Re: [R] Problem with retreaving numeric data
dvkirankumar wrote: I am trying to get a value from a dataset in data set its stored as 001 but while i am trying to retreave it its giving as 1 can any one help me to retreave it as 001 I have to guess if you used a boomerang or a sling to retrieve your data. My blind guess is you used read.table, or odbc. Assuming read.table: use the parameter colClasses to force that column to be read in as a string instead of a number. The function uses the first few lines to guess the data type, which can be wrong. Dieter -- View this message in context: http://n4.nabble.com/Problem-with-retreaving-numeric-data-tp1476934p1476943.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running rscript in windows
How did you change directory? Does dir() show that your directory is the desktop? Presumably the desktop folder is something like C:/Users/someone/Desktop. Sourcing test.R from there should work. But the simplest way is source(file.choose()) and then navigate to where test.R is located. -Peter Ehlers vikrant wrote: Hi, I saved the function in test.R file on Desktop. Then after starting R I changed my directory to desktop. and tried the command source(test.R) it gave me following error Error in file(file, r, encoding = encoding) : cannot open the connection In addition: Warning message: In file(file, r, encoding = encoding) : cannot open file 'test.R': No such file or directory -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Proxy settings
Thanks, especially to Greg for the help with the proxy settings required for Windows. I have managed to solve the problem, with Greg's latest suggestion. Jacob Jacob L van Wyk Department of Statistics University of Johannesburg (APK) PO Box 524, Auckland Park, 2006 Office ph: 011 559 3080 Fax: 011 559 2499 This email and all contents are subject to the following disclaimer: http://www.uj.ac.za/UJ_email_legal_disclaimer.htm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] question about boxplot,does it accept ad hoc data
Guanhua Chen wrote: I have a question about boxplot(), does it accept ad hoc data , for example, I only provide quartile information to the function,but get the boxplot as usual, is it possible , or if there is any other function can do this. Thank you very much! boxplot calls bxp which is documented and accepts the summary data for plotting. Dieter -- View this message in context: http://n4.nabble.com/question-about-boxplot-does-it-accept-ad-hoc-data-tp1476784p1476949.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with retreaving numeric data
My guess is that you cannot keep it numeric, but that you have to convert it to a string (the gurus may know better). x=001 x x=001 x Daniel - cuncta stricte discussurus - -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of venkata kirankumar Sent: Thursday, February 11, 2010 2:47 AM To: r-help@r-project.org Subject: [R] Problem with retreaving numeric data Hi all, I am trying to get a value from a dataset in data set its stored as 001 but while i am trying to retreave it its giving as 1 can any one help me to retreave it as 001 thanks in advance kiran [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question about rank() function
To follow up on Moshe's post, do rank(fmodel) rank(round(fmodel,4)) rank(fmodel)==rank(round(fmodel,4)) If the two are not identical, you have the explanation Moshe suggested, just that this approach is somewhat more comprehensive as it works on the entire fmodel vector. See the example below: x=c(1.0001,1.0002,1.0003,1.0004,2.0001,2.0002,2.0003,3.0001,3.0002,4) rank(x) rank(round(x,2)) rank(x)==rank(round(x,2)) HTH, Daniel - cuncta stricte discussurus - -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Something Something Sent: Thursday, February 11, 2010 2:23 AM To: r-help@r-project.org Subject: [R] Question about rank() function Hello, I am trying to get the 'rank' function to work for me, but not sure what I am doing wrong. Please help. I ran the following commands: data = read.table(test1.csv, head=T, as.is=T, na.string=., row.nam=NULL) X1 = as.factor(data[[3]]) X2 = as.factor(data[[4]]) X3 = as.factor(data[[5]]) Y = data[[2]] model = lm(Y ~ X1*X2*X3, na.action = na.exclude) fmodel = fitted(model) fmodel (First line is shown below.) 12345678 9 10 11 12 13 14 15 16 17 180.3763 180.3763 180.3763 180.3763 180.4546 180.3763 177.9245 177.9245 181.3859 180.3763 NA 180.4546 180.3763 180.4546 180.3763 180.3763 180.4546 Then I run: fmodel.rank = rank(fmodel) fmodel.rank (First line is shown below) 1 2 3 4 5 6 7 8 9101112 13141516171819202122232425 26 375.0 222.0 68.5 68.5 402.5 222.0 33.5 33.5 465.5 222.0 500.0 402.5 222.0 402.5 222.0 222.0 378.5 222.0 222.0 222.0 222.0 222.0 402.5 222.0 33.5 222.0 As you can see, first 4 values of 'fmodel' are 180.3763, so after running rank(fmodel) I expected the ranks of first 4 to be the same, but they are not. What am I doing wrong? Please let me know. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] SAS and RODBC
I am using R-2.10.1 binary from CRAN on a WinXP Pro system. I also use SAS
v9.2 on the same box. I just started using the SAS ODBC driver that comes with
version 9 of SAS. I have been able to set up an ODBC source for SAS datasets
using the driver, and then with RODBC I am able to read a sample SAS dataset.
library(RODBC)
ch - odbcConnect('sasodbc', believeNRows=FALSE)
df - sqlQuery(ch, 'select * from sasodbc.class', as.is=TRUE)
df
Name Sex Age Height Weight
1 Alfred M 14 69.0 112.5
2Alice F 13 56.5 84.0
3 Barbara F 13 65.3 98.0
4Carol F 14 62.8 102.5
5Henry M 14 63.5 102.5
6James M 12 57.3 83.0
7 Jane F 12 59.8 84.5
8Janet F 15 62.5 112.5
9 Jeffrey M 13 62.5 84.0
10John M 12 59.0 99.5
11 Joyce F 11 51.3 50.5
12Judy F 14 64.3 90.0
13 Louise F 12 56.3 77.0
14Mary F 15 66.5 112.0
15 Philip M 16 72.0 150.0
16 Robert M 12 64.8 128.0
17 Ronald M 15 67.0 133.0
18 Thomas M 11 57.5 85.0
19 William M 15 66.5 112.0
str(df)
'data.frame': 19 obs. of 5 variables:
$ Name : chr Alfred Alice Barbara Carol ...
$ Sex : chr M F F F ...
$ Age : num 14 13 13 14 14 12 12 15 13 12 ...
$ Height: num 69 56.5 65.3 62.8 63.5 57.3 59.8 62.5 62.5 59 ...
$ Weight: num 112 84 98 102 102 ...
However, I am not able to save a dataframe back to a SAS dataset. When I try
to use sqlSave I get the following error.
sqlSave(ch, df, tablename='sasodbc.class2')
Error in sqlSave(ch, df, tablename = sasodbc.class2) : 0 0
[RODBC] ERROR: Could not SQLExecDirect 'CREATE TABLE sasodbc.class2
(rownames varchar(255), Name varchar(255), Sex varchar(255), Age num,
Height num, Weight num)'
Can anyone suggest how I might go about tracking down the problem? I don't
know much about ODBC in general or what RODBC is doing under the hood, or how
the SAS ODBC driver is written, but it would be useful if I could get R to
write SAS datasets, and not just read them.
Thanks,
Dan
Daniel Nordlund
Bothell, WA USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] ff package: How to save and open ff(df) files.
Hello to everyone, I'm a newbie with ff package and I´m starting to use it. I´ve been reading the ff.pdf guide and another documents and questions , but I´m really confused about some procedures I can´t see how to do. I´d want to know if it´s possible (and how) to save a ffdf file(s) and open it in another session, via saving it in an permanet location. Let´s supose we´re reading from a text file to a ffdf object, with read.table.ffdf and we want to save the files and information in a permanent path and file. First of all I read about GetOption(fftempdir) but I don´t know how to change this parameter. I read also about the pattern option, and I asume that this option changes the prefix of the files created phisically under the ffdf object. Isn´t it? Can I use this parameter to create a permanent location (via putting the entire path) for the files? Can I use this option after reading the file as ffdf , applying the pattern to the ffdf object I created before? The next and related quetion is, if I can save the files in a permanent location , how can I load them? Can I use the generic load of an image of the R session? Thanks in advance for reading this question and please apologize if my english is not very accurate and/or the question is too simple. Regards Daniel. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running rscript in windows
Thanks a lot, really. dir() option showd my desktop files and test.R was shown as test.R.txt when I run source(test.R.txt) it worked. Just for your information, I changed the directory using Menu options File- change dir. I verified the same using getwd() command in R. ' -- View this message in context: http://n4.nabble.com/Running-rscript-in-windows-tp1475671p1476962.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SAS and RODBC
On Thu, 11 Feb 2010, Daniel Nordlund wrote:
I am using R-2.10.1 binary from CRAN on a WinXP Pro system. I also use SAS
v9.2 on the same box. I just started using the SAS ODBC driver that comes with
version 9 of SAS. I have been able to set up an ODBC source for SAS datasets
using the driver, and then with RODBC I am able to read a sample SAS dataset.
library(RODBC)
ch - odbcConnect('sasodbc', believeNRows=FALSE)
df - sqlQuery(ch, 'select * from sasodbc.class', as.is=TRUE)
df
Name Sex Age Height Weight
1 Alfred M 14 69.0 112.5
2Alice F 13 56.5 84.0
3 Barbara F 13 65.3 98.0
4Carol F 14 62.8 102.5
5Henry M 14 63.5 102.5
6James M 12 57.3 83.0
7 Jane F 12 59.8 84.5
8Janet F 15 62.5 112.5
9 Jeffrey M 13 62.5 84.0
10John M 12 59.0 99.5
11 Joyce F 11 51.3 50.5
12Judy F 14 64.3 90.0
13 Louise F 12 56.3 77.0
14Mary F 15 66.5 112.0
15 Philip M 16 72.0 150.0
16 Robert M 12 64.8 128.0
17 Ronald M 15 67.0 133.0
18 Thomas M 11 57.5 85.0
19 William M 15 66.5 112.0
str(df)
'data.frame': 19 obs. of 5 variables:
$ Name : chr Alfred Alice Barbara Carol ...
$ Sex : chr M F F F ...
$ Age : num 14 13 13 14 14 12 12 15 13 12 ...
$ Height: num 69 56.5 65.3 62.8 63.5 57.3 59.8 62.5 62.5 59 ...
$ Weight: num 112 84 98 102 102 ...
However, I am not able to save a dataframe back to a SAS dataset. When I try
to use sqlSave I get the following error.
sqlSave(ch, df, tablename='sasodbc.class2')
Error in sqlSave(ch, df, tablename = sasodbc.class2) : 0 0
[RODBC] ERROR: Could not SQLExecDirect 'CREATE TABLE sasodbc.class2 (rownames varchar(255), Name varchar(255),
Sex varchar(255), Age num, Height num, Weight num)'
Can anyone suggest how I might go about tracking down the problem?
I don't know much about ODBC in general or what RODBC is doing under
the hood, or how the SAS ODBC driver is written, but it would be
useful if I could get R to write SAS datasets, and not just read
them.
What 'RODBC is doing under the hood' is in that error message: sending
an SQL query to create a table. Unfortunately, the SAS ODBC driver is
not returning a useful error message, and this really becomes a
question for SAS support. Maybe that function is not supported, the
connection is read-only, the SAS dialect requires different quotes
(although RODBC asked the driver about quoting) ... only someone
familiar with the ODBC driver will know.
This is really off-topic here: r-sig-db would be more appropriate but
only marginally so,
Thanks,
Dan
Daniel Nordlund
Bothell, WA USA
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regarding a error while plotting R chart using qcc package.
On 11 Feb 2010, at 06:53, Vikrant Shimpi wrote:
Dear Luka ,
I am using qcc package in R to plot SPC charts. BUt while plotting
R chart I had a error. My question is it necessary while plotting
R Chart the group sample size must be 25 ?. Because when I took
group sample size as 1000 it gave me error, till I took group sample
size as 26, But as sooon as I changed the group sample size to 25
the R chart was plotted successfully.
I had a discussion in the R forum, at the end of it was suggested to
write to you regarding the error. I am giving the link for the same.
http://n4.nabble.com/problems-with-SPC-charts-in-R-td1467901.html#a1469800
Also I am attaching the dataset and the code which gave me error
while plotting R chart.
R code is as follows: -
SAMPLE_SIZE-1000
y-read.csv(data.csv,sep=,,header=TRUE)
y-subset(y, !is.null(y[,1]),)
unique_b_vals = unique(y[,2])
final_set - NULL
for(b_val in unique_b_vals)
{
temp1 = subset(y,week==b_val,)
temp1 = temp1[sample(dim(temp1)[1], SAMPLE_SIZE),]
if (is.null(final_set))
final_set - temp1
else
final_set - rbind(final_set,temp1)
print(b_val)
}
First of all, here I got an error:
Error in sample(dim(temp1)[1], SAMPLE_SIZE) :
cannot take a sample larger than the population when 'replace =
FALSE'
The final_set matrix has however dimension
dim(final_set)
[1] 17000 3
and I will continue with this.
library(qcc)
attach(final_set)
a- qcc.groups(ST,week)
dim(a)
obj - qcc(a[,],type=R)
summary(obj)
detach(final_set)
Here I am selecting a sample of size 1000 for each group. And it
gives me following error
Error in limits.R(center = 62614.0571428571, std.dev = NA_real_,
sizes = c(1000L, :
group size must be less than 51 when giving nsigmas
Yes and it must be like that. You shouldn't use R charts for
monitoring dispersion using sample sizes larger than 20, and for
sample sizes greater than 25 you get an error. From theory, R chart
used the distribution of relative range for estimating sigma, which is
tabulated up to a sample size of 25
qcc.options(exp.R.unscaled)
The number 51 comes from another tabulated data
qcc.options(se.R.unscaled)
In this case you must simply use an S chart:
obj - qcc(a,type=S)
Some sparse notes:
- don't use a[,] to select a whole matrix, simply a, i.e. qcc(a)
- don't use - for assignment (it has another meaning...), - is enough
I hope this help.
Luca Scrucca
--
Luca Scrucca
Dipartimento di Economia, Finanza e Statistica
Sezione di Statistica
Università degli Studi di Perugia
Via A. Pascoli, 20
06123 PERUGIA (ITALY)
Tel. +39-075-5855233
Fax: +39-075-5855950
E-mail: l...@stat.unipg.it
Web page: http://www.stat.unipg.it/luca
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] SAS and RODBC
There is a SASxport package on CRAN that may be of interest.
On Thu, Feb 11, 2010 at 3:38 AM, Daniel Nordlund djnordl...@verizon.net wrote:
I am using R-2.10.1 binary from CRAN on a WinXP Pro system. I also use SAS
v9.2 on the same box. I just started using the SAS ODBC driver that comes
with version 9 of SAS. I have been able to set up an ODBC source for SAS
datasets using the driver, and then with RODBC I am able to read a sample SAS
dataset.
library(RODBC)
ch - odbcConnect('sasodbc', believeNRows=FALSE)
df - sqlQuery(ch, 'select * from sasodbc.class', as.is=TRUE)
df
Name Sex Age Height Weight
1 Alfred M 14 69.0 112.5
2 Alice F 13 56.5 84.0
3 Barbara F 13 65.3 98.0
4 Carol F 14 62.8 102.5
5 Henry M 14 63.5 102.5
6 James M 12 57.3 83.0
7 Jane F 12 59.8 84.5
8 Janet F 15 62.5 112.5
9 Jeffrey M 13 62.5 84.0
10 John M 12 59.0 99.5
11 Joyce F 11 51.3 50.5
12 Judy F 14 64.3 90.0
13 Louise F 12 56.3 77.0
14 Mary F 15 66.5 112.0
15 Philip M 16 72.0 150.0
16 Robert M 12 64.8 128.0
17 Ronald M 15 67.0 133.0
18 Thomas M 11 57.5 85.0
19 William M 15 66.5 112.0
str(df)
'data.frame': 19 obs. of 5 variables:
$ Name : chr Alfred Alice Barbara Carol ...
$ Sex : chr M F F F ...
$ Age : num 14 13 13 14 14 12 12 15 13 12 ...
$ Height: num 69 56.5 65.3 62.8 63.5 57.3 59.8 62.5 62.5 59 ...
$ Weight: num 112 84 98 102 102 ...
However, I am not able to save a dataframe back to a SAS dataset. When I try
to use sqlSave I get the following error.
sqlSave(ch, df, tablename='sasodbc.class2')
Error in sqlSave(ch, df, tablename = sasodbc.class2) : 0 0
[RODBC] ERROR: Could not SQLExecDirect 'CREATE TABLE sasodbc.class2
(rownames varchar(255), Name varchar(255), Sex varchar(255), Age num,
Height num, Weight num)'
Can anyone suggest how I might go about tracking down the problem? I don't
know much about ODBC in general or what RODBC is doing under the hood, or how
the SAS ODBC driver is written, but it would be useful if I could get R to
write SAS datasets, and not just read them.
Thanks,
Dan
Daniel Nordlund
Bothell, WA USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R2HTML
I am using R 2.10.1 for Mac OS. But Bart's Tip to use 'HTML(summary(iris))' completely solved the problem. Thanks to everybody for helping. Regina Am 10.02.2010 um 20:01 schrieb Greg Snow: When I copy/paste/run your code below I get a file with the summary output in a nice table. Telling us your version, operating system, and other information requested in the posting guide may help. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Regina Schinner Sent: Wednesday, February 10, 2010 1:44 AM To: r-help@r-project.org Subject: [R] R2HTML I am having difficulties with R2HTML. If I try to generate a HTML file with the below code, the titles, horizontal line, and scatter plot are there, but the data summary [summary(iris)] is not. --- library(R2HTML) HTMLStart(file=myreport, extension=html, echo=FALSE, HTMLframe=TRUE) HTML.title(Data Description, HR=3) summary(iris) HTMLhr() HTML.title(Scatter Plot, HR=3) plot(iris$Sepal.Length~iris$Sepal.Width) HTMLplot() HTMLStop() --- How do I add summary data to a HTML file? Thanks for any help you can provide Regina Schinner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ZOO object colnames refering to Dates
Hello, I have large zoo objects (about 100 or more time series merged next to eachother). Example: X05.Oct.99 X05.Nov.99 X05.Dec.99 X05.Jan.00 X05.Feb.00 X05.Mar.00 X05.Apr.00 X05.May.00 X05.Jun.00 [1,] 5649.3 5679.4 5679.4 5679.4 5679.4 5679.4 5679.4 5679.4 5679.4 [2,] 5682.7 5719.2 5719.2 5719.2 5719.2 5719.2 5719.2 5719.2 5719.2 [3,] 5697.5 5745.5 5745.5 5745.5 5745.5 5745.5 5745.5 5745.5 5745.5 [4,] 5723.9 5767.8 5767.8 5767.8 5767.8 5767.8 5767.8 5767.8 5767.8 [5,] 5782.1 5829.8 5829.8 5829.8 5829.8 5829.8 5829.8 5829.8 5829.8 [6,] 5815.0 5850.9 5850.9 5850.9 5850.9 5850.9 5850.9 5850.9 5850.9 The column names contain dates, i.e., X05.Oct.99 stands for a time sequence that was obtained on 05/10/1999. Each column is obtained month + 1 from the previous one. Is it possible to access these columns (time series data) via a for/next loop (or a while) that uses dates i/o (i in 1:8) in the above example? Say: if month==Oct and year==1999 choose column X05.Oct.99 ... Could I also generate automatically a variable, appropriately named from the corresponding columns name that would contain the data and access it by that date? Any pointers really appreciated. Thanks in advance, Costas __ Information from ESET Smart Security, version of virus signature database 4857 (20100211) __ The message was checked by ESET Smart Security. http://www.eset.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweve/cacheSweave
Hi there
I have a problem with using Sweave in combination with the option driver =
cacheSweave.
Whichever code I try to run - when it comes to converting the tex file into
pdf it comes up with the same errors (\csname \endcsname errors). Does anybody
have an idea what it going wrong?
Sweave(pgfSweave-example.Rnw,driver = cacheSweaveDriver)
Writing to file pgfSweave-example.tex
Processing code chunks ...
1 : term verbatim (label=setup)
2 : echo term verbatim (label=data)
3 : term verbatim eps pdf (label=boxplot)
You can now run LaTeX on 'pgfSweave-example.tex'
tools::texi2dvi(pgfSweave-example.tex, pdf=TRUE)
Error in tools::texi2dvi(pgfSweave-example.tex, pdf = TRUE) :
running 'texi2dvi' on 'pgfSweave-example.tex' failed
LaTeX errors:
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: LaTeX E
rror: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H return for immediate help
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
I am running this under Windows XP, R version 2.9.2 (2009-08-24),
package.version(cacheSweave)
[1] 0.4-3.
Any help or advice on this would be highly appreciated!
Best wishes
Kristian
_
Dr Kristian Unger
Bioinformaticist Chernobyl Tissue Bank
Division of Surgery and Cancer
Imperial College London
Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS
Tel +44-20-8383-2443
Mob +44-795-1080619
Skype kristianunger
http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
http://www.chernobyltissuebank.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Biclustering package
Hello, I am looking for R package which can perform biclustering a part from biclust package. thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave, lty = 3 line incorect in pdf output
Ken,
I can't contribute much, just that I tried to look into it and can't
replicate it. I tried it both with .Stex and .Rnw yielding identical
results, just like plotting it interactively (on my default X11) and
printing it via dev.copy2pdf(). All of the approaches seemed to yield the
same output which looks ok.
Just for the record...
Z
R sessionInfo()
R version 2.10.1 (2009-12-14)
i486-pc-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fortunes_1.3-7
On Thu, 11 Feb 2010, Ken Knoblauch wrote:
I'm having a problem with dotted lines (lty = 3) in the pdf output
in documents generated with Sweave. In the displayed pdf, the
dotted line does not show up and in the printed output, it is
there but does not seem to respect the lwd argument, for example, it
is very faint despite using lwd = 3. The dotted line is correct
in a quartz window and if I save the Quartz window to a pdf
and include it in the tex document, then the dotted line is there
at the correct line width. Here is a short example, using the Stex
convention for Sweave. I saved the quartz window in a file called
quartzSave.pdf after running the document through Sweave a first
time without the \includegraphics{quartzSave} line.
\documentclass[10pt]{article}
\usepackage{graphicx}
\begin{document}
Test of lty = 3 argument.
\begin{Scode}{fig=TRUE,eps=FALSE}
x - 1:10
plot(x, type = l, lty = 3, lwd = 3)
lines(x, 0.5 * x, type = l)
\end{Scode}
Saved from Quartz window:
\includegraphics{quartzSave}
\end{document}
I have attached the pdf created by Sweave (which is missing the dotted
lines) in case it can get through the filter to R-help.
sessionInfo()
R version 2.10.1 Patched (2010-02-01 r51089)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] tools_2.10.1
Thanks for any help.
Ken
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Biclustering package
Alex, the isa2 package implements the biclustering algorithm discussed in Bergmann S, Ihmels J, and Barkai N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Rev E Stat Nonlin Soft Matter Phys 2003 Mar; 67(3 Pt 1) 031902 Best, Gabor On Thu, Feb 11, 2010 at 10:51 AM, Alex Roy alexroy2...@gmail.com wrote: Hello, I am looking for R package which can perform biclustering a part from biclust package. thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gabor Csardi gabor.csa...@unil.ch UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unexpected output in first iteration of for-loop
Ok, you're right - may I rephrase:
How should I modify the assignment of result - latentVariableNames
so it produces the output without the first line?
I thought result - NULL should do the job, but it didn't because of the
following names(result) assignment (which I understand, but not how I
can workaround it).
Here's the output and code again:
latentVariable Indiv Group
1 rPlanning rIterat rTDD
2 rPlanning0.79 0.84
3rIterat0.79 0.83
4 rTDD 0.9 0.96
5 rStandup0.83 0.82
6rRetros 0.9 0.95
7rAccess0.91 0.92
8 rAccTest0.87 0.9
#
LV - c(rPlanning, rIterat, rTDD, rStandup, rRetros, rAccess,
rAccTest)
#
loopCronbach - function(latentVariableNames, groupingVariable)
{
result - latentVariableNames
names(result) - c(latentVariable, Indiv, Group)
for (currentName in latentVariableNames)
{
print(currentName)
print(result)
tmp1 - calculateIndividualCronbach(get(currentName))
tmp2 - calculateGroupCronbach(get(currentName), groupingVariable)
result - rbind(result,data.frame(latentVariable=currentName,
Indiv=tmp1,Group=tmp2))
}
return(result)
}
On Thu, Feb 11, 2010 at 3:31 AM, jim holtman jholt...@gmail.com wrote:
It doing exactly what you asked it to do. You have the assignment:
result - latentVariableNames
and then you print it out in the loop. What were you expecting?
On Wed, Feb 10, 2010 at 9:06 PM, Chaehan So chaehan...@gmail.com wrote:
Dear r-helpers,
why do I get an output in the first iteration of the for-loop
which contains the string values of the input vector,
and how can I avoid that?
Here's the output (only line 1 is wrong)
latentVariable Indiv Group
1 rPlanning rIterat rTDD
2 rPlanning0.79 0.84
3rIterat0.79 0.83
4 rTDD 0.9 0.96
5 rStandup0.83 0.82
6rRetros 0.9 0.95
7rAccess0.91 0.92
8 rAccTest0.87 0.9
#
LV - c(rPlanning, rIterat, rTDD, rStandup, rRetros, rAccess,
rAccTest)
#
loopCronbach - function(latentVariableNames, groupingVariable)
{
result - latentVariableNames
names(result) - c(latentVariable, Indiv, Group)
for (currentName in latentVariableNames)
{
print(currentName)
print(result)
tmp1 - calculateIndividualCronbach(get(currentName))
tmp2 - calculateGroupCronbach(get(currentName), groupingVariable)
result - rbind(result,data.frame(latentVariable=currentName,
Indiv=tmp1,Group=tmp2))
}
return(result)
}
a - loopCronbach(LV, u_proj)
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
--
Humboldt University Berlin, Germany
Institute of Psychology
Rudower Chaussee 18, Room 1221
12489 Berlin
Germany
Office: +49 30 2093 - 9337
Mobile: +49 171- 626 9373
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave, lty = 3 line incorect in pdf output
Hi Achim,
Thanks for trying. Maybe, it's a Mac-thing. I'll wait to
see if I get other replies. It's strange, as the quartz
graphic is correct but the pdf produced by Sweave doesn't
contain the dotted line, with the caveat, on my Mac for the
moment.
Ken
Quoting Achim Zeileis achim.zeil...@uibk.ac.at:
Ken,
I can't contribute much, just that I tried to look into it and can't
replicate it. I tried it both with .Stex and .Rnw yielding identical
results, just like plotting it interactively (on my default X11) and
printing it via dev.copy2pdf(). All of the approaches seemed to yield
the same output which looks ok.
Just for the record...
Z
R sessionInfo()
R version 2.10.1 (2009-12-14)
i486-pc-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fortunes_1.3-7
On Thu, 11 Feb 2010, Ken Knoblauch wrote:
I'm having a problem with dotted lines (lty = 3) in the pdf output
in documents generated with Sweave. In the displayed pdf, the
dotted line does not show up and in the printed output, it is
there but does not seem to respect the lwd argument, for example, it
is very faint despite using lwd = 3. The dotted line is correct
in a quartz window and if I save the Quartz window to a pdf
and include it in the tex document, then the dotted line is there
at the correct line width. Here is a short example, using the Stex
convention for Sweave. I saved the quartz window in a file called
quartzSave.pdf after running the document through Sweave a first
time without the \includegraphics{quartzSave} line.
\documentclass[10pt]{article}
\usepackage{graphicx}
\begin{document}
Test of lty = 3 argument.
\begin{Scode}{fig=TRUE,eps=FALSE}
x - 1:10
plot(x, type = l, lty = 3, lwd = 3)
lines(x, 0.5 * x, type = l)
\end{Scode}
Saved from Quartz window:
\includegraphics{quartzSave}
\end{document}
I have attached the pdf created by Sweave (which is missing the dotted
lines) in case it can get through the filter to R-help.
sessionInfo()
R version 2.10.1 Patched (2010-02-01 r51089)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] tools_2.10.1
Thanks for any help.
Ken
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] ZOO object colnames refering to Dates
On Thu, 11 Feb 2010, Research wrote: Hello, I have large zoo objects (about 100 or more time series merged next to eachother). Example: X05.Oct.99 X05.Nov.99 X05.Dec.99 X05.Jan.00 X05.Feb.00 X05.Mar.00 X05.Apr.00 X05.May.00 X05.Jun.00 [1,] 5649.3 5679.4 5679.4 5679.4 5679.4 5679.4 5679.4 5679.4 5679.4 [2,] 5682.7 5719.2 5719.2 5719.2 5719.2 5719.2 5719.2 5719.2 5719.2 [3,] 5697.5 5745.5 5745.5 5745.5 5745.5 5745.5 5745.5 5745.5 5745.5 [4,] 5723.9 5767.8 5767.8 5767.8 5767.8 5767.8 5767.8 5767.8 5767.8 [5,] 5782.1 5829.8 5829.8 5829.8 5829.8 5829.8 5829.8 5829.8 5829.8 [6,] 5815.0 5850.9 5850.9 5850.9 5850.9 5850.9 5850.9 5850.9 5850.9 The column names contain dates, i.e., X05.Oct.99 stands for a time sequence that was obtained on 05/10/1999. Each column is obtained month + 1 from the previous one. Is it possible to access these columns (time series data) via a for/next loop (or a while) that uses dates i/o (i in 1:8) in the above example? Say: if month==Oct and year==1999 choose column X05.Oct.99 ... You can switch back and forth between character representations and timedate representations using strptime() and format() along with formatting strings, e.g., R strptime(X05.Oct.99, X%d.%b.%y) [1] 1999-10-05 R format(strptime(X05.Oct.99, X%d.%b.%y), X%d.%b.%y) [1] X05.Oct.99 R format(strptime(X05.Oct.99, X%d.%b.%y), %d/%m/%Y) [1] 05/10/1999 And so on. See Grothendieck G, Petzoldt T (2004). R Help Desk: Date and Time Classes in R. R News, 4(1), 2932. URL http://www.R-project.org/doc/Rnews/Rnews_2004-1.pdf for more details. I wonder why you have the time information in the columns rather than in the rows though... If your measurements on that day represent intra-day measurements, simply use some time/date class, e.g., POSIXct (or chron or timeDate) for that. If the measurements correspond to some replications they can just go into the columns rather than the rows of the series. For examples in zoo, see the vignettes of the package. hth, Z Could I also generate automatically a variable, appropriately named from the corresponding columns name that would contain the data and access it by that date? Any pointers really appreciated. Thanks in advance, Costas __ Information from ESET Smart Security, version of virus signature database 4857 (20100211) __ The message was checked by ESET Smart Security. http://www.eset.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] gdata
Hi Using R 2.10.1 on a mac os 10.6.2, I have have a problem with gdata package. When I use the command read.xls, I get this error-message: Erreur dans xls2sep(xls, sheet, verbose = verbose, ..., method = method, : Unable to read translated csv file '/var/folders/gb/gbzQ4sqTF-KK3D5m6v-IJE+++TI/-Tmp-//Rtmp3Hprw9/file10d63af1.csv'. Erreur dans file.exists(tfn) : argument 'file' incorrect dyld: lazy symbol binding failed: Symbol not found: _Perl_Tstack_sp_ptr Referenced from: /Library/Frameworks/R.framework/Resources/library/gdata/perl/darwin-thread-multi-2level/auto/Compress/Raw/Zlib/Zlib.bundle Expected in: dynamic lookup dyld: Symbol not found: _Perl_Tstack_sp_ptr Referenced from: /Library/Frameworks/R.framework/Resources/library/gdata/perl/darwin-thread-multi-2level/auto/Compress/Raw/Zlib/Zlib.bundle Expected in: dynamic lookup I never had this problem with the previous version of R... Could somebody help me? Thank you! Guillaume -- View this message in context: http://n4.nabble.com/gdata-tp1477079p1477079.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ZOO object colnames refering to Dates
Here are a few more examples:
ym - seq(from = as.Date(1999-10-05), to = as.Date(2000-06-05),
+ by = month)
z - zoo(matrix(seq_len(length(ym) * 5), 5))
colnames(z) - format(ym, X%d.%b.%y)
z
X05.Oct.99 X05.Nov.99 X05.Dec.99 X05.Jan.00 X05.Feb.00 X05.Mar.00 X05.Apr.00
1 1 6 11 16 21 26 31
2 2 7 12 17 22 27 32
3 3 8 13 18 23 28 33
4 4 9 14 19 24 29 34
5 5 10 15 20 25 30 35
X05.May.00 X05.Jun.00
1 36 41
2 37 42
3 38 43
4 39 44
5 40 45
to.header - function(month, year) {
+ d - as.Date(paste(year, month, 5, sep = -), %Y-%b-%d)
+ format(d, X%d.%b.%y)
+ }
to.header(Oct, 1999)
[1] X05.Oct.99
for(j in 1:NCOL(z)) print(z[,j])
1 2 3 4 5
1 2 3 4 5
1 2 3 4 5
6 7 8 9 10
1 2 3 4 5
11 12 13 14 15
1 2 3 4 5
16 17 18 19 20
1 2 3 4 5
21 22 23 24 25
1 2 3 4 5
26 27 28 29 30
1 2 3 4 5
31 32 33 34 35
1 2 3 4 5
36 37 38 39 40
1 2 3 4 5
41 42 43 44 45
for(nm in colnames(z)) print(z[,nm])
1 2 3 4 5
1 2 3 4 5
1 2 3 4 5
6 7 8 9 10
1 2 3 4 5
11 12 13 14 15
1 2 3 4 5
16 17 18 19 20
1 2 3 4 5
21 22 23 24 25
1 2 3 4 5
26 27 28 29 30
1 2 3 4 5
31 32 33 34 35
1 2 3 4 5
36 37 38 39 40
1 2 3 4 5
41 42 43 44 45
On Thu, Feb 11, 2010 at 5:04 AM, Achim Zeileis achim.zeil...@uibk.ac.at wrote:
On Thu, 11 Feb 2010, Research wrote:
Hello,
I have large zoo objects (about 100 or more time series merged next to
eachother). Example:
X05.Oct.99 X05.Nov.99 X05.Dec.99 X05.Jan.00 X05.Feb.00 X05.Mar.00
X05.Apr.00 X05.May.00 X05.Jun.00
[1,] 5649.3 5679.4 5679.4 5679.4 5679.4 5679.4
5679.4 5679.4 5679.4
[2,] 5682.7 5719.2 5719.2 5719.2 5719.2 5719.2
5719.2 5719.2 5719.2
[3,] 5697.5 5745.5 5745.5 5745.5 5745.5 5745.5
5745.5 5745.5 5745.5
[4,] 5723.9 5767.8 5767.8 5767.8 5767.8 5767.8
5767.8 5767.8 5767.8
[5,] 5782.1 5829.8 5829.8 5829.8 5829.8 5829.8
5829.8 5829.8 5829.8
[6,] 5815.0 5850.9 5850.9 5850.9 5850.9 5850.9
5850.9 5850.9 5850.9
The column names contain dates, i.e., X05.Oct.99 stands for a time
sequence that was obtained on 05/10/1999. Each column is obtained month + 1
from the previous one.
Is it possible to access these columns (time series data) via a for/next
loop (or a while) that uses dates i/o (i in 1:8) in the above example?
Say: if month==Oct and year==1999 choose column X05.Oct.99 ...
You can switch back and forth between character representations and timedate
representations using strptime() and format() along with formatting strings,
e.g.,
R strptime(X05.Oct.99, X%d.%b.%y)
[1] 1999-10-05
R format(strptime(X05.Oct.99, X%d.%b.%y), X%d.%b.%y)
[1] X05.Oct.99
R format(strptime(X05.Oct.99, X%d.%b.%y), %d/%m/%Y)
[1] 05/10/1999
And so on. See
Grothendieck G, Petzoldt T (2004). R Help Desk: Date and Time
Classes in R. R News, 4(1), 2932.
URL http://www.R-project.org/doc/Rnews/Rnews_2004-1.pdf
for more details.
I wonder why you have the time information in the columns rather than in the
rows though... If your measurements on that day represent intra-day
measurements, simply use some time/date class, e.g., POSIXct (or chron or
timeDate) for that. If the measurements correspond to some replications they
can just go into the columns rather than the rows of the series.
For examples in zoo, see the vignettes of the package.
hth,
Z
Could I also generate automatically a variable, appropriately named from
the corresponding columns name that would contain the data and access it by
that date?
Any pointers really appreciated.
Thanks in advance,
Costas
__ Information from ESET Smart Security, version of virus
signature database 4857 (20100211) __
The message was checked by ESET Smart Security.
http://www.eset.com
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read
Re: [R] Sweave, lty = 3 line incorect in pdf output
Some follow-up after Achim's message,
If I open the Sweave created pdf, lty3Test-001.pdf, attached
to the first mail, with the display command from imageMagick,
indeed, the dotted line is present, but faintly, as with the
hardcopy printout, i.e., not respecting the lwd = 3 argument.
But, the dotted line is absent if viewed with Mac's Preview.app
and the pdf viewer of TeXShop. I don't have acrobat on my
Mac to test that, but it seems to in part, at least, viewer related.
Still, it would be good to track this down and ideally solve
it.
Thanks.
Ken
Quoting Achim Zeileis achim.zeil...@uibk.ac.at:
Ken,
I can't contribute much, just that I tried to look into it and can't
replicate it. I tried it both with .Stex and .Rnw yielding identical
results, just like plotting it interactively (on my default X11) and
printing it via dev.copy2pdf(). All of the approaches seemed to yield
the same output which looks ok.
Just for the record...
Z
R sessionInfo()
R version 2.10.1 (2009-12-14)
i486-pc-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fortunes_1.3-7
On Thu, 11 Feb 2010, Ken Knoblauch wrote:
I'm having a problem with dotted lines (lty = 3) in the pdf output
in documents generated with Sweave. In the displayed pdf, the
dotted line does not show up and in the printed output, it is
there but does not seem to respect the lwd argument, for example, it
is very faint despite using lwd = 3. The dotted line is correct
in a quartz window and if I save the Quartz window to a pdf
and include it in the tex document, then the dotted line is there
at the correct line width. Here is a short example, using the Stex
convention for Sweave. I saved the quartz window in a file called
quartzSave.pdf after running the document through Sweave a first
time without the \includegraphics{quartzSave} line.
\documentclass[10pt]{article}
\usepackage{graphicx}
\begin{document}
Test of lty = 3 argument.
\begin{Scode}{fig=TRUE,eps=FALSE}
x - 1:10
plot(x, type = l, lty = 3, lwd = 3)
lines(x, 0.5 * x, type = l)
\end{Scode}
Saved from Quartz window:
\includegraphics{quartzSave}
\end{document}
I have attached the pdf created by Sweave (which is missing the dotted
lines) in case it can get through the filter to R-help.
sessionInfo()
R version 2.10.1 Patched (2010-02-01 r51089)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] tools_2.10.1
Thanks for any help.
Ken
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html
--
Ken Knoblauch
Inserm U846
Stem-cell and Brain Research Institute
Department of Integrative Neurosciences
18 avenue du Doyen Lépine
69500 Bron
France
tel: +33 (0)4 72 91 34 77
fax: +33 (0)4 72 91 34 61
portable: +33 (0)6 84 10 64 10
http://www.sbri.fr/members/kenneth-knoblauch.html
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] gdata
The most recent version of gdata uses certain perl packages not used by the older versions and perhaps that is causing the problem. You could try installing the latest version of active perl or if that fails you could try an older version of gdata: http://www.activestate.com/activeperl/ http://cran.r-project.org/src/contrib/Archive/gdata/ On Thu, Feb 11, 2010 at 5:06 AM, Casimir gcar...@gmail.com wrote: Hi Using R 2.10.1 on a mac os 10.6.2, I have have a problem with gdata package. When I use the command read.xls, I get this error-message: Erreur dans xls2sep(xls, sheet, verbose = verbose, ..., method = method, : Unable to read translated csv file '/var/folders/gb/gbzQ4sqTF-KK3D5m6v-IJE+++TI/-Tmp-//Rtmp3Hprw9/file10d63af1.csv'. Erreur dans file.exists(tfn) : argument 'file' incorrect dyld: lazy symbol binding failed: Symbol not found: _Perl_Tstack_sp_ptr Referenced from: /Library/Frameworks/R.framework/Resources/library/gdata/perl/darwin-thread-multi-2level/auto/Compress/Raw/Zlib/Zlib.bundle Expected in: dynamic lookup dyld: Symbol not found: _Perl_Tstack_sp_ptr Referenced from: /Library/Frameworks/R.framework/Resources/library/gdata/perl/darwin-thread-multi-2level/auto/Compress/Raw/Zlib/Zlib.bundle Expected in: dynamic lookup I never had this problem with the previous version of R... Could somebody help me? Thank you! Guillaume -- View this message in context: http://n4.nabble.com/gdata-tp1477079p1477079.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] AFTREG with ID argument
Göran, thanks! One more thing that I found: As soon as you have at least one NA in the independent vars, the trick that you mentioned does not work anymore. Example: testdata start stop censor groupvar var1 1 01 01 0.1284928 2 12 01 0.4896125 3 23 01 0.7012899 4 34 01NA 5 01 02 0.7964361 6 12 02 0.8466039 7 23 12 0.2234271 aftreg(Surv(start, stop, censor)~var1, data=testdata, id=testdata$groupvar) Error in order(id, Y[, 1]) : Different length of arguments (* I translated this from the German Output *) Do you think there is a simple hack which excludes all subjects that have at least on NA in their independent vars? If it was only one dependent var it would probably be easy by just using subset, but I have lots of different combinations of vars that I'd like to test ;) Best Philipp PS: Conerning the benmark: For a large dataset (~ 1600 observations on ~300 subjects) processing takes about 40 seconds (core 2 duo @ 2.46 GHz, T9300). Interestingly, processing the testdata-set above with only 7 observations on 2 subjects takes 2 minutes... Göran Broström wrote: Philipp Rappold wrote: Dear all, I have some trouble using the id-argument with aftreg (accelerated failure time regression analysis from the eha library). As far as I understand it, the id argument is used to group individuals together if there are time-varying covariates and the data is arranged in counting process style. Unfortunately, i cannot figure out how to use the id-argument. The most straight-forward way would be to simply state the grouping variable, but it throws an error. I've included an example below: the dataframe for regression is called test, with the grouping variable person. test start end censor person var1 1 0 1 0 1 0.5 2 1 2 0 1 0.4 3 2 3 0 1 0.6 4 3 4 1 1 -0.3 5 0 1 0 2 0.6 6 1 2 0 2 0.7 7 2 3 0 2 0.6 fit - aftreg(Surv(start, end, censor)~var1, data=test, id=person) Error in order(id, Y[, 1]) : argument 1 is not a vector You have caught the _function_ 'person' (package: utils) instead of the variable 'person' in the data frame. That explains the odd error message. If you change the variable name to, e.g., ID, you'll get the error message Error in order(id, Y[, 1]) : object 'id' not found which would hint you in the right direction. You need to specify 'id' by a full name, in your case 'test$person'. This is of course a deficiency in the interface of aftreg. I will fix it asap. So the temporary fix is 'id = test$person'. Thanks for the report, Göran fit - aftreg(Surv(start, end, censor)~var1, data=test, id=test[person]) Error in `[.data.frame`(id, ord) : undefined columns selected What would be the correct way to fit this example model? Thanks + all the best Philipp __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R wiki link ?
PhGr == Philippe Grosjean phgrosj...@sciviews.org on Mon, 08 Feb 2010 19:55:08 +0100 writes: PhGr Prof. John C Nash wrote: Is this a transient problem, or has the link to the R wiki on the R home page (www.r-project.org) to http://wiki.r-project.org/ been corrupted? I can find http://rwiki.sciviews.org that works. PhGr Yes, the problem is known. I have to fix it. and it has been fixed, late yesterday, thanks to Stefan Theussl's kind and swift cooperation. Martin Maechler, ETH Zurich PhGr Best, PhGr Philippe Grosjean __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweve/cacheSweave
Unger, Kristian wrote:
Hi there
I have a problem with using Sweave in combination with the option driver =
cacheSweave.
Whichever code I try to run - when it comes to converting the tex file into
pdf it comes up with the same errors (\csname \endcsname errors). Does anybody
have an idea what it going wrong?
Sweave(pgfSweave-example.Rnw,driver = cacheSweaveDriver)
Writing to file pgfSweave-example.tex
Processing code chunks ...
1 : term verbatim (label=setup)
2 : echo term verbatim (label=data)
3 : term verbatim eps pdf (label=boxplot)
You can now run LaTeX on 'pgfSweave-example.tex'
tools::texi2dvi(pgfSweave-example.tex, pdf=TRUE)
Error in tools::texi2dvi(pgfSweave-example.tex, pdf = TRUE) :
running 'texi2dvi' on 'pgfSweave-example.tex' failed
LaTeX errors:
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: LaTeX E
rror: Missing \begin{document}.
I think this is the important error: it looks as though your .tex file
isn't a complete LaTeX document. The other errors likely follow from this.
Duncan Murdoch
See the LaTeX manual or LaTeX Companion for explanation.
Type H return for immediate help
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
I am running this under Windows XP, R version 2.9.2 (2009-08-24),
package.version(cacheSweave)
[1] 0.4-3.
Any help or advice on this would be highly appreciated!
Best wishes
Kristian
_
Dr Kristian Unger
Bioinformaticist Chernobyl Tissue Bank
Division of Surgery and Cancer
Imperial College London
Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS
Tel +44-20-8383-2443
Mob +44-795-1080619
Skype kristianunger
http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
http://www.chernobyltissuebank.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running rscript in windows
vikrant wrote: Thanks a lot, really. dir() option showd my desktop files and test.R was shown as test.R.txt when I run source(test.R.txt) it worked. Just for your information, I changed the directory using Menu options File- change dir. I verified the same using getwd() command in R. ' This is due to the bizarre default in Windows of suppressing file extensions. Turn that off, so you can see what files are really named, and you will not be confused by secret renamings like this one. Duncan Muroch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweve/cacheSweave
On 11/02/2010 6:06 AM, Duncan Murdoch wrote:
Unger, Kristian wrote:
Hi there
I have a problem with using Sweave in combination with the option driver =
cacheSweave.
Whichever code I try to run - when it comes to converting the tex file into
pdf it comes up with the same errors (\csname \endcsname errors). Does anybody
have an idea what it going wrong?
Sweave(pgfSweave-example.Rnw,driver = cacheSweaveDriver)
Writing to file pgfSweave-example.tex
Processing code chunks ...
1 : term verbatim (label=setup)
2 : echo term verbatim (label=data)
3 : term verbatim eps pdf (label=boxplot)
You can now run LaTeX on 'pgfSweave-example.tex'
tools::texi2dvi(pgfSweave-example.tex, pdf=TRUE)
Error in tools::texi2dvi(pgfSweave-example.tex, pdf = TRUE) :
running 'texi2dvi' on 'pgfSweave-example.tex' failed
LaTeX errors:
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: LaTeX E
rror: Missing \begin{document}.
I think this is the important error: it looks as though your .tex file
isn't a complete LaTeX document. The other errors likely follow from this.
From an offline followup: the .tex was complete, but it included a
path to Sweave.sty that contained TeX-special characters, and that was
the source of the error. See ?RweaveLatex for a discussion of how to
avoid this.
Duncan Murdoch
Duncan Murdoch
See the LaTeX manual or LaTeX Companion for explanation.
Type H return for immediate help
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10: Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
I am running this under Windows XP, R version 2.9.2 (2009-08-24),
package.version(cacheSweave)
[1] 0.4-3.
Any help or advice on this would be highly appreciated!
Best wishes
Kristian
_
Dr Kristian Unger
Bioinformaticist Chernobyl Tissue Bank
Division of Surgery and Cancer
Imperial College London
Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS
Tel +44-20-8383-2443
Mob +44-795-1080619
Skype kristianunger
http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
http://www.chernobyltissuebank.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] ACF and PACF
Hi helpers, can you help me in plotting acf and pacf functions in R. I am using the code acf(variable name) but it is not working. Expecting your reply. Thanks -- View this message in context: http://n4.nabble.com/ACF-and-PACF-tp1477149p1477149.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (linux) display messages in R startup screen
Dear guRus, I'm maintaining central R installation (Linux) for our institute. The startup screen of R traditionally echoes some messages (starting with R version ...Copyright (C).. The R Foundation for Statistical Computing...) and I'd like to display for example right after these messages some other messages about our specific setup, how to contact me etc ... What would be the best place to add this ? I've been looking into the bin/ directory (ie /linux/local/lib64/R/bin) but I'm not shure about the best place/way for such messages. On Windows I've used the etc/Rprofile.site for somehow similar issues, but I haven't seen any equivalent on our linux installation. Any suggestions ? Thank's in advance Wolfgang For completeness: sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et Génomique Intégratives CNRS UMR7104, IGBMC, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger (at) igbmc.fr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Coda or R or input error? (Error in lowess(xp, yp[, k]) :...)
I have been using R with the packages locfit and coda to analyse output from a population genetics program (msvar) which I have been running on an external server (http://cbsuapps.tc.cornell.edu/ index.aspx). One of the first steps is to read the msvar output tables into R and then use coda to analyse the MCMC object. Sometimes, this works perfectly and sometimes, when I try to plot the output, it does not! The error message I get is- Error in lowess(xp, yp[, k]) : NA/NaN/Inf in foreign function call (arg 2) Someone mentioned that this may be because R is very memory hungry and it may be too much for my laptop to cope with. So I tried running it on another computer and this time I cannot even get as far as creating the MCMC object, I get a message telling me that there are non-numeric values: Error in mcmc(data = D1) : Data frame contains non- numeric values I find it difficult to believe that there are any non-numeric values as I have run the msvar analysis on 5 different projects and treated the outputs in exactly the same way; 2 have worked perfectly but the other 3 all produce these same messages. I have checked for empty lines at the end of the files. Is it likely to be because the files are too large? Any help or suggestions would be gratefully received. Many thanks I have pasted the R transcripts below, just in case anyone fancies a read! Laptop- Lowess error A1-read.table(file=hparsA1.dat,sep= ) A2-read.table(file=hparsA2.dat,sep= ) A3-read.table(file=hparsA3.dat,sep= ) dim(A1) [1] 20 11 dim(A2) [1] 20 11 dim(A3) [1] 20 11 mcmc.A1-mcmc(data=A1) mcmc.A2-mcmc(data=A2) mcmc.A3-mcmc(data=A3) plot(mcmc.A1) Error in lowess(xp, yp[, k]) : NA/NaN/Inf in foreign function call (arg 2) plot(mcmc.A2) Error in lowess(xp, yp[, k]) : NA/NaN/Inf in foreign function call (arg 2) plot(mcmc.A3) Error in lowess(xp, yp[, k]) : NA/NaN/Inf in foreign function call (arg 2) Desktop- Non-numeric error D1-read.table(file=hparsD1.dat,sep= ) D2-read.table(file=hparsD2.dat,sep= ) D3-read.table(file=hparsD3.dat,sep= ) mcmc.D1-mcmc(data=D1) Error in mcmc(data = D1) : Data frame contains non-numeric values mcmc.D2-mcmc(data=D2) Error in mcmc(data = D2) : Data frame contains non-numeric values mcmc.D3-mcmc(data=D3) Error in mcmc(data = D3) : Data frame contains non-numeric values __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Zero-inflated Negat. Binom. model
Dear R crew: I am sorry this question has been posted before, but I can't seem to solve this problem yet. I have a simple dataset consisting of two variables: cestode intensity and chick size (defined as CAPI). Intensity is a count and clearly overdispersed, with way too many zeroes. I'm interested in looking at the association between these two variables, i.e. how well does chick size predict tape intensity? Since I have a small sample size, I fit a zero inflated negat. Binomial (not Poisson) model using the pscl package. I built tried two models and got the outputs below. model - zeroinfl(Int_Cesto ~ CAPI, dist = negbin, EM = TRUE) Call: zeroinfl(formula = Int_Cesto ~ CAPI, dist = negbin, EM = TRUE) Count model coefficients (negbin with log link): (Intercept) CAPI -2.99182 0.06817 Theta = 0.4528 Zero-inflation model coefficients (binomial with logit link): (Intercept) CAPI 12.1364 -0.1572 summary(model) Call: zeroinfl(formula = Int_Cesto ~ CAPI, dist = negbin, EM = TRUE) Pearson residuals: Min 1Q Median 3Q Max -0.62751 -0.38842 -0.21303 -0.06899 7.29566 Count model coefficients (negbin with log link): Estimate Std. Error z value Pr(|z|) (Intercept) -2.991823.39555 -0.881 0.3783 CAPI 0.068170.04098 1.664 0.0962 . Log(theta) -0.792220.45031 -1.759 0.0785 . Zero-inflation model coefficients (binomial with logit link): Estimate Std. Error z value Pr(|z|) (Intercept) 12.136363.71918 3.263 0.00110 ** CAPI-0.157200.04989 -3.151 0.00163 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Theta = 0.4528 Number of iterations in BFGS optimization: 1 Log-likelihood: -140.2 on 5 Df QUESTIONS 1. Is my model adequately specified? 2. CAPI is included in blocks 1 of output containing negative binomial regression coefficients for CAPI, and is also included also in block 2 corresponding to the inflation model. Does this make sense? If I specify my model slightly differently, I get what I believe is more reasonable results: model12 - zeroinfl(Int_Cesto ~ 1|CAPI, dist = negbin, EM = TRUE) model12 Call: zeroinfl(formula = Int_Cesto ~ 1 | CAPI, dist = negbin, EM = TRUE) Count model coefficients (negbin with log link): (Intercept) 2.692 Theta = 0.4346 Zero-inflation model coefficients (binomial with logit link): (Intercept) CAPI 13.2476 -0.1708 summary(model12) Call: zeroinfl(formula = Int_Cesto ~ 1 | CAPI, dist = negbin, EM = TRUE) Pearson residuals: Min 1Q Median 3Q Max -0.61616 -0.36902 -0.19466 -0.0 4.85481 Count model coefficients (negbin with log link): Estimate Std. Error z value Pr(|z|) (Intercept) 2.6924 0.3031 8.883 2e-16 *** Log(theta) -0.8334 0.4082 -2.042 0.0412 * Zero-inflation model coefficients (binomial with logit link): Estimate Std. Error z value Pr(|z|) (Intercept) 13.247573.64531 3.634 0.000279 *** CAPI-0.170780.04921 -3.471 0.000519 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Theta = 0.4346 Number of iterations in BFGS optimization: 1 Log-likelihood: -141.9 on 4 Df QUESTION: 1.Is this model specification and output more reasonable? 2.CAPI appears only in the second block that corresponds to the inflation model. Thanks in advance! Luciano [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (linux) display messages in R startup screen
On 11 February 2010 at 12:08, Wolfgang Raffelsberger wrote: | I'm maintaining central R installation (Linux) for our institute. The | startup screen of R traditionally echoes some messages (starting with R | version ...Copyright (C).. The R Foundation for Statistical | Computing...) and I'd like to display for example right after these | messages some other messages about our specific setup, how to contact me | etc ... | What would be the best place to add this ? | | I've been looking into the bin/ directory (ie /linux/local/lib64/R/bin) | but I'm not shure about the best place/way for such messages. | On Windows I've used the etc/Rprofile.site for somehow similar issues, | but I haven't seen any equivalent on our linux installation. You can use the same file -- $(R_HOME)/etc/Rprofile.site -- see help(Startup). For Debian/Ubuntu we also store it in /etc/R/Rprofile.site and soft-link it back to $(R_HOME)/etc but R only knows the latter location. Hth, Dirk -- Registration is open for the 2nd International conference R / Finance 2010 See http://www.RinFinance.com for details, and see you in Chicago in April! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] cluster/distance large matrix
Hi all, I've stumbled upon some memory limitations for the analysis that I want to run. I've a matrix of distances between 38000 objects. These distances were calculated outside of R. I want to cluster these objects. For smaller sets (egn=100) this is how I proceed: A-matrix(scan(file, n=100*100),100,100, byrow=TRUE) ad-as.dist(A) ahc-hclust(ad,method=ward,members=NULL) However if I try this with the real dataset I end up with memory problems. I've the 64bit version of R installed on a machine with 40Gb RAM (Windows 2003 64bit version). I'm thinking about using only the lower triangle of the matrix but I can't create a distance object for the clustering from the lower.tri Can someone help me with a suggestion for which way to go? Best Regards Bart Thijs -- View this message in context: http://n4.nabble.com/cluster-distance-large-matrix-tp1477237p1477237.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] GWRM package
I'd like to announce the availability of the GWRM package. It provides a set of functions for fitting Generalized Waring Regression Models. It also includes the dataset and the example of Rodriguez-Avi, J; Conde-Sanchez, A; Saez-Castillo, A.J., Olmo-Jimenez, M. J. and Martinez Rodriguez, A. M.(2009). A generalized Waring regression model for count data. Computational Statistics and Data Analysis, 53, pp. 3717-3725. The package has been uploaded to CRAN and is now available under the GPL-2 license. Antonio Jose Saez-Castillo, Ph.D. ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweve/cacheSweave
Thank you very much Duncan! Adding the line \usepackage{Sweave} fixed the
problem.
Best wishes
Kristian
_
Dr Kristian Unger
Bioinformaticist Chernobyl Tissue Bank
Division of Surgery and Cancer
Imperial College London
Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS
Tel +44-20-8383-2443
Mob +44-795-1080619
Skype kristianunger
http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
http://www.chernobyltissuebank.com
-Original Message-
From: Duncan Murdoch [mailto:murd...@stats.uwo.ca]
Sent: 11 February 2010 12:06
To: Unger, Kristian
Cc: 'r-help@r-project.org'
Subject: Re: [R] Sweve/cacheSweave
On 11/02/2010 6:06 AM, Duncan Murdoch wrote:
Unger, Kristian wrote:
Hi there
I have a problem with using Sweave in combination with the option driver =
cacheSweave.
Whichever code I try to run - when it comes to converting the tex file into
pdf it comes up with the same errors (\csname \endcsname errors). Does
anybody have an idea what it going wrong?
Sweave(pgfSweave-example.Rnw,driver = cacheSweaveDriver)
Writing to file pgfSweave-example.tex
Processing code chunks ...
1 : term verbatim (label=setup)
2 : echo term verbatim (label=data)
3 : term verbatim eps pdf (label=boxplot)
You can now run LaTeX on 'pgfSweave-example.tex'
tools::texi2dvi(pgfSweave-example.tex, pdf=TRUE)
Error in tools::texi2dvi(pgfSweave-example.tex, pdf = TRUE) :
running 'texi2dvi' on 'pgfSweave-example.tex' failed
LaTeX errors:
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10:
Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10:
LaTeX E
rror: Missing \begin{document}.
I think this is the important error: it looks as though your .tex file
isn't a complete LaTeX document. The other errors likely follow from this.
From an offline followup: the .tex was complete, but it included a
path to Sweave.sty that contained TeX-special characters, and that was
the source of the error. See ?RweaveLatex for a discussion of how to
avoid this.
Duncan Murdoch
Duncan Murdoch
See the LaTeX manual or LaTeX Companion for explanation.
Type H return for immediate help
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10:
Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10:
Missing
\endcsname inserted
The control sequence marked to be read again should
not appear between \csname and \endcsname.
C:/Imperial/Sileida/DOUBLECHECK/ALL/eval_amps/pgfSweave-example.tex:10:
Extra \
endcsname
I'm ignoring this, since I wasn't doing a \csname.
I am running this under Windows XP, R version 2.9.2 (2009-08-24),
package.version(cacheSweave)
[1] 0.4-3.
Any help or advice on this would be highly appreciated!
Best wishes
Kristian
_
Dr Kristian Unger
Bioinformaticist Chernobyl Tissue Bank
Division of Surgery and Cancer
Imperial College London
Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS
Tel +44-20-8383-2443
Mob +44-795-1080619
Skype kristianunger
http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
http://www.chernobyltissuebank.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] cluster/distance large matrix
Dear Bart, a strange thing in your question is that the term Ward's method usually refers to a method based on the k-means criterion, which, in its standard form, is not based on dissimilarities, but on objects*variables-data. So I wonder how and why you want to use Ward's method on a dissimilarity matrix in the first place (I know that the k-means criterion can in principle be translated to dissimilarity data - this is probably what hclust's method=ward does if fed with a dissimilarity matrix, but I'm not sure -, but then it loses its justification). One thing you could think about is using the function pam in library cluster. Chances are that this won't work on 38,000 cases either, but you may cluster a subsample of, say, 2,000 cases and assign all further objects to the most similar cluster medoid. It is well know that hierarchical methods are problematic with too large dissimilarity matrices; even if you resolve the memory problem, the number of operations required is enormous. Hope this helps, Christian On Thu, 11 Feb 2010, Bart Thijs wrote: Hi all, I've stumbled upon some memory limitations for the analysis that I want to run. I've a matrix of distances between 38000 objects. These distances were calculated outside of R. I want to cluster these objects. For smaller sets (egn=100) this is how I proceed: A-matrix(scan(file, n=100*100),100,100, byrow=TRUE) ad-as.dist(A) ahc-hclust(ad,method=ward,members=NULL) However if I try this with the real dataset I end up with memory problems. I've the 64bit version of R installed on a machine with 40Gb RAM (Windows 2003 64bit version). I'm thinking about using only the lower triangle of the matrix but I can't create a distance object for the clustering from the lower.tri Can someone help me with a suggestion for which way to go? Best Regards Bart Thijs -- View this message in context: http://n4.nabble.com/cluster-distance-large-matrix-tp1477237p1477237.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. *** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 chr...@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ACF and PACF
On 11.02.2010 12:48, sathiya_mtm wrote: Hi helpers, can you help me in plotting acf and pacf functions in R. I am using the code acf(variable name) but it is not working. For me it is, hence citing the footer of al R-help messages: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Uwe Ligges Expecting your reply. Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] WMF conversion
Could you save the original graphics as a pdf, and include the pdf in Powerpoint? -- begin included message -- Unfortunately, after placed in the PowerPoint and the PowerPoint is converted to PDF via MS Office's built in conversion utility, the resulting image have diagonal streaks across them from the y-axis down to the x-axis. The rest of the document is perfect, but the WMF images now have streaks across them. It looks like it may be caused, somehow, by the dotted grid. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Total least squares linear regression
This is also called Deming regression and perhaps many other things.
It is a lively topic in the validation of competing assay methods in the
laboratory. I have a function 'deming.R' that does a generalized form
of this, based on the (very nice) article below, the code is attached.
(The attachments will be stripped by R-help, but the original requestor
will get them.) If someone thinks this to be of general enough interest
to package up on CRAN I'm happy donate the code to them -- I won't have
the time for some while.
Terry T.
BD Ripley and M Thompson, Regression techniques for the detection
of analytical bias, Analyst 112:377-383, 1987.
- begin included message ---
After a thorough research, I still find myself unable to find a
function
that does linear regression of 2 vectors of data using the total least
squares, also called orthogonal regression (see :
http://en.wikipedia.org/wiki/Total_least_squares) instead of the
ordinary least squares method. Indeed, the lm function has a
method argument but the manual says that there is only one option so
far.
However, since the samples I am studying have the type of relationship
that requires orthogonal regression, I am bound to use it.
x se.x y se.y
871 192 735 207
701 156 792 223
328 76 340 096
560 126 544 153
155 39 207 59
175 43 229 65
73 22 66 19
366 84 343 97
90 25 125 36
939 207 658 185
439 100 331 93
369 84 272 77
34 13 232 66
194 47 150 43
207 50 350 99
138 36 117 33
181 45 231 66
127 33 188 54
82 23 44 13
188 46 137 40
566 127 704 198
0 06 0 1
0 6 49 15
40 15 129 37
0 6 37 12
198 48 216 62
1021 224 1253 351
464 105 390 110
566 127 466 131
1925 418 1586 445
\name{deming}
\alias{deming}
\title{Fit a generalized Deming regression}
\description{
Find the MLE line relating x and y when both are measured with
error. When the variances are constant and equal, this is the
special case of Deming regression.
For laboratory analytes this is rarely true, however.
}
\usage{
ripleyfit(x, y, xstd, ystd, jackknife = TRUE, dfbeta = FALSE, scale=T)
}
\arguments{
\item{x}{A numeric vector}
\item{y}{A numeric vector}
\item{xstd}{Either a numeric vector of the same length as \code{x}
giving the standard error for each of the elements, or a vector of
length 2 giving the error formula.}
\item{ystd}{Either a numeric vector of the same length as \code{y}
giving the standard error for each of the elements, or a vector of
length 2 giving the error formula.}
\item{jackknife}{Produce jackknife estimates of standard error.}
\item{dfbeta}{Return the dfbeta matrix}
\item{scale}{Compute an estimate of residual variance or scale.
If FALSE, the estimates of variance \code{xstd} and \code{ystd} are
assumed to be perfectly calibrated.}
}
\details{
The \code{xstd} specification can be a pair of
values a, b; if so then the standard deviation of \code{x} is assumed
to be \code{a + b*x}; similarly for \code{ystd}.
An assumption of constant variance (homoscedasticity) correponds to \code{b=0}.
If \code{b} is 0 for both \code{x} and \code{y},
then the result depends only on the
ratio of the \code{a} values, which is the ratio of the variances.
To fit a Deming regression for instance use \code{c(1,0)} for
both specifications. (Use of (k,0) for both would give the same answer
for any value k).
When \code{a} is zero this is a model assuming constant coefficient of
variation.
Values of stdx= (0,k) and stdy = (0,1) correspond to the case of contant
proportional errors discussed by Linnet.
The most realistic case is where both \code{a} and \code{b} are
non-zero and have been estimated from prior data.
}
\value{
If \code{jackknife} is FALSE the result is a vector containing the
intercept and the slope, otherwise it is a list with components:
\item{coefficient}{The coefficient vector, containing the intercept and
slope.}
\item{variance}{The jackknife estimate of variance}
\item{dfbeta}{Optionally, the dfbeta residuals. A 2 column matrix,
each row is the change in the coefficient vector if that observation is
removed from the data.}
}
\details{
The standard printout includes test of intercept=0 and of slope=1.}
\references{
BD Ripley and M Thompson, Regression techniques for the detection
of analytical bias, Analyst 112:377-383, 1987.
K Linnet, Estimation of the linear relationship between the
measurements of two methods with proportional errors.
Statistics in Medicine 9:1463-1473, 1990.
}
\author{Terry Therneau}
\examples{
# Data from Ripley
arsenic - data.frame(
x=c(871, 701, 328, 560, 155, 175, 73, 366, 90, 939, 439, 369, 34, 194,
207, 138, 181, 127, 82, 188, 566, 0, 0, 40, 0, 198, 1021, 464, 566,
1925)/100,
y=c(735, 792, 340, 544, 207, 229, 66, 343, 125, 658, 331, 272, 232, 150,
350, 117, 231, 188, 44, 137, 704, 0, 49, 129, 37, 216, 1253, 390,
466, 1586)/100,
se.x=c(192, 156, 76, 126, 39, 43, 22, 84, 25, 207, 100, 84, 13, 47,
50, 36, 45, 33, 23, 46,
[R] Odp: Simplify the code
Hi
I did not see the answer yet, probably nobody is much interested in such
function, so I will try.
r-help-boun...@r-project.org napsal dne 10.02.2010 21:57:42:
Hi all,
I wrote the following code for the function that is attached.
I want to simply the code.
Why. If it works there is no problem until you encounter performance
issues. If it does not work you shall specify what is wrong with it.
Many functions are vectorised (including choose and beta) so you could
probably get rid of nested cycles but I am far from elaborating how to
change your code and make it simpler (shorter, quicker ???)
Regards
Petr
Can some one give me some help?
The function is attached and the following is the code:
## f1 is the function calculate the value outside the sum
f1 - function(t, a, b) {t/beta(a, b)}
## f2 is the function that calculates the summand
f2 - function(j, k, t, a, b){choose(j-1,k-1)*(1-t)^(j-1) * beta(a+k,
b+j-
k)}
## f3 calculates the sum
f3 - function(n, t, a, b){
ss - matrix(0, nrow=n, ncol=n)
for (j in 1:n){
for (i in 1:j) {
ss[i,j]- f2(j,i, t, a, b)
}
}
sum - sum(ss)
return(sum)
}
## f is the final function
f - function(n,t, a, b) {f1(t,a ,b)*f3(n,t,a,b)}
##
Many thanks!
Hannah
[příloha question to R-heip.pdf odstraněna uživatelem Petr PIKAL/CTCAP]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Question re model development
Dear Sir/Madam I'm trying quite a long shot here... I have used R previously, and would just like to know if any software/model has been designed which will allow me to project the future risk profile of a group of insured lives (by factors such as age, gender etc.), based on past and exisiting risk profiles of the covered lives? If you could point me in the direction of a similar project or code it would be much appreciated. Thank you. Stratos Laskarides [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] for loop the can be skipped
Hello,
there is compact way to skip a for loop when the requested number of
iterations is 0 ?
For example, something equivalent to the following code:
for (i in some_function(from=1,to=iteration_cycles)) { ... }
Where the loop is skipped when iteration_cycles==0
Thanks in advance.
F: Pollastri
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] for loop the can be skipped
On 11/02/2010 9:28 AM, Fabrizio Pollastri wrote:
Hello,
there is compact way to skip a for loop when the requested number of
iterations is 0 ?
For example, something equivalent to the following code:
for (i in some_function(from=1,to=iteration_cycles)) { ... }
Where the loop is skipped when iteration_cycles==0
Sure:
for (i in seq_len(iteration_cycles)) { ... }
will execute 0 times if requested.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Biclustering package
Thank you very much Gabor. Alex On Thu, Feb 11, 2010 at 10:55 AM, Gábor Csárdi csa...@rmki.kfki.hu wrote: Alex, the isa2 package implements the biclustering algorithm discussed in Bergmann S, Ihmels J, and Barkai N. Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Rev E Stat Nonlin Soft Matter Phys 2003 Mar; 67(3 Pt 1) 031902 Best, Gabor On Thu, Feb 11, 2010 at 10:51 AM, Alex Roy alexroy2...@gmail.com wrote: Hello, I am looking for R package which can perform biclustering a part from biclust package. thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gabor Csardi gabor.csa...@unil.ch UNIL DGM [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cluster/distance large matrix (fwd)
On Thu, 11 Feb 2010, Christian Hennig wrote: It is well know that hierarchical methods are problematic with too large dissimilarity matrices; even if you resolve the memory problem, the number of operations required is enormous. There is at least one exception to this. Single-linkage hierarchical clustering with a convex distance such as Euclidean distance is feasible for quite large data sets using algorithms for the Euclidean minimum spanning tree. For tens to hundreds of thousands of points (flow cytometry data) the algorithm in the nnclust package is competitive in speed with model-based clustering (on a 32-bit system). It's slower than pam(), but it is deterministic. This doesn't apply to the original question, of course. -thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Suprising behavior of paste or cat?
If the list would provide additional reports I'd appreciate it. I replicated the effect this morning on another Windows XP machine... R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.1 ... and I replicated it using the current development build... R version 2.11.0 Under development (unstable) (2010-02-09 r51113) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base In additionally I've determined that when h.long = 150; both cat and write fail, but when h.long = 100 only the file write with cat fails. Please advise. Best, Russell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R ANOVA gives diferent results than SPSS
I guess my subject says it all. But I loaded a dataset in spss and used the foreign package to read and save it in R. Running an anova (using the aov command) gives a different F and p value in R than it does in SPSS. ANy idea what is going on? -- View this message in context: http://n4.nabble.com/R-ANOVA-gives-diferent-results-than-SPSS-tp1477322p1477322.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Using Rscript in combination with eval() results in error
Dear List,
I'm having trouble running a .bat file which calls an R-Script via the
command line (using Rscript).
I put the following line in a file called test.bat:
Rscript --vanilla test.R
Then I tried to launch test.bat via Windows' CMD (I plan to make this a
scheduled Windows task).
The actual R-script (test.R) is executed just fine until it gets to a line
containing an eval() expression:
eval(parse(file=C:/temp/another.script.R))
and R (or Windows' CMD, respectively) throws the following error
Error in if (file == ) - stdin() else { : Argument is of length 0
Calls: source - eval.with.vis - eval.wtih.vis - source
Execution stopped
Usually such eval() expressions work just fine in my scripts.
I tried the following already:
1) to.load.file - file(C:/temp/another.script.R, open=rt);
eval(parse(file=to.load.file): No luck
2) Running test.R within a Rterm session: Works fine.
3) Calling the following from within a Rterm session:
system(Rscript C:/temp/test.R, wait=TRUE, invisible=FALSE)
That works too!
Is there something one needs to be aware of regarding eval() or source()
when launching a script via a CMD call to a .bat file?
Im running Windows XP and R-2.10.1
Any hints greatly appreciated!
Thanks,
Janko
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] trouble with read.table and colClasses='raw'
Hi all, First off, it is surprising that there are no examples of how to use read.table() under ?read.table ! I am trying to read in a flat file of type 'raw'. It has 1000 rows and 600K columns. I have the RAM to accomplish this, but can't get the data into R using read.table: x - read.table(data,header=TRUE,colClasses=rep(,60)) #returns error: no method or default for coercing character to raw Then I thought that maybe the colClasses vector needed to actually *be* the mode needed (here's where an example under ?read.table would help): x - read.table(data,header=TRUE,colClasses=rep(as.raw(1),60)) I waited on the latter command for a couple of hours before killing the process. What should the colClasses argument be? Should I be using another method to read the data into R? Previous experience using scan() and readLines() showed that read.table() was faster, at least for those examples, so I've stopped trying to use those other functions. Thank you, JJ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R ANOVA gives diferent results than SPSS
On Thu, 11 Feb 2010, Protzko wrote: I guess my subject says it all. But I loaded a dataset in spss and used the foreign package to read and save it in R. Running an anova (using the aov command) gives a different F and p value in R than it does in SPSS. ANy idea what is going on? Yes. Either you specified a different model or different tests for the same model in the two systems, or you are interpreting the output incorrectly, or the results are different. Without more detail it is hard to be sure, but the first two possibilities seem more likely. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unexpected output in first iteration of for-loop
You have a mistake in how you're setting up the object named result
before the loop.
You set result - latentVariableNames. It is a vector of length 6,
when you call the function with LV. The printout from the first
iteration shows this.
But then you rbind result with a data frame that has three columns.
These are basically incompatible, but R (apparently silently) wraps
the vector of length 6 into two rows of three columns.
Here's an example:
foo - letters[1:6]
names(foo) - c('a','b','c')
foo
abc NA NA NA
a b c d e f
rbind(foo, data.frame(a='X', b='Y', c='Z',stringsAsFactors=FALSE))
a b c
1 a b c
2 X Y Z
What I would do is something like this (untested):
loopCronbach - function(latentVariableNames, groupingVariable) {
n - length(latentVariableNames)
tmp1 - tmp2 - numeric(n)
for (i in 1:n) {
tmp1[i] - calculateIndividualCronbach(get(latentVariableNames[i]))
tmp2[i] - calculateGroupCronbach(get(latentVariableNames[i]),
groupingVariable)
}
result -
data.frame(latentVariable=latentVariableNames,Indiv=tmp1,Group=tmp2)
names(result) - c(latentVariable, Indiv, Group)
result ## no need to use return()
}
Building up a dataframe row by row using rbind() is in general an
expensive way to do things -- although in this instance it's such a
small dataframe that it doesn't matter.
-Don
At 10:56 AM +0100 2/11/10, Chaehan So wrote:
Ok, you're right - may I rephrase:
How should I modify the assignment of result - latentVariableNames
so it produces the output without the first line?
I thought result - NULL should do the job, but it didn't because of the
following names(result) assignment (which I understand, but not how I
can workaround it).
Here's the output and code again:
latentVariable Indiv Group
1 rPlanning rIterat rTDD
2 rPlanning0.79 0.84
3rIterat0.79 0.83
4 rTDD 0.9 0.96
5 rStandup0.83 0.82
6rRetros 0.9 0.95
7rAccess0.91 0.92
8 rAccTest0.87 0.9
#
LV - c(rPlanning, rIterat, rTDD, rStandup, rRetros, rAccess,
rAccTest)
#
loopCronbach - function(latentVariableNames, groupingVariable)
{
result - latentVariableNames
names(result) - c(latentVariable, Indiv, Group)
for (currentName in latentVariableNames)
{
print(currentName)
print(result)
tmp1 - calculateIndividualCronbach(get(currentName))
tmp2 - calculateGroupCronbach(get(currentName), groupingVariable)
result - rbind(result,data.frame(latentVariable=currentName,
Indiv=tmp1,Group=tmp2))
}
return(result)
}
On Thu, Feb 11, 2010 at 3:31 AM, jim holtman jholt...@gmail.com wrote:
It doing exactly what you asked it to do. You have the assignment:
result - latentVariableNames
and then you print it out in the loop. What were you expecting?
On Wed, Feb 10, 2010 at 9:06 PM, Chaehan So chaehan...@gmail.com wrote:
Dear r-helpers,
why do I get an output in the first iteration of the for-loop
which contains the string values of the input vector,
and how can I avoid that?
Here's the output (only line 1 is wrong)
latentVariable Indiv Group
1 rPlanning rIterat rTDD
2 rPlanning0.79 0.84
3rIterat0.79 0.83
4 rTDD 0.9 0.96
5 rStandup0.83 0.82
6rRetros 0.9 0.95
7rAccess0.91 0.92
8 rAccTest0.87 0.9
#
LV - c(rPlanning, rIterat, rTDD, rStandup, rRetros, rAccess,
rAccTest)
#
loopCronbach - function(latentVariableNames, groupingVariable)
{
result - latentVariableNames
names(result) - c(latentVariable, Indiv, Group)
for (currentName in latentVariableNames)
{
print(currentName)
print(result)
tmp1 - calculateIndividualCronbach(get(currentName))
tmp2 - calculateGroupCronbach(get(currentName), groupingVariable)
result - rbind(result,data.frame(latentVariable=currentName,
Indiv=tmp1,Group=tmp2))
}
return(result)
}
a - loopCronbach(LV, u_proj)
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
--
Humboldt University Berlin, Germany
Institute of Psychology
Rudower Chaussee 18, Room 1221
12489 Berlin
Germany
Office: +49 30 2093 - 9337
Mobile: +49 171- 626 9373
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
--
Don
Re: [R] histogam plots
Thank you very much for your reply. That was very helpful.
I also want to add two density curves on top of each histgram. One is the
density curve of a standard normal random variable. The other is the
denstity curve according to the histgram.
I was trying to use the function
panel.mathdensity, but not successful.
Can anyone give me some help?
Thank you!
2010/2/11 bill.venab...@csiro.au
One way round this is to use lattice. With your matrix 'w' you might
W - data.frame(w = as.vector(w),
r = factor(as.vector(row(w))) )
require(lattice)
histogram(~w|r, W)
Identical axis systems will be used for all panels.
Bill Venables
CSIRO/CMIS Cleveland Laboratories
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of li li
Sent: Thursday, 11 February 2010 2:52 PM
To: r-help
Subject: [R] histogam plots
Hi all,
I want to draw a histgram for each row of a matrix and compare them.
However the plot I
got does not have the same y range and x range, which makes it difficult to
make the comparison.
Is there a easy way to fix the x range and y range in a xy plot for
several
plots, instead of specifying
them for each plot.
The following is my code for generalizing the matrix and draw the
histogram.
gen is the function to generate the dta
gen - function(m, rho) {
library(MASS)
set.seed(103)
theta - 0
theta1 - 2
pi0 - 0.9
mzero - pi0*m
mean - c(rep(theta, mzero), rep(theta1,m-mzero))
J - rep(1, m)
var - function(rho) {(1-rho)*diag(m)+ rho*J%*%t(J)}
t - mvrnorm(1, mean, var(rho))
return(t)
}
### w is the matrix. A histgram is drawn for each of the rows.
n - 1000
r - seq(0,0.9, by=0.1)
w - matrix(0, ncol=n, nrow=length(r))
for (i in 1: length(r)){w[i,]- gen(n,r[i])}
par(mfrow=c(2,5))
hist(w[1,], breaks=100)
hist(w[2,], breaks=100)
hist(w[3,], breaks=100)
hist(w[4,], breaks=100)
hist(w[5,], breaks=100)
hist(w[6,], breaks=100)
hist(w[7,], breaks=100)
hist(w[8,], breaks=100)
hist(w[9,], breaks=100)
hist(w[10,], breaks=100)
##
Thank you !
Li
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating a new Access database with R
I am facing the same problem as well, I would like to code with following
concept but wondering how to cope it.
if (*mdb file exist)
{ add new row/col }
else
{ add new *mdb file }
--
From: Uri Shimron UriShimron_at_optiver.com
Date: Thu 21 Sep 2006 - 13:27:35 GMT
First of all, since this is my first posting, I would like to thank
anybody who works/has worked on R, and made it such a beautiful open
source package!
My question is: how do I create a new Access database with R? I need a
channel before I can do anything, but if the mdb-file doesn't exist, I
can't connect to it with odbcConnectAccess.
I've looked at the RODBC.pdf on CRAN, searched the mailing-lists, and
looked at test.R file in the package. But probably I've overlooked
something.
It is of course possible to keep a clean new mdb-file somewhere and then
copy it to the required directory with:
shell(copy EmptyDB.mdb NewLocation.mdb)
But that isn't very elegant...
Thanks in advance,
Uri Shimron
_
USB$B%a%b%jBe$o$j$K$*;H$$$/$...@$5$$!#l5na$g;H$($k(B25GB$B!#(B
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble with read.table and colClasses='raw'
Hi! |colClasses| character. A vector of classes to be assumed for the columns. I'm not an R expert and I don't know what your flat file raw is, but the colClasses argument is to define whether the column will be treated as containing factors, logical, integer etc... For more on read.table, read the manual R Data Import/Export available on the R-project website. I don't know if it helps, but I hope it does! Ivan Le 2/11/2010 16:36, Johan Jackson a écrit : Hi all, First off, it is surprising that there are no examples of how to use read.table() under ?read.table ! I am trying to read in a flat file of type 'raw'. It has 1000 rows and 600K columns. I have the RAM to accomplish this, but can't get the data into R using read.table: x- read.table(data,header=TRUE,colClasses=rep(,60)) #returns error: no method or default for coercing character to raw Then I thought that maybe the colClasses vector needed to actually *be* the mode needed (here's where an example under ?read.table would help): x- read.table(data,header=TRUE,colClasses=rep(as.raw(1),60)) I waited on the latter command for a couple of hours before killing the process. What should the colClasses argument be? Should I be using another method to read the data into R? Previous experience using scan() and readLines() showed that read.table() was faster, at least for those examples, so I've stopped trying to use those other functions. Thank you, JJ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simplify the code
Thank you for your reply. I was just trying to make the code less
complicated.
I got your point.
Thanks!
2010/2/11 Petr PIKAL petr.pi...@precheza.cz
Hi
I did not see the answer yet, probably nobody is much interested in such
function, so I will try.
r-help-boun...@r-project.org napsal dne 10.02.2010 21:57:42:
Hi all,
I wrote the following code for the function that is attached.
I want to simply the code.
Why. If it works there is no problem until you encounter performance
issues. If it does not work you shall specify what is wrong with it.
Many functions are vectorised (including choose and beta) so you could
probably get rid of nested cycles but I am far from elaborating how to
change your code and make it simpler (shorter, quicker ???)
Regards
Petr
Can some one give me some help?
The function is attached and the following is the code:
## f1 is the function calculate the value outside the sum
f1 - function(t, a, b) {t/beta(a, b)}
## f2 is the function that calculates the summand
f2 - function(j, k, t, a, b){choose(j-1,k-1)*(1-t)^(j-1) * beta(a+k,
b+j-
k)}
## f3 calculates the sum
f3 - function(n, t, a, b){
ss - matrix(0, nrow=n, ncol=n)
for (j in 1:n){
for (i in 1:j) {
ss[i,j]- f2(j,i, t, a, b)
}
}
sum - sum(ss)
return(sum)
}
## f is the final function
f - function(n,t, a, b) {f1(t,a ,b)*f3(n,t,a,b)}
##
Many thanks!
Hannah
[pøíloha question to R-heip.pdf odstranìna u¾ivatelem Petr PIKAL/CTCAP]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Zero-inflated Negat. Binom. model
On Thu, 11 Feb 2010, Luciano La Sala wrote: Dear R crew: I am sorry this question has been posted before, but I can't seem to solve this problem yet. Just for the others reader who might not recall that you asked virtually the same question last week. This was my reply: https://stat.ethz.ch/pipermail/r-help/2010-February/227040.html I have a simple dataset consisting of two variables: cestode intensity and chick size (defined as CAPI). Intensity is a count and clearly overdispersed, with way too many zeroes. I'm interested in looking at the association between these two variables, i.e. how well does chick size predict tape intensity? Since I have a small sample size, I fit a zero inflated negat. Binomial (not Poisson) model using the pscl package. I built tried two models and got the outputs below. model - zeroinfl(Int_Cesto ~ CAPI, dist = negbin, EM = TRUE) Call: zeroinfl(formula = Int_Cesto ~ CAPI, dist = negbin, EM = TRUE) Count model coefficients (negbin with log link): (Intercept) CAPI -2.99182 0.06817 Theta = 0.4528 Zero-inflation model coefficients (binomial with logit link): (Intercept) CAPI 12.1364 -0.1572 summary(model) Call: zeroinfl(formula = Int_Cesto ~ CAPI, dist = negbin, EM = TRUE) Pearson residuals: Min 1Q Median 3Q Max -0.62751 -0.38842 -0.21303 -0.06899 7.29566 Count model coefficients (negbin with log link): Estimate Std. Error z value Pr(|z|) (Intercept) -2.991823.39555 -0.881 0.3783 CAPI 0.068170.04098 1.664 0.0962 . Log(theta) -0.792220.45031 -1.759 0.0785 . Zero-inflation model coefficients (binomial with logit link): Estimate Std. Error z value Pr(|z|) (Intercept) 12.136363.71918 3.263 0.00110 ** CAPI-0.157200.04989 -3.151 0.00163 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Theta = 0.4528 Number of iterations in BFGS optimization: 1 Log-likelihood: -140.2 on 5 Df QUESTIONS 1. Is my model adequately specified? See my reply linked above. I guess it's hard to say more than that. 2. CAPI is included in blocks 1 of output containing negative binomial regression coefficients for CAPI, and is also included also in block 2 corresponding to the inflation model. Does this make sense? Dito. If I specify my model slightly differently, I get what I believe is more reasonable results: model12 - zeroinfl(Int_Cesto ~ 1|CAPI, dist = negbin, EM = TRUE) model12 Call: zeroinfl(formula = Int_Cesto ~ 1 | CAPI, dist = negbin, EM = TRUE) Count model coefficients (negbin with log link): (Intercept) 2.692 Theta = 0.4346 Zero-inflation model coefficients (binomial with logit link): (Intercept) CAPI 13.2476 -0.1708 summary(model12) Call: zeroinfl(formula = Int_Cesto ~ 1 | CAPI, dist = negbin, EM = TRUE) Pearson residuals: Min 1Q Median 3Q Max -0.61616 -0.36902 -0.19466 -0.0 4.85481 Count model coefficients (negbin with log link): Estimate Std. Error z value Pr(|z|) (Intercept) 2.6924 0.3031 8.883 2e-16 *** Log(theta) -0.8334 0.4082 -2.042 0.0412 * Zero-inflation model coefficients (binomial with logit link): Estimate Std. Error z value Pr(|z|) (Intercept) 13.247573.64531 3.634 0.000279 *** CAPI-0.170780.04921 -3.471 0.000519 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Theta = 0.4346 Number of iterations in BFGS optimization: 1 Log-likelihood: -141.9 on 4 Df QUESTION: 1.Is this model specification and output more reasonable? 2.CAPI appears only in the second block that corresponds to the inflation model. You can apply standard model selection techniques. Hands-on examples for that are in the vignette that I pointed you to last week: vignette(countreg, package = pscl) Different model selection strategies may however yield different models. AIC will prefer the model with CAPI in the count equation. In contrast, a Wald test at 5% level would drop it. You could also look at the BIC and at the LR test. My guess is though that the answer will be: CAPI has some weak but practically not very relevant influence on the mean in the count component. But I strongly recommend that you try to get more familiar with the zero-inflated model and the general model selection strategies. Or you could try to get help from a local statistician to obtain an appropriate model and interpret its results. hth, Z Thanks in advance! Luciano [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list
Re: [R] trouble with read.table and colClasses='raw'
Well, it's too complicated for me! Here are what I would do (limited
since I'm still a newbie)
1) the syntax seems correct, it should work. The problem is somewhere
else, coming from your own file. Did you try skipping the colClasses
argument? To see how it looks like... If you can import it that way, try
str(x) to see what you have. It might help you.
2) I've never had that much data to import, and for me read.table works
well.
You might want to wait for the experts!
Ivan
Le 2/11/2010 17:14, Johan Jackson a écrit :
Hi Ivan,
Thanks for the reply. Damn IT! My original post was screwed up. HERE
is what I did:
x - read.table(data,header=TRUE,colClasses=rep('raw',60))
#returns error: no method or default for coercing character to raw
I've read the ?read.table and the colClasses argument. I'm still unclear:
1) colClasses is a character vector, is that right? That seems to be
what the help says, but I get an error when I do the above.
2) what is the most efficient way to read in huge amounts of data? In
the past I found that scan() and readLines() were slower than read.table.
Thanks,
JJ
On Thu, Feb 11, 2010 at 8:53 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de mailto:ivan.calan...@uni-hamburg.de
wrote:
Hi!
|colClasses| character. A vector of classes to be assumed
for the
columns.
I'm not an R expert and I don't know what your flat file raw is, but
the colClasses argument is to define whether the column will be
treated
as containing factors, logical, integer etc...
For more on read.table, read the manual R Data Import/Export
available
on the R-project website.
I don't know if it helps, but I hope it does!
Ivan
Le 2/11/2010 16:36, Johan Jackson a écrit :
Hi all,
First off, it is surprising that there are no examples of how to use
read.table() under ?read.table !
I am trying to read in a flat file of type 'raw'. It has 1000
rows and 600K
columns. I have the RAM to accomplish this, but can't get the
data into R
using read.table:
x- read.table(data,header=TRUE,colClasses=rep(,60))
#returns error: no method or default for coercing character
to raw
Then I thought that maybe the colClasses vector needed to
actually *be* the
mode needed (here's where an example under ?read.table would help):
x- read.table(data,header=TRUE,colClasses=rep(as.raw(1),60))
I waited on the latter command for a couple of hours before
killing the
process. What should the colClasses argument be?
Should I be using another method to read the data into R? Previous
experience using scan() and readLines() showed that read.table()
was faster,
at least for those examples, so I've stopped trying to use those
other
functions.
Thank you,
JJ
[[alternative HTML version deleted]]
__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] AFTREG with ID argument
On Feb 11, 2010, at 5:58 AM, Philipp Rappold wrote: Göran, thanks! One more thing that I found: As soon as you have at least one NA in the independent vars, the trick that you mentioned does not work anymore. Example: testdata start stop censor groupvar var1 1 01 01 0.1284928 2 12 01 0.4896125 3 23 01 0.7012899 4 34 01NA 5 01 02 0.7964361 6 12 02 0.8466039 7 23 12 0.2234271 aftreg(Surv(start, stop, censor)~var1, data=testdata, id=testdata $groupvar) Error in order(id, Y[, 1]) : Different length of arguments (* I translated this from the German Output *) Do you think there is a simple hack which excludes all subjects that have at least on NA in their independent vars? If it was only one dependent var it would probably be easy by just using subset, but I have lots of different combinations of vars that I'd like to test ;) I don't know if it's a hack, but there are a set of functions that perform such subsetting: ?na.omit There is a parameter that would accomplish that goal inside aftreg. You may want to check what your defaults are for na.action. -- David. Best Philipp PS: Conerning the benmark: For a large dataset (~ 1600 observations on ~300 subjects) processing takes about 40 seconds (core 2 duo @ 2.46 GHz, T9300). Interestingly, processing the testdata-set above with only 7 observations on 2 subjects takes 2 minutes... Göran Broström wrote: Philipp Rappold wrote: Dear all, I have some trouble using the id-argument with aftreg (accelerated failure time regression analysis from the eha library). As far as I understand it, the id argument is used to group individuals together if there are time-varying covariates and the data is arranged in counting process style. Unfortunately, i cannot figure out how to use the id-argument. The most straight-forward way would be to simply state the grouping variable, but it throws an error. I've included an example below: the dataframe for regression is called test, with the grouping variable person. test start end censor person var1 1 0 1 0 1 0.5 2 1 2 0 1 0.4 3 2 3 0 1 0.6 4 3 4 1 1 -0.3 5 0 1 0 2 0.6 6 1 2 0 2 0.7 7 2 3 0 2 0.6 fit - aftreg(Surv(start, end, censor)~var1, data=test, id=person) Error in order(id, Y[, 1]) : argument 1 is not a vector You have caught the _function_ 'person' (package: utils) instead of the variable 'person' in the data frame. That explains the odd error message. If you change the variable name to, e.g., ID, you'll get the error message Error in order(id, Y[, 1]) : object 'id' not found which would hint you in the right direction. You need to specify 'id' by a full name, in your case 'test$person'. This is of course a deficiency in the interface of aftreg. I will fix it asap. So the temporary fix is 'id = test$person'. Thanks for the report, Göran fit - aftreg(Surv(start, end, censor)~var1, data=test, id=test[person]) Error in `[.data.frame`(id, ord) : undefined columns selected What would be the correct way to fit this example model? Thanks + all the best Philipp __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Access variables by string
Dear all,
I have two probably very easy questions:
(1) Is there a way to access certain variables by their string-based
name representation?
Example:
numbers - c(one, two, three)
varname - numbers
print(varname[2])
(2) I need this functionality for a customized na.exclude() function
that I am building, which should only exclude rows that have NA in
certain columns. Maybe there is already a function which does
exactly what I need, so I'd highly appreciate if someone could point
me there ;)
My current implementation looks like this:
naexlcude - function(data, varnames)
{
for(v in varnames){
data = subset(data, !is.na(v))
}
data
}
Best
Philipp
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Suprising behavior of paste or cat?
On Feb 11, 2010, at 10:17 AM, Russell Pierce wrote: If the list would provide additional reports I'd appreciate it. I replicated the effect this morning on another Windows XP machine... Worked as expected on a Mac OSX 10.5.8, R 2.10.1, [R.app GUI 1.30 (5534) x86_64-apple-darwin9.8.0] -- David. R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.1 ... and I replicated it using the current development build... R version 2.11.0 Under development (unstable) (2010-02-09 r51113) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base In additionally I've determined that when h.long = 150; both cat and write fail, but when h.long = 100 only the file write with cat fails. Please advise. Best, Russell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question re model development
On Feb 11, 2010, at 9:10 AM, Stratos Laskarides wrote: Dear Sir/Madam I'm trying quite a long shot here... I have used R previously, and would just like to know if any software/model has been designed which will allow me to project the future risk profile of a group of insured lives (by factors such as age, gender etc.), based on past and exisiting risk profiles of the covered lives? If you could point me in the direction of a similar project or code it would be much appreciated. R has been used in actuarial research. There is an actuar package, although I do not use it for my work on insurance related topics. I have been using survival models and R has a rich set of tools for that purpose. Perhaps you could be more specific. Thank you. Stratos Laskarides [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integral of function of dnorm
This is exactly what I mean. I need to find integrate(dnorm(mean=8,sd=1)*log(dnorm(mean=8,sd=1)), -Inf, Inf) Which doesn't work like that, because it says: Error in dnorm(mean = 8, sd = 1) : element 1 is empty; the part of the args list of '.Internal' being evaluated was: (x, mean, sd, log) So how can I define x? THanks a lot Dear all, How is it possible in R to calculate the following integral: Integral(-Inf, Inf)[log(dnorm(mean = 3, sd = 1))] how can I define that the density dnorm is taken on (-Inf, Inf) Thanks a lot! Er, if you mean integral with respect to the x argument in dnorm, then the answer is -Inf because log(dnorm(x,...)) goes quadratically to -Inf in both directions. If you meant otherwise, please tell us what you meant... [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble with read.table and colClasses='raw'
The error message says there is no method for
converting from 'character' to 'raw'.
Apparently, R is seeing character data in the
file, and is trying to convert it to raw, since
you specified raw, and it can't.
See, for example,
as('aa','raw')
Error in as(aa, raw) :
no method or default for coercing character to raw
(same error message)
So I would ask, what are your data, really? Why
are you asking for raw? Have you checked the help
page for raw to make sure it's what you want?
-Don
At 5:23 PM +0100 2/11/10, Ivan Calandra wrote:
Content-Type: text/plain
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-length: 3983
Well, it's too complicated for me! Here are what I would do (limited
since I'm still a newbie)
1) the syntax seems correct, it should work. The problem is somewhere
else, coming from your own file. Did you try skipping the colClasses
argument? To see how it looks like... If you can import it that way, try
str(x) to see what you have. It might help you.
2) I've never had that much data to import, and for me read.table works
well.
You might want to wait for the experts!
Ivan
Le 2/11/2010 17:14, Johan Jackson a écrit :
Hi Ivan,
Thanks for the reply. Damn IT! My original post was screwed up. HERE
is what I did:
x - read.table(data,header=TRUE,colClasses=rep('raw',60))
#returns error: no method or default for coercing character to raw
I've read the ?read.table and the colClasses argument. I'm still unclear:
1) colClasses is a character vector, is that right? That seems to be
what the help says, but I get an error when I do the above.
2) what is the most efficient way to read in huge amounts of data? In
the past I found that scan() and readLines() were slower than read.table.
Thanks,
JJ
On Thu, Feb 11, 2010 at 8:53 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de mailto:ivan.calan...@uni-hamburg.de
wrote:
Hi!
|colClasses| character. A vector of classes to be assumed
for the
columns.
I'm not an R expert and I don't know what your flat file raw is, but
the colClasses argument is to define whether the column will be
treated
as containing factors, logical, integer etc...
For more on read.table, read the manual R Data Import/Export
available
on the R-project website.
I don't know if it helps, but I hope it does!
Ivan
Le 2/11/2010 16:36, Johan Jackson a écrit :
Hi all,
First off, it is surprising that there are no examples of how to use
read.table() under ?read.table !
I am trying to read in a flat file of type 'raw'. It has 1000
rows and 600K
columns. I have the RAM to accomplish this, but can't get the
data into R
using read.table:
x- read.table(data,header=TRUE,colClasses=rep(,60))
#returns error: no method or default for coercing character
to raw
Then I thought that maybe the colClasses vector needed to
actually *be* the
mode needed (here's where an example under ?read.table would help):
x- read.table(data,header=TRUE,colClasses=rep(as.raw(1),60))
I waited on the latter command for a couple of hours before
killing the
process. What should the colClasses argument be?
Should I be using another method to read the data into R? Previous
experience using scan() and readLines() showed that read.table()
was faster,
at least for those examples, so I've stopped trying to use those
other
functions.
Thank you,
JJ
[[alternative HTML version deleted]]
__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062
__
R-help@r-project.org
Re: [R] Access variables by string
Philipp Rappold wrote:
Dear all,
I have two probably very easy questions:
(1) Is there a way to access certain variables by their string-based
name representation?
Example:
numbers - c(one, two, three)
varname - numbers
print(varname[2])
(2) I need this functionality for a customized na.exclude() function
that I am building, which should only exclude rows that have NA in
certain columns. Maybe there is already a function which does exactly
what I need, so I'd highly appreciate if someone could point me there ;)
My current implementation looks like this:
naexlcude - function(data, varnames)
{
for(v in varnames){
data = subset(data, !is.na(v))
}
data
}
Well, you can use get(varname)[2] or more generally things like
eval(bquote(.(as.name(varname))[2])), but for this particular
application, why not just use the standard indexing techniques?
I think this will do
ix - apply(is.na(data[varnames]), 1, any)
data[!ix,]
e.g.
table(apply(is.na(airquality[c(Wind,Ozone)]),1, any))
FALSE TRUE
11637
colSums(is.na(airquality))
Ozone Solar.RWindTemp Month Day
37 7 0 0 0 0
table(apply(is.na(airquality[c(Solar.R,Ozone)]),1, any))
FALSE TRUE
11142
(Using functions like subset inside another function often leads to
problems because of the nonstandard evaluation tricks that it uses. It
is mainly useful to save tying on the command line.)
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Access variables by string
For your first question, use the get() function
-Don
At 5:18 PM +0100 2/11/10, Philipp Rappold wrote:
Dear all,
I have two probably very easy questions:
(1) Is there a way to access certain variables by their string-based
name representation?
Example:
numbers - c(one, two, three)
varname - numbers
print(varname[2])
(2) I need this functionality for a customized na.exclude() function
that I am building, which should only exclude rows that have NA in
certain columns. Maybe there is already a function which does
exactly what I need, so I'd highly appreciate if someone could point
me there ;)
My current implementation looks like this:
naexlcude - function(data, varnames)
{
for(v in varnames){
data = subset(data, !is.na(v))
}
data
}
Best
Philipp
__
R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R ANOVA gives diferent results than SPSS
I've always found exactly the same results. If you post code that allows us to reproduce this, I suspect someone would be able to shed light on it. And output too. J On 11 February 2010 06:47, Protzko prot...@gmail.com wrote: I guess my subject says it all. But I loaded a dataset in spss and used the foreign package to read and save it in R. Running an anova (using the aov command) gives a different F and p value in R than it does in SPSS. ANy idea what is going on? -- View this message in context: http://n4.nabble.com/R-ANOVA-gives-diferent-results-than-SPSS-tp1477322p1477322.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jeremy Miles Psychology Research Methods Wiki: www.researchmethodsinpsychology.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Suprising behavior of paste or cat?
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Russell Pierce
Sent: Wednesday, February 10, 2010 9:21 PM
To: r-help@r-project.org
Subject: [R] Suprising behavior of paste or cat?
I may be making a simple error, but I've looked at the str() of the
resulting objects and I can't see any obvious reason I'm having the
problem I am having, so I am reaching out to the R-help group. I am
generating a string in my code. When I make a slight modification
(add a comma at the end using my lastcomma function), I can no
longer successfully write that string to a file. Specifically, the
resulting file contains only the ⰱ character.
That character (which prints as an unfilled square when
I look at it in Outlook) is (when I copy and paste it
to R 2.10.0 on Windows):
ⰱ
[1] \u2c31
The 2 bytes in it would be comma and one in ascii:
\x2c
[1] ,
\x31
[1] 1
It looks like a ascii/UTF-8 mismatch. Is the square Outlook's
way of saying it is illegal UTF-8?
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
This occurs in:
R version 2.10.0 (2009-10-26) R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
but not in...
R version 2.7.1 (2008-06-23)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
TE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=
en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
NT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Sample code:
h.long - 150
task - c(rep(1,h.long),rep(2,h.long))
ord - sample(1:length(task))
task - task[ord]
taskout - paste(task,collapse=,)
write(file=please.txt,taskout)
lastcomma - function(x) {return(paste(x,,,collapse=,sep=))}
res - lastcomma(taskout)
write(file=fail.txt,res)
cat(file=catfail.txt,res)
Any ideas as to how to avoid this problem would be appriciated as well
as suggestions as to whether this is expected behavior, or whether it
ought to be reported as a bug.
Best,
Russell Pierce
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R ANOVA gives diferent results than SPSS
Thomas Lumley wrote: On Thu, 11 Feb 2010, Protzko wrote: I guess my subject says it all. But I loaded a dataset in spss and used the foreign package to read and save it in R. Running an anova (using the aov command) gives a different F and p value in R than it does in SPSS. ANy idea what is going on? Yes. Either you specified a different model or different tests for the same model in the two systems, or you are interpreting the output incorrectly, or the results are different. Also beware of unbalanced data sets, aov() will not handle Error() terms properly in an unbalanced design, and in general tests will be order dependent (type 1 tests in SAS terminology). Without more detail it is hard to be sure, but the first two possibilities seem more likely. Yes, many people on the list can probably spot the issue when seeing the two anova tables. -thomas Thomas LumleyAssoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integral of function of dnorm
Here's a suggestion: Plot the function: x - seq(3, 13, length=101) plot(x, y=dnorm(x, mean=8,sd=1)*log(dnorm(x,mean=8,sd=1))) x - seq(7.5, 8.5, length=101) plot(x, y=dnorm(x, mean=8,sd=1)*log(dnorm(x,mean=8,sd=1))) x - seq(7.9, 8.1, length=101) plot(x, y=dnorm(x, mean=8,sd=1)*log(dnorm(x,mean=8,sd=1))) This suggests to me that you can integrate over restricted domains of x, and sum the intermediate results. Charles Annis, P.E. charles.an...@statisticalengineering.com 561-352-9699 http://www.StatisticalEngineering.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Trafim Vanishek Sent: Thursday, February 11, 2010 11:49 AM To: Peter Dalgaard Cc: r-help@r-project.org Subject: Re: [R] Integral of function of dnorm This is exactly what I mean. I need to find integrate(dnorm(mean=8,sd=1)*log(dnorm(mean=8,sd=1)), -Inf, Inf) Which doesn't work like that, because it says: Error in dnorm(mean = 8, sd = 1) : element 1 is empty; the part of the args list of '.Internal' being evaluated was: (x, mean, sd, log) So how can I define x? THanks a lot Dear all, How is it possible in R to calculate the following integral: Integral(-Inf, Inf)[log(dnorm(mean = 3, sd = 1))] how can I define that the density dnorm is taken on (-Inf, Inf) Thanks a lot! Er, if you mean integral with respect to the x argument in dnorm, then the answer is -Inf because log(dnorm(x,...)) goes quadratically to -Inf in both directions. If you meant otherwise, please tell us what you meant... [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating a new Access database with R
As a workaround, you can keep an empty mdb file on your filesystem. When you need a new database, you can copy and rename the empty file. -- View this message in context: http://n4.nabble.com/Re-Creating-a-new-Access-database-with-R-tp1477400p1477533.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] aggregate function / custom column names?
This question is about column names returned by the aggregate function.
Consider the following example
df - data.frame(
id = c(rep('11',30),rep('22',30),rep('33',30)),
value = c(rnorm(30,2,0.5), rnorm(30,3,0.5), rnorm(30,6,0.5))
)
aggregate(df[,c(value),drop=FALSE], by=list(id=df$id), max)
output:
idvalue
1 11 2.693528
2 22 3.868400
3 33 6.942519
aggregate(df$value, by=list(id=df$id), max)
output:
idx
1 11 2.693528
2 22 3.868400
3 33 6.942519
(YMMV on output values since data is randomly generated)
I would like to be able to name the output column as max.value. I realize I
can add the following statement:
colnames(df)[match(value,colnames(df))] - max.value
Is there a way of having aggregate return computed column names which can be
specified when calling the function (i.e. aggregate)?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble with read.table and colClasses='raw'
Hi Don and all,
I guess we're getting somewhere. Thanks. The file (first three columns,
first five rows) looks like this:
X10 X20 X30
00 0001
00 02 02
00 00 00
00 01 01
00 00 00
I guess R is reading 00 as a character? But here's the weird thing: this
data (a raw matrix in R) was written out by R itself:
write.table(dat,data,col.names=T,row.names=F,quote=F)
*If* I understand correctly, then this seems like very *bad behavior* on R's
part: you should be able to write out a matrix and read it right back into R
without hassles like this (but everytime I blame R, it turns out to be user
error, so...),
JJ
On Thu, Feb 11, 2010 at 9:59 AM, Don MacQueen m...@llnl.gov wrote:
The error message says there is no method for converting from 'character'
to 'raw'.
Apparently, R is seeing character data in the file, and is trying to
convert it to raw, since you specified raw, and it can't.
See, for example,
as('aa','raw')
Error in as(aa, raw) :
no method or default for coercing character to raw
(same error message)
So I would ask, what are your data, really? Why are you asking for raw?
Have you checked the help page for raw to make sure it's what you want?
-Don
At 5:23 PM +0100 2/11/10, Ivan Calandra wrote:
Content-Type: text/plain
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-length: 3983
Well, it's too complicated for me! Here are what I would do (limited
since I'm still a newbie)
1) the syntax seems correct, it should work. The problem is somewhere
else, coming from your own file. Did you try skipping the colClasses
argument? To see how it looks like... If you can import it that way, try
str(x) to see what you have. It might help you.
2) I've never had that much data to import, and for me read.table works
well.
You might want to wait for the experts!
Ivan
Le 2/11/2010 17:14, Johan Jackson a écrit :
Hi Ivan,
Thanks for the reply. Damn IT! My original post was screwed up. HERE
is what I did:
x - read.table(data,header=TRUE,colClasses=rep('raw',60))
#returns error: no method or default for coercing character to raw
I've read the ?read.table and the colClasses argument. I'm still
unclear:
1) colClasses is a character vector, is that right? That seems to be
what the help says, but I get an error when I do the above.
2) what is the most efficient way to read in huge amounts of data? In
the past I found that scan() and readLines() were slower than
read.table.
Thanks,
JJ
On Thu, Feb 11, 2010 at 8:53 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de mailto:ivan.calan...@uni-hamburg.de
wrote:
Hi!
|colClasses| character. A vector of classes to be assumed
for the
columns.
I'm not an R expert and I don't know what your flat file raw is,
but
the colClasses argument is to define whether the column will be
treated
as containing factors, logical, integer etc...
For more on read.table, read the manual R Data Import/Export
available
on the R-project website.
I don't know if it helps, but I hope it does!
Ivan
Le 2/11/2010 16:36, Johan Jackson a écrit :
Hi all,
First off, it is surprising that there are no examples of how to
use
read.table() under ?read.table !
I am trying to read in a flat file of type 'raw'. It has 1000
rows and 600K
columns. I have the RAM to accomplish this, but can't get the
data into R
using read.table:
x- read.table(data,header=TRUE,colClasses=rep(,60))
#returns error: no method or default for coercing character
to raw
Then I thought that maybe the colClasses vector needed to
actually *be* the
mode needed (here's where an example under ?read.table would help):
x- read.table(data,header=TRUE,colClasses=rep(as.raw(1),60))
I waited on the latter command for a couple of hours before
killing the
process. What should the colClasses argument be?
Should I be using another method to read the data into R? Previous
experience using scan() and readLines() showed that read.table()
was faster,
at least for those examples, so I've stopped trying to use those
other
functions.
Thank you,
JJ
[[alternative HTML version deleted]]
__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://*stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://*www.*R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailto:R-help@r-project.org mailing list
Re: [R] aggregate function / custom column names?
Try this:
aggregate(list(Max = df$value), df['id'], max)
id Max
1 11 2.610491
2 22 3.796836
3 33 6.562515
or if using value rather than Max is ok then just:
aggregate(df['value'], df['id'], max)
idvalue
1 11 2.610491
2 22 3.796836
3 33 6.562515
On Thu, Feb 11, 2010 at 12:18 PM, Chuck White chuckwhi...@charter.net wrote:
This question is about column names returned by the aggregate function.
Consider the following example
df - data.frame(
id = c(rep('11',30),rep('22',30),rep('33',30)),
value = c(rnorm(30,2,0.5), rnorm(30,3,0.5), rnorm(30,6,0.5))
)
aggregate(df[,c(value),drop=FALSE], by=list(id=df$id), max)
output:
id value
1 11 2.693528
2 22 3.868400
3 33 6.942519
aggregate(df$value, by=list(id=df$id), max)
output:
id x
1 11 2.693528
2 22 3.868400
3 33 6.942519
(YMMV on output values since data is randomly generated)
I would like to be able to name the output column as max.value. I realize I
can add the following statement:
colnames(df)[match(value,colnames(df))] - max.value
Is there a way of having aggregate return computed column names which can be
specified when calling the function (i.e. aggregate)?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Access variables by string
On Thu, Feb 11, 2010 at 4:18 PM, Philipp Rappold
philipp.rapp...@gmail.com wrote:
Dear all,
I have two probably very easy questions:
(1) Is there a way to access certain variables by their string-based name
representation?
Example:
numbers - c(one, two, three)
varname - numbers
print(varname[2])
print(get(varname)[2])
(2) I need this functionality for a customized na.exclude() function that I
am building, which should only exclude rows that have NA in certain columns.
Maybe there is already a function which does exactly what I need, so I'd
highly appreciate if someone could point me there ;)
My current implementation looks like this:
naexlcude - function(data, varnames)
{
for(v in varnames){
data = subset(data, !is.na(v))
}
data
}
f = function(x, vars) x[complete.cases(x[vars]),]
b
Best
Philipp
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: Recall function: evaluation nested too deeply: infinite recursion / options(expressions=)?
hello all
i searched the archives and couldn't get a solution to the following question.
i have the following function:
F=function(z,v)
{
if (v==-.5) return(1) else return(2*v/z + 1/Recall(z,v-1))
}
and while testing whether it works (ie F(z,v) is approx =
besselK(z,1+v)/besselK(z,V). the recursion formula allows one to calculate
besselK(z,1+v)/besselK(z,V) for large values of z ) i got the following error :
evaluation nested too deeply: infinite recursion / options(expressions=)?
i.e.
zz=1
nn=1000
R=array(0,dim=nn)
for (i in 1:nn)
{
print(i)
R[i]=F(zz,-0.5+(i-1))
}
the error occurs when i==713
but when one evaluates F(1,-.5+(713-1)) i get [1] 1423.001
note also that if v starts getting large, evaluation of F also gives the error.
e.g. F(1, 713.5)
any help?
seems like looping works nicely here
F2=function(z,v)
{
#check that the v is correct! ie -.5, .5, 3/2, 5/2, .
if (v==-0.5)
{
return(1)
}else
{
ntimes = v+1.5
R=array(0,dim=ntimes)
R[1]=1
for (i in 2:ntimes)
{
R[i]= 2*v/z + 1/R[i-1]
}
return(R[ntimes])
}
}
Allan Clark
Lecturer in Statistical Sciences Department
University of Cape Town
7701 Rondebosch
South Africa
TEL (Office): +27-21-650-3228
FAX: +27-21-650-4773
http://web.uct.ac.za/depts/stats/aclark.htm
Allan Clark
Lecturer in Statistical Sciences Department
University of Cape Town
7701 Rondebosch
South Africa
TEL (Office): +27-21-650-3228
FAX: +27-21-650-4773
http://web.uct.ac.za/depts/stats/aclark.htm
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integral of function of dnorm
Here's another suggestion: evaluate
-0.5 * (log(2 * pi) + 1) ## -1.418939
Or you can do the integral:
f - function(x, mu = 8, s = 1){
dnorm(x, mu, s) * log(dnorm(x, mu, s))}
integrate(f, lower = -2, upper = 18)
#-1.418939 with absolute error 2.8e-10
Try other values for lower= and upper= and see
if you can understand why -Inf, Inf won't work.
You can also plot your function with, e.g.
curve(f, 7, 9)
-Peter Ehlers
Charles Annis, P.E. wrote:
Here's a suggestion: Plot the function:
x - seq(3, 13, length=101)
plot(x, y=dnorm(x, mean=8,sd=1)*log(dnorm(x,mean=8,sd=1)))
x - seq(7.5, 8.5, length=101)
plot(x, y=dnorm(x, mean=8,sd=1)*log(dnorm(x,mean=8,sd=1)))
x - seq(7.9, 8.1, length=101)
plot(x, y=dnorm(x, mean=8,sd=1)*log(dnorm(x,mean=8,sd=1)))
This suggests to me that you can integrate over restricted domains of x, and
sum the intermediate results.
Charles Annis, P.E.
charles.an...@statisticalengineering.com
561-352-9699
http://www.StatisticalEngineering.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Trafim Vanishek
Sent: Thursday, February 11, 2010 11:49 AM
To: Peter Dalgaard
Cc: r-help@r-project.org
Subject: Re: [R] Integral of function of dnorm
This is exactly what I mean.
I need to find integrate(dnorm(mean=8,sd=1)*log(dnorm(mean=8,sd=1)), -Inf,
Inf)
Which doesn't work like that, because it says:
Error in dnorm(mean = 8, sd = 1) : element 1 is empty;
the part of the args list of '.Internal' being evaluated was:
(x, mean, sd, log)
So how can I define x?
THanks a lot
Dear all,
How is it possible in R to calculate the following integral:
Integral(-Inf, Inf)[log(dnorm(mean = 3, sd = 1))]
how can I define that the density dnorm is taken on (-Inf, Inf)
Thanks a lot!
Er, if you mean integral with respect to the x argument in dnorm, then the
answer is -Inf because log(dnorm(x,...)) goes quadratically to -Inf in
both
directions. If you meant otherwise, please tell us what you meant...
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Peter Ehlers
University of Calgary
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integral of function of dnorm
Try: tmpfun - function(x) dnorm(x,mean=8,sd=1)*log(dnorm(x,mean=8,sd=1)) integrate( tmpfun, -Inf, Inf) Also you may want to look at the log argument to dnorm rather than taking the log of the function. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Trafim Vanishek Sent: Thursday, February 11, 2010 9:49 AM To: Peter Dalgaard Cc: r-help@r-project.org Subject: Re: [R] Integral of function of dnorm This is exactly what I mean. I need to find integrate(dnorm(mean=8,sd=1)*log(dnorm(mean=8,sd=1)), - Inf, Inf) Which doesn't work like that, because it says: Error in dnorm(mean = 8, sd = 1) : element 1 is empty; the part of the args list of '.Internal' being evaluated was: (x, mean, sd, log) So how can I define x? THanks a lot Dear all, How is it possible in R to calculate the following integral: Integral(-Inf, Inf)[log(dnorm(mean = 3, sd = 1))] how can I define that the density dnorm is taken on (-Inf, Inf) Thanks a lot! Er, if you mean integral with respect to the x argument in dnorm, then the answer is -Inf because log(dnorm(x,...)) goes quadratically to -Inf in both directions. If you meant otherwise, please tell us what you meant... [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble with read.table and colClasses='raw'
Hi Ivan,
Thanks for the reply. Damn IT! My original post was screwed up. HERE is what
I did:
x - read.table(data,header=TRUE,colClasses=rep('raw',60))
#returns error: no method or default for coercing character to raw
I've read the ?read.table and the colClasses argument. I'm still unclear:
1) colClasses is a character vector, is that right? That seems to be what
the help says, but I get an error when I do the above.
2) what is the most efficient way to read in huge amounts of data? In the
past I found that scan() and readLines() were slower than read.table.
Thanks,
JJ
On Thu, Feb 11, 2010 at 8:53 AM, Ivan Calandra ivan.calan...@uni-hamburg.de
wrote:
Hi!
|colClasses| character. A vector of classes to be assumed for the
columns.
I'm not an R expert and I don't know what your flat file raw is, but
the colClasses argument is to define whether the column will be treated
as containing factors, logical, integer etc...
For more on read.table, read the manual R Data Import/Export available
on the R-project website.
I don't know if it helps, but I hope it does!
Ivan
Le 2/11/2010 16:36, Johan Jackson a écrit :
Hi all,
First off, it is surprising that there are no examples of how to use
read.table() under ?read.table !
I am trying to read in a flat file of type 'raw'. It has 1000 rows and
600K
columns. I have the RAM to accomplish this, but can't get the data into R
using read.table:
x- read.table(data,header=TRUE,colClasses=rep(,60))
#returns error: no method or default for coercing character to raw
Then I thought that maybe the colClasses vector needed to actually *be*
the
mode needed (here's where an example under ?read.table would help):
x- read.table(data,header=TRUE,colClasses=rep(as.raw(1),60))
I waited on the latter command for a couple of hours before killing the
process. What should the colClasses argument be?
Should I be using another method to read the data into R? Previous
experience using scan() and readLines() showed that read.table() was
faster,
at least for those examples, so I've stopped trying to use those other
functions.
Thank you,
JJ
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fwd: Recall function: evaluation nested too deeply: infinite recursion / options(expressions=)?
You might be impacted by FAQ 7.31.
Your statement if(v == -.5)
might be suspect. You might want to use 'all.equal'
On Thu, Feb 11, 2010 at 11:40 AM, Allan Clark allan.cl...@uct.ac.za wrote:
hello all
i searched the archives and couldn't get a solution to the following question.
i have the following function:
F=function(z,v)
{
if (v==-.5) return(1) else return(2*v/z + 1/Recall(z,v-1))
}
and while testing whether it works (ie F(z,v) is approx =
besselK(z,1+v)/besselK(z,V). the recursion formula allows one to calculate
besselK(z,1+v)/besselK(z,V) for large values of z ) i got the following error
: evaluation nested too deeply: infinite recursion / options(expressions=)?
i.e.
zz=1
nn=1000
R=array(0,dim=nn)
for (i in 1:nn)
{
print(i)
R[i]=F(zz,-0.5+(i-1))
}
the error occurs when i==713
but when one evaluates F(1,-.5+(713-1)) i get [1] 1423.001
note also that if v starts getting large, evaluation of F also gives the
error. e.g. F(1, 713.5)
any help?
seems like looping works nicely here
F2=function(z,v)
{
#check that the v is correct! ie -.5, .5, 3/2, 5/2, .
if (v==-0.5)
{
return(1)
}else
{
ntimes = v+1.5
R=array(0,dim=ntimes)
R[1]=1
for (i in 2:ntimes)
{
R[i]= 2*v/z + 1/R[i-1]
}
return(R[ntimes])
}
}
Allan Clark
Lecturer in Statistical Sciences Department
University of Cape Town
7701 Rondebosch
South Africa
TEL (Office): +27-21-650-3228
FAX: +27-21-650-4773
http://web.uct.ac.za/depts/stats/aclark.htm
Allan Clark
Lecturer in Statistical Sciences Department
University of Cape Town
7701 Rondebosch
South Africa
TEL (Office): +27-21-650-3228
FAX: +27-21-650-4773
http://web.uct.ac.za/depts/stats/aclark.htm
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble with read.table and colClasses='raw'
The read.table function does not know how to convert the character
representation that it reads into raw variables. Try using 'integer' for the
colClasses to read the data in as integers, then convert those back to raw (if
that is really what you need).
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Johan Jackson
Sent: Thursday, February 11, 2010 10:29 AM
To: Don MacQueen
Cc: r-help@r-project.org
Subject: Re: [R] trouble with read.table and colClasses='raw'
Hi Don and all,
I guess we're getting somewhere. Thanks. The file (first three columns,
first five rows) looks like this:
X10 X20 X30
00 0001
00 02 02
00 00 00
00 01 01
00 00 00
I guess R is reading 00 as a character? But here's the weird thing:
this
data (a raw matrix in R) was written out by R itself:
write.table(dat,data,col.names=T,row.names=F,quote=F)
*If* I understand correctly, then this seems like very *bad behavior*
on R's
part: you should be able to write out a matrix and read it right back
into R
without hassles like this (but everytime I blame R, it turns out to be
user
error, so...),
JJ
On Thu, Feb 11, 2010 at 9:59 AM, Don MacQueen m...@llnl.gov wrote:
The error message says there is no method for converting from
'character'
to 'raw'.
Apparently, R is seeing character data in the file, and is trying to
convert it to raw, since you specified raw, and it can't.
See, for example,
as('aa','raw')
Error in as(aa, raw) :
no method or default for coercing character to raw
(same error message)
So I would ask, what are your data, really? Why are you asking for
raw?
Have you checked the help page for raw to make sure it's what you
want?
-Don
At 5:23 PM +0100 2/11/10, Ivan Calandra wrote:
Content-Type: text/plain
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-length: 3983
Well, it's too complicated for me! Here are what I would do (limited
since I'm still a newbie)
1) the syntax seems correct, it should work. The problem is
somewhere
else, coming from your own file. Did you try skipping the colClasses
argument? To see how it looks like... If you can import it that way,
try
str(x) to see what you have. It might help you.
2) I've never had that much data to import, and for me read.table
works
well.
You might want to wait for the experts!
Ivan
Le 2/11/2010 17:14, Johan Jackson a écrit :
Hi Ivan,
Thanks for the reply. Damn IT! My original post was screwed up.
HERE
is what I did:
x - read.table(data,header=TRUE,colClasses=rep('raw',60))
#returns error: no method or default for coercing character to
raw
I've read the ?read.table and the colClasses argument. I'm still
unclear:
1) colClasses is a character vector, is that right? That seems to
be
what the help says, but I get an error when I do the above.
2) what is the most efficient way to read in huge amounts of data?
In
the past I found that scan() and readLines() were slower than
read.table.
Thanks,
JJ
On Thu, Feb 11, 2010 at 8:53 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de mailto:ivan.calan...@uni-
hamburg.de
wrote:
Hi!
|colClasses| character. A vector of classes to be
assumed
for the
columns.
I'm not an R expert and I don't know what your flat file raw
is,
but
the colClasses argument is to define whether the column will be
treated
as containing factors, logical, integer etc...
For more on read.table, read the manual R Data Import/Export
available
on the R-project website.
I don't know if it helps, but I hope it does!
Ivan
Le 2/11/2010 16:36, Johan Jackson a écrit :
Hi all,
First off, it is surprising that there are no examples of
how to
use
read.table() under ?read.table !
I am trying to read in a flat file of type 'raw'. It has 1000
rows and 600K
columns. I have the RAM to accomplish this, but can't get the
data into R
using read.table:
x- read.table(data,header=TRUE,colClasses=rep(,60))
#returns error: no method or default for coercing
character
to raw
Then I thought that maybe the colClasses vector needed to
actually *be* the
mode needed (here's where an example under ?read.table would
help):
x-
read.table(data,header=TRUE,colClasses=rep(as.raw(1),60))
I waited on the latter command for a couple of hours before
killing the
process. What should the colClasses argument be?
Should I be using another method to read the data into R?
Previous
Re: [R] histogam plots
Hi:
## Histogram + density plots in lattice and ggplot2
# example data frame
x - data.frame(x = rnorm(600), g = factor(rep(1:6, each = 100)))
# lattice
library(lattice)
histogram(~ x | g, data = dd, type = 'density',
panel = function(x, subscripts, ...) {
panel.histogram(x, ...)
panel.mathdensity(dnorm, col = 'red', ...)
panel.densityplot(x, plot.points = FALSE, col = 'navy',...)
} )
# ggplot2
library(ggplot2)
p - ggplot(data = dd, aes(x = x, group = g))
p + geom_histogram(aes(y = ..density..), binwidth = 0.5) +
geom_density(color = 'navy') + stat_function(fun = 'dnorm') +
facet_wrap(~ g, ncol = 3) + ylab(Density)
If you prefer the ordering given by ggplot2, then in the lattice invocation,
addas.table = TRUE, in the line above the panel function call.
HTH,
Dennis
On Thu, Feb 11, 2010 at 7:50 AM, li li hannah@gmail.com wrote:
Thank you very much for your reply. That was very helpful.
I also want to add two density curves on top of each histgram. One is the
density curve of a standard normal random variable. The other is the
denstity curve according to the histgram.
I was trying to use the function
panel.mathdensity, but not successful.
Can anyone give me some help?
Thank you!
2010/2/11 bill.venab...@csiro.au
One way round this is to use lattice. With your matrix 'w' you might
W - data.frame(w = as.vector(w),
r = factor(as.vector(row(w))) )
require(lattice)
histogram(~w|r, W)
Identical axis systems will be used for all panels.
Bill Venables
CSIRO/CMIS Cleveland Laboratories
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of li li
Sent: Thursday, 11 February 2010 2:52 PM
To: r-help
Subject: [R] histogam plots
Hi all,
I want to draw a histgram for each row of a matrix and compare them.
However the plot I
got does not have the same y range and x range, which makes it difficult
to
make the comparison.
Is there a easy way to fix the x range and y range in a xy plot for
several
plots, instead of specifying
them for each plot.
The following is my code for generalizing the matrix and draw the
histogram.
gen is the function to generate the dta
gen - function(m, rho) {
library(MASS)
set.seed(103)
theta - 0
theta1 - 2
pi0 - 0.9
mzero - pi0*m
mean - c(rep(theta, mzero), rep(theta1,m-mzero))
J - rep(1, m)
var - function(rho) {(1-rho)*diag(m)+ rho*J%*%t(J)}
t - mvrnorm(1, mean, var(rho))
return(t)
}
### w is the matrix. A histgram is drawn for each of the rows.
n - 1000
r - seq(0,0.9, by=0.1)
w - matrix(0, ncol=n, nrow=length(r))
for (i in 1: length(r)){w[i,]- gen(n,r[i])}
par(mfrow=c(2,5))
hist(w[1,], breaks=100)
hist(w[2,], breaks=100)
hist(w[3,], breaks=100)
hist(w[4,], breaks=100)
hist(w[5,], breaks=100)
hist(w[6,], breaks=100)
hist(w[7,], breaks=100)
hist(w[8,], breaks=100)
hist(w[9,], breaks=100)
hist(w[10,], breaks=100)
##
Thank you !
Li
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
http://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Recall function: evaluation nested too deeply: infinite recursion / options(expressions=)?
hello all
i searched the archives and couldn't get a solution to the following question.
i have the following function:
F=function(z,v)
{
if (v==-.5) return(1) else return(2*v/z + 1/Recall(z,v-1))
}
and while testing whether it works (ie F(z,v) is approx =
besselK(z,1+v)/besselK(z,V). the recursion formula allows one to calculate
besselK(z,1+v)/besselK(z,V) for large values of z ) i got the following error :
evaluation nested too deeply: infinite recursion / options(expressions=)?
i.e.
zz=1
nn=1000
R=array(0,dim=nn)
for (i in 1:nn)
{
print(i)
R[i]=F(zz,-0.5+(i-1))
}
the error occurs when i==713
but when one evaluates F(1,-.5+(713-1)) i get [1] 1423.001
note also that if v starts getting large, evaluation of F also gives the error.
e.g. F(1, 713.5)
any help?
seems like looping works nicely here
F2=function(z,v)
{
#check that the v is correct! ie -.5, .5, 3/2, 5/2, .
if (v==-0.5)
{
return(1)
}else
{
ntimes = v+1.5
R=array(0,dim=ntimes)
R[1]=1
for (i in 2:ntimes)
{
R[i]= 2*v/z + 1/R[i-1]
}
return(R[ntimes])
}
}
Allan Clark
Lecturer in Statistical Sciences Department
University of Cape Town
7701 Rondebosch
South Africa
TEL (Office): +27-21-650-3228
FAX: +27-21-650-4773
http://web.uct.ac.za/depts/stats/aclark.htm
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R ANOVA gives diferent results than SPSS
a one-way ANOVA should be a one-way ANOVA I guess, model is simple enough I thought. The F value seems pretty clear, I'm doing nothing fancy here, just trying to figure out how to do in R what I'm doing in SPSS. -- View this message in context: http://n4.nabble.com/R-ANOVA-gives-diferent-results-than-SPSS-tp1477322p1477468.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Access variables by string
Philipp Rappold philipp.rappold at gmail.com writes:
Dear all,
[...]
(2) I need this functionality for a customized na.exclude() function
that I am building, which should only exclude rows that have NA in
certain columns. Maybe there is already a function which does
exactly what I need, so I'd highly appreciate if someone could point
me there ;)
I would use something like
naexclude - function(data, varnames)
d[rowSums(is.na(data[,varnames,drop=FALSE])) == 0,]
Dan
My current implementation looks like this:
naexlcude - function(data, varnames)
{
for(v in varnames){
data = subset(data, !is.na(v))
}
data
}
Best
Philipp
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Dual Category X-Axis (Multi-Level)
Hello, I was wondering if anyone knows of a way to produce multilevel x-axis groupings similar to Excel's pivotcharts. (If you're not sure what I'm talking about, here's an example: http://peltiertech.com/WordPress/chart-with-a-dual-category-axis/). I realize that I could use mtext to manually insert text where desired, but I was hoping for a more systematic approach. Thanks in advance, -eric [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating a new Access database with R
Paul- wrote: As a workaround, you can keep an empty mdb file on your filesystem. When you need a new database, you can copy and rename the empty file. Creating a new database is not part of (R)ODBC because there are too many differences between implementations. You you use some RDCOM method to do that, though. Dieter -- View this message in context: http://n4.nabble.com/Re-Creating-a-new-Access-database-with-R-tp1477400p1477613.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble with read.table and colClasses='raw'
The other possibility is that you could create the function to convert from
character to raw (possibly wrapping as.raw around as.integer) so that
read.table knows what to do.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Greg Snow
Sent: Thursday, February 11, 2010 11:06 AM
To: Johan Jackson; Don MacQueen
Cc: r-help@r-project.org
Subject: Re: [R] trouble with read.table and colClasses='raw'
The read.table function does not know how to convert the character
representation that it reads into raw variables. Try using 'integer'
for the colClasses to read the data in as integers, then convert those
back to raw (if that is really what you need).
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Johan Jackson
Sent: Thursday, February 11, 2010 10:29 AM
To: Don MacQueen
Cc: r-help@r-project.org
Subject: Re: [R] trouble with read.table and colClasses='raw'
Hi Don and all,
I guess we're getting somewhere. Thanks. The file (first three
columns,
first five rows) looks like this:
X10 X20 X30
00 0001
00 02 02
00 00 00
00 01 01
00 00 00
I guess R is reading 00 as a character? But here's the weird thing:
this
data (a raw matrix in R) was written out by R itself:
write.table(dat,data,col.names=T,row.names=F,quote=F)
*If* I understand correctly, then this seems like very *bad behavior*
on R's
part: you should be able to write out a matrix and read it right back
into R
without hassles like this (but everytime I blame R, it turns out to
be
user
error, so...),
JJ
On Thu, Feb 11, 2010 at 9:59 AM, Don MacQueen m...@llnl.gov wrote:
The error message says there is no method for converting from
'character'
to 'raw'.
Apparently, R is seeing character data in the file, and is trying
to
convert it to raw, since you specified raw, and it can't.
See, for example,
as('aa','raw')
Error in as(aa, raw) :
no method or default for coercing character to raw
(same error message)
So I would ask, what are your data, really? Why are you asking for
raw?
Have you checked the help page for raw to make sure it's what you
want?
-Don
At 5:23 PM +0100 2/11/10, Ivan Calandra wrote:
Content-Type: text/plain
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-length: 3983
Well, it's too complicated for me! Here are what I would do
(limited
since I'm still a newbie)
1) the syntax seems correct, it should work. The problem is
somewhere
else, coming from your own file. Did you try skipping the
colClasses
argument? To see how it looks like... If you can import it that
way,
try
str(x) to see what you have. It might help you.
2) I've never had that much data to import, and for me read.table
works
well.
You might want to wait for the experts!
Ivan
Le 2/11/2010 17:14, Johan Jackson a écrit :
Hi Ivan,
Thanks for the reply. Damn IT! My original post was screwed up.
HERE
is what I did:
x - read.table(data,header=TRUE,colClasses=rep('raw',60))
#returns error: no method or default for coercing character
to
raw
I've read the ?read.table and the colClasses argument. I'm still
unclear:
1) colClasses is a character vector, is that right? That seems
to
be
what the help says, but I get an error when I do the above.
2) what is the most efficient way to read in huge amounts of
data?
In
the past I found that scan() and readLines() were slower than
read.table.
Thanks,
JJ
On Thu, Feb 11, 2010 at 8:53 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de mailto:ivan.calan...@uni-
hamburg.de
wrote:
Hi!
|colClasses| character. A vector of classes to be
assumed
for the
columns.
I'm not an R expert and I don't know what your flat file
raw
is,
but
the colClasses argument is to define whether the column will
be
treated
as containing factors, logical, integer etc...
For more on read.table, read the manual R Data
Import/Export
available
on the R-project website.
I don't know if it helps, but I hope it does!
Ivan
Le 2/11/2010 16:36, Johan Jackson a écrit :
Hi all,
First off, it is surprising that there are no examples of
how to
use
read.table() under ?read.table !
I am trying to read in a flat file of type 'raw'. It has
1000
Re: [R] histogam plots
Dennis Murphy wrote:
## Histogram + density plots in lattice and ggplot2
There was a typo in your example (should be dd - data.frame), but anyway.
ggplot2 needs 10 times as long. While Bill Venables (?) would argue what
are you going to do with 3 seconds in your life, it adds up in lengthy
Sweave reports (yes... caching would be an option).
Still preferring lattice.
Dieter
# example data frame
library(ggplot2)
library(lattice)
dd - data.frame(x = rnorm(600), g = factor(rep(1:6, each = 100)))
# lattice
system.time(
print(histogram(~ x | g, data = dd, type = 'density',
panel = function(x, subscripts, ...) {
panel.histogram(x, ...)
panel.mathdensity(dnorm, col = 'red', ...)
panel.densityplot(x, plot.points = FALSE, col = 'navy',...)
} ))
)
# 0.33 seconds
# ggplot2
system.time(
print( ggplot(data = dd, aes(x = x, group = g)) +
geom_histogram(aes(y = ..density..), binwidth = 0.5) +
geom_density(color = 'navy') + stat_function(fun = 'dnorm') +
facet_wrap(~ g, ncol = 3) + ylab(Density))
)
# 3.7 seconds
--
View this message in context:
http://n4.nabble.com/histogam-plots-tp1476859p1477632.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Reading raw intensity data from getGEO's gse object
Hello, I am trying to download a SOFT matrix file for GSE series to extract
raw intensity data.
gse- getGEO('GSE', AnnotGPL=T)
However, I am not able to use the function Table(gse), which returns the
following error
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function Table, for signature
GSE
If I try to use the GDS file, I get only the adjusted log 2 ratio of
intensities.
Is there any way to get to the raw intensity data contained within GSE
object?
Thanks,
Dipen
--
View this message in context:
http://n4.nabble.com/Reading-raw-intensity-data-from-getGEO-s-gse-object-tp1477633p1477633.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble with read.table and colClasses='raw'
Johan Jackson wrote: Hi Don and all, I guess we're getting somewhere. Thanks. The file (first three columns, first five rows) looks like this: X10 X20 X30 00 0001 00 02 02 00 00 00 00 01 01 00 00 00 I guess R is reading 00 as a character? But here's the weird thing: this data (a raw matrix in R) was written out by R itself: write.table(dat,data,col.names=T,row.names=F,quote=F) *If* I understand correctly, then this seems like very *bad behavior* on R's part: you should be able to write out a matrix and read it right back into R without hassles like this (but everytime I blame R, it turns out to be user error, so...), JJ Well, R is stupid, of course, so there's not much sense in blaming R. You could blame the designers/programmers, but I wouldn't do that - they seem like pretty smart people. Still, I can sympathize. When I first got my Porsche, I couldn't figure out how to make it go faster and why it kept making so much noise. Then someone told me that the left foot pedal wasn't just a footrest. And thus I discovered that there are non-automatics in this world. -:) Anyway, I just read your sample data into R, saved it with your write() command and read it back with dat - read.table(file=data, header=TRUE, colClasses=character) I suspect that you really don't know what 'raw' type means and haven't bothered to check ?raw. It's also pretty clear that you haven't read the colClasses description in ?read.table very carefully. The one thing R help pages are pretty good at is careful definition of arguments. I do hope that your day will improve. -Peter Ehlers [..] -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Suprising behavior of paste or cat?
Thank you for your input so far r-help denizens. Neither David nor
Peter were able to replicate my result. Has anybody other than me
been able to generate the failure I'm describing? So far I've
experienced it on 3 machines, Windows XP/P4/2.1.10, Windows
XP/Atom/2.1.10/2.1.11(release), Windows Vista/Centrino/2.1.10, but
found no problem on linux/2.7.1/x86_64.
Bill's idea is interesting. There may be a mismatch between types
occurring somewhere, but I haven't exactly where yet. To test our his
idea, I tried changing the order of the values in my vector task so
my output would start off with 2, rather than 1,. But I did not
observe a change in behavior.
I've generated further sample code to demonstrate the idiosyncraticy
of what I'm observing.
This code segment does not create a failure.
#No failure
lastcomma - function(x) {return(paste(x,,,collapse=,sep=))}
h.long - 150
task1 - c(rep(1,h.long),rep(2,h.long))
task2- c(rep(2,h.long),rep(1,h.long))
res1 - lastcomma(paste(task1,collapse=,))
res2 - lastcomma(paste(task2,collapse=,))
write(file=write-okay1.txt,res1)
cat(file=cat-okay2.txt,res2)
This code segment, where the task vector is reordered using sample as
an index, creates invalid files.
#Failure of write and cat
ord - sample(1:(h.long*2))
task1 - task1[ord]
task2 - task2[ord]
res1.bad - lastcomma(paste(task1,collapse=,))
res2.bad - lastcomma(paste(task2,collapse=,))
write(file=write-bad1.txt,res1.bad)
cat(file=cat-bad2.txt,res2.bad)
This code segment, where the task vector is shorter and reordered,
creates invalid files with cat, but not with write, and only when task
has been passed through my lastcomma function.
#Inconsistent; cat fails but write does not, cat only fails when
string has been passed through lastcomma
h.long - 100
task1 - c(rep(1,h.long),rep(2,h.long))
task2- c(rep(2,h.long),rep(1,h.long))
ord - sample(1:(h.long*2))
task1 - task1[ord]
task2 - task2[ord]
res1.no.lastcomma - paste(task1,collapse=,)
res2.no.lastcomma - paste(task2,collapse=,)
res1.yes.lastcomma - lastcomma(res1.no.lastcomma)
res2.yes.lastcomma - lastcomma(res2.no.lastcomma)
write(file=write-1-nlc.txt,res1.no.lastcomma) #okay
write(file=write-2-nlc.txt,res2.no.lastcomma) #okay
cat(file=cat-1-nlc.txt,res1.no.lastcomma) #okay
cat(file=cat-2-nlc.txt,res2.no.lastcomma) #okay
write(file=write-1-lc.txt,res1.yes.lastcomma) #okay
write(file=write-2-lc.txt,res2.yes.lastcomma) #okay
cat(file=cat-1-lc.txt,res1.yes.lastcomma) #bad
cat(file=cat-2-lc.txt,res2.yes.lastcomma) #bad
Thanks,
Russell
On Thu, Feb 11, 2010 at 9:05 AM, William Dunlap wdun...@tibco.com wrote:
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Russell Pierce
Sent: Wednesday, February 10, 2010 9:21 PM
To: r-help@r-project.org
Subject: [R] Suprising behavior of paste or cat?
I may be making a simple error, but I've looked at the str() of the
resulting objects and I can't see any obvious reason I'm having the
problem I am having, so I am reaching out to the R-help group. I am
generating a string in my code. When I make a slight modification
(add a comma at the end using my lastcomma function), I can no
longer successfully write that string to a file. Specifically, the
resulting file contains only the ⰱ character.
That character (which prints as an unfilled square when
I look at it in Outlook) is (when I copy and paste it
to R 2.10.0 on Windows):
ⰱ
[1] \u2c31
The 2 bytes in it would be comma and one in ascii:
\x2c
[1] ,
\x31
[1] 1
It looks like a ascii/UTF-8 mismatch. Is the square Outlook's
way of saying it is illegal UTF-8?
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
This occurs in:
R version 2.10.0 (2009-10-26) R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
but not in...
R version 2.7.1 (2008-06-23)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
TE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=
en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
NT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Sample code:
h.long - 150
task - c(rep(1,h.long),rep(2,h.long))
ord - sample(1:length(task))
task - task[ord]
taskout - paste(task,collapse=,)
write(file=please.txt,taskout)
lastcomma - function(x) {return(paste(x,,,collapse=,sep=))}
res - lastcomma(taskout)
write(file=fail.txt,res)
cat(file=catfail.txt,res)
Any ideas as to how to avoid this problem would be appriciated as well
as suggestions as to whether this is expected
Re: [R] R ANOVA gives diferent results than SPSS
A couple of possibilities: The data is not the same, e.g. something in the file was interpreted differently by the 2 programs, one of the programs may have stopped reading at an unrecognized value, while the other skipped it and went on. Or it used to be common to encode missing values as -999, if one program recognizes that as missing, but you did not tell the other one too, then it could treat that as a legitimate value. The model is not the same, e.g. one program may be interpreting your grouping variable as a continuous variable and the other as categorical, which would result in 2 very different models and outcomes. If you show us your data/code/output as has been requested, then we may be able to tell which it is. Without that information you are expecting either R or the members of the list to read your mind. I keep making notes to my future self to use the timetravel package (not written yet, that's why I need my future self to use it) to send a copy of the esp package (also not written yet) back in time to me so I can use it for situations like this. But so far that has not worked (maybe my future self is even more lazy than my present self, or my near future self does something to offend my far future self enough that he is unwilling to do this small favor for my current past self, darn, either way means I should probably do better on the diet/exercise). The short version of the above rambling is that we want to help, but cannot help you until you help us to help you. Show us your data/code/output (or data/code/output for simulated/example data if you can't show your real data). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Protzko Sent: Thursday, February 11, 2010 9:38 AM To: r-help@r-project.org Subject: Re: [R] R ANOVA gives diferent results than SPSS a one-way ANOVA should be a one-way ANOVA I guess, model is simple enough I thought. The F value seems pretty clear, I'm doing nothing fancy here, just trying to figure out how to do in R what I'm doing in SPSS. -- View this message in context: http://n4.nabble.com/R-ANOVA-gives- diferent-results-than-SPSS-tp1477322p1477468.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Find each time a value changes
It was brought to my attention that the rle() answer to this question was not posted. The following gives the correct answer once the last value is deleted. x-seq(1:100) y1-rep(1,10) y2-rep(2,10) y-c(y1,y2,y1,y1,y1,y2,y1,y2,y1,y2) xy-cbind(x,y) print(xy) print(str(xy)) # SEE WHAT RLE GIVES test - rle(xy[,2]) print(str(test) # USE JIMS TRICK OF CUMULATIVE SUMMING # TO GET THE LOCATIONS result - cumsum(c(1,rle(xy[,2])$lengths)) Tim Clark Department of Zoology University of Hawaii --- On Wed, 2/10/10, Ben Tupper ben.bigh...@gmail.com wrote: From: Ben Tupper ben.bigh...@gmail.com Subject: Re: [R] Find each time a value changes To: r-help@r-project.org Cc: Tim Clark mudiver1...@yahoo.com Date: Wednesday, February 10, 2010, 4:16 PM Hi, On Feb 10, 2010, at 8:58 PM, Tim Clark wrote: Dear List, I am trying to find each time a value changes in a dataset. The numbers are variables for day vs. night values, so what I am really getting is the daily sunrise and sunset. A simplified example is the following: x-seq(1:100) y1-rep(1,10) y2-rep(2,10) y-c(y1,y2,y1,y1,y1,y2,y1,y2,y1,y2) xy-cbind(x,y) I would like to know each time the numbers change. Correct answer should be: x=1,11,21,51,61,71,81,91 I think this gets close... which(diff(y) != 0) [1] 10 20 50 60 70 80 90 You'll need to fiddle to get exactly what you want. Cheers, Ben I would appreciate any help or suggestions. It seems like it should be simple but I’m stuck! Thanks, Tim Tim Clark Department of Zoology University of Hawaii __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Suprising behavior of paste or cat?
I don't think you have said how you are examining the output files. Is
it possible that your text editor is assuming that the files are UCS-2
(Unicode), even
though R is writing ASCII?
Duncan Murdoch
On 11/02/2010 1:44 PM, Russell Pierce wrote:
Thank you for your input so far r-help denizens. Neither David nor
Peter were able to replicate my result. Has anybody other than me
been able to generate the failure I'm describing? So far I've
experienced it on 3 machines, Windows XP/P4/2.1.10, Windows
XP/Atom/2.1.10/2.1.11(release), Windows Vista/Centrino/2.1.10, but
found no problem on linux/2.7.1/x86_64.
Bill's idea is interesting. There may be a mismatch between types
occurring somewhere, but I haven't exactly where yet. To test our his
idea, I tried changing the order of the values in my vector task so
my output would start off with 2, rather than 1,. But I did not
observe a change in behavior.
I've generated further sample code to demonstrate the idiosyncraticy
of what I'm observing.
This code segment does not create a failure.
#No failure
lastcomma - function(x) {return(paste(x,,,collapse=,sep=))}
h.long - 150
task1 - c(rep(1,h.long),rep(2,h.long))
task2- c(rep(2,h.long),rep(1,h.long))
res1 - lastcomma(paste(task1,collapse=,))
res2 - lastcomma(paste(task2,collapse=,))
write(file=write-okay1.txt,res1)
cat(file=cat-okay2.txt,res2)
This code segment, where the task vector is reordered using sample as
an index, creates invalid files.
#Failure of write and cat
ord - sample(1:(h.long*2))
task1 - task1[ord]
task2 - task2[ord]
res1.bad - lastcomma(paste(task1,collapse=,))
res2.bad - lastcomma(paste(task2,collapse=,))
write(file=write-bad1.txt,res1.bad)
cat(file=cat-bad2.txt,res2.bad)
This code segment, where the task vector is shorter and reordered,
creates invalid files with cat, but not with write, and only when task
has been passed through my lastcomma function.
#Inconsistent; cat fails but write does not, cat only fails when
string has been passed through lastcomma
h.long - 100
task1 - c(rep(1,h.long),rep(2,h.long))
task2- c(rep(2,h.long),rep(1,h.long))
ord - sample(1:(h.long*2))
task1 - task1[ord]
task2 - task2[ord]
res1.no.lastcomma - paste(task1,collapse=,)
res2.no.lastcomma - paste(task2,collapse=,)
res1.yes.lastcomma - lastcomma(res1.no.lastcomma)
res2.yes.lastcomma - lastcomma(res2.no.lastcomma)
write(file=write-1-nlc.txt,res1.no.lastcomma) #okay
write(file=write-2-nlc.txt,res2.no.lastcomma) #okay
cat(file=cat-1-nlc.txt,res1.no.lastcomma) #okay
cat(file=cat-2-nlc.txt,res2.no.lastcomma) #okay
write(file=write-1-lc.txt,res1.yes.lastcomma) #okay
write(file=write-2-lc.txt,res2.yes.lastcomma) #okay
cat(file=cat-1-lc.txt,res1.yes.lastcomma) #bad
cat(file=cat-2-lc.txt,res2.yes.lastcomma) #bad
Thanks,
Russell
On Thu, Feb 11, 2010 at 9:05 AM, William Dunlap wdun...@tibco.com wrote:
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Russell Pierce
Sent: Wednesday, February 10, 2010 9:21 PM
To: r-help@r-project.org
Subject: [R] Suprising behavior of paste or cat?
I may be making a simple error, but I've looked at the str() of the
resulting objects and I can't see any obvious reason I'm having the
problem I am having, so I am reaching out to the R-help group. I am
generating a string in my code. When I make a slight modification
(add a comma at the end using my lastcomma function), I can no
longer successfully write that string to a file. Specifically, the
resulting file contains only the ⰱ character.
That character (which prints as an unfilled square when
I look at it in Outlook) is (when I copy and paste it
to R 2.10.0 on Windows):
ⰱ
[1] \u2c31
The 2 bytes in it would be comma and one in ascii:
\x2c
[1] ,
\x31
[1] 1
It looks like a ascii/UTF-8 mismatch. Is the square Outlook's
way of saying it is illegal UTF-8?
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
This occurs in:
R version 2.10.0 (2009-10-26) R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
but not in...
R version 2.7.1 (2008-06-23)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLA
TE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=
en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
NT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Sample code:
h.long - 150
task - c(rep(1,h.long),rep(2,h.long))
ord - sample(1:length(task))
task - task[ord]
taskout - paste(task,collapse=,)
write(file=please.txt,taskout)
Re: [R] Creating a new Access database with R
On Thu, Feb 11, 2010 at 6:23 PM, Dieter Menne dieter.me...@menne-biomed.de wrote: Paul- wrote: As a workaround, you can keep an empty mdb file on your filesystem. When you need a new database, you can copy and rename the empty file. Creating a new database is not part of (R)ODBC because there are too many differences between implementations. You you use some RDCOM method to do that, though. Create an empty mdb file in the usual way, then read it into R using a binary file connection, save it as an R object. To create, spew the raw bytes back out to another connection. Something like: mdb = readBin(test1.mdb,what=raw,n=7) length(mdb) [1] 65536 Ooh, 64kbytes. If that's too big, run length encoding will shrink it somewhat: rle(mdb) Run Length Encoding lengths: int [1:3953] 1 1 2 1 1 1 1 1 1 1 ... values : raw [1:3953] 00 01 00 53 ... However, I just created two via the MS ODBC dialog, and they aren't identical. They are wildly different. I suspect it's just creation dates and times in the system tables. You should be okay. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dual Category X-Axis (Multi-Level)
Using mtext is probably one of the most straight forward ways. You can also use something like: par(mfrow=c(1,3), mar=c(5.1,0,4.1,0), oma=c(0,4.1,0,1.1)) one - 1:3 two - 2:5 three - 6:4 names(one) - LETTERS[1:3] names(two) - letters[2:5] names(three) - state.abb[6:4] tmp.ylim - range(0,one,two,three) barplot(one, col='red', bty='n', xlab='one', ylim=tmp.ylim) barplot(two, col='green', bty='n', xlab='two', ylim=tmp.ylim, ylab='', yaxt='n') barplot(three, col='blue', xlab='three', bty='n', ylim=tmp.ylim, ylab='', yaxt='n') Or you could put that in a loop. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Powell, Eric Sent: Thursday, February 11, 2010 9:16 AM To: 'r-help@r-project.org' Subject: [R] Dual Category X-Axis (Multi-Level) Hello, I was wondering if anyone knows of a way to produce multilevel x-axis groupings similar to Excel's pivotcharts. (If you're not sure what I'm talking about, here's an example: http://peltiertech.com/WordPress/chart-with-a-dual-category-axis/). I realize that I could use mtext to manually insert text where desired, but I was hoping for a more systematic approach. Thanks in advance, -eric [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Find each time a value changes
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tim Clark Sent: Thursday, February 11, 2010 10:53 AM To: r-help@r-project.org Subject: Re: [R] Find each time a value changes It was brought to my attention that the rle() answer to this question was not posted. The following gives the correct answer once the last value is deleted. x-seq(1:100) y1-rep(1,10) y2-rep(2,10) y-c(y1,y2,y1,y1,y1,y2,y1,y2,y1,y2) xy-cbind(x,y) print(xy) print(str(xy)) # SEE WHAT RLE GIVES test - rle(xy[,2]) print(str(test) # USE JIMS TRICK OF CUMULATIVE SUMMING # TO GET THE LOCATIONS result - cumsum(c(1,rle(xy[,2])$lengths)) This cumsum undoes the diff that rle does. You could do what the first half of rle does with isFirstInRun - function(x)c(TRUE, x[-1]!=x[-length(x)] or isLastInRun - function(x)c(x[-1]!=x[-length(x)], TRUE) Use as which(isFirstInRun(xy[,2])) Tim Clark Department of Zoology University of Hawaii --- On Wed, 2/10/10, Ben Tupper ben.bigh...@gmail.com wrote: From: Ben Tupper ben.bigh...@gmail.com Subject: Re: [R] Find each time a value changes To: r-help@r-project.org Cc: Tim Clark mudiver1...@yahoo.com Date: Wednesday, February 10, 2010, 4:16 PM Hi, On Feb 10, 2010, at 8:58 PM, Tim Clark wrote: Dear List, I am trying to find each time a value changes in a dataset. The numbers are variables for day vs. night values, so what I am really getting is the daily sunrise and sunset. A simplified example is the following: x-seq(1:100) y1-rep(1,10) y2-rep(2,10) y-c(y1,y2,y1,y1,y1,y2,y1,y2,y1,y2) xy-cbind(x,y) I would like to know each time the numbers change. Correct answer should be: x=1,11,21,51,61,71,81,91 I think this gets close... which(diff(y) != 0) [1] 10 20 50 60 70 80 90 You'll need to fiddle to get exactly what you want. Cheers, Ben I would appreciate any help or suggestions. It seems like it should be simple but I'm stuck! Thanks, Tim Tim Clark Department of Zoology University of Hawaii __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
