date:20120412

Hi

see inline

 
 Hello,
 
 I've got a small dataset on box turtle shell measurements that I would 
 like to perform a detrended correspondence analysis on. I thought that 
it 
 would be interesting to examine the morphometrics for each species in 
the 
 area of overlap and in areas where neither species occurs. 
 
 I've taken a look at the dune and dune.env datasets in vegan. Using the 
 str() command gives me 
 
  str(dune)
 'data.frame':   20 obs. of  30 variables:
  $ Belper: num  3 0 2 0 0 0 0 2 0 0 ...
  $ Empnig: num  0 0 0 0 0 0 0 0 0 0 ...
  $ Junbuf: num  0 3 0 0 0 0 0 0 0 0 ...
  $ Junart: num  0 0 0 3 0 0 4 0 0 3 ...
  ...
 
 However, when I try looking directly at the data frame using the edit 
 command I see that there is a column called row.names to the left of 
Belper.
 
 Likewise, when I use the str() command on dune.env I get
 
  str(dune.env)
 'data.frame':   20 obs. of  5 variables:
  $ A1: num  3.5 6 4.2 5.7 4.3 2.8 4.2 6.3 4 11.5 ...
  $ Moisture  : Ord.factor w/ 4 levels 1245: 1 4 2 4 1 1 4 1 2 
4 ...
  $ Management: Factor w/ 4 levels BF,HF,NM,..: 1 4 4 4 2 4 2 2 3 3 
...
  $ Use   : Ord.factor w/ 3 levels HayfieldHaypastu..: 2 2 2 3 
2 
 2 3 1 1 2 ...
  $ Manure: Ord.factor w/ 5 levels 0123..: 3 4 5 4 3 5 4 
3 1 1 ...
 
 but using the edit() command shows a column named row.names.

No. This is not a column but it is what it says row.names

 str(rosin)
'data.frame':   10 obs. of  5 variables:
 $ pytel: int  1 2 3 4 5 6 7 8 9 10
 $ rstr : num  1.022 0.981 0.992 1.01 0.976 ...
 $ gama : num  1.4 1.44 1.41 1.43 1.39 ...
 $ cas  : int  0 3 6 9 12 15 18 21 24 27
 $ typ  : chr  anatas anatas anatas anatas 


 head(rosin)
  pytel  rstr gama castyp
1 1 1.0216621 1.397885   0 anatas
2 2 0.9809663 1.442439   3 anatas
3 3 0.9916211 1.411767   6 anatas
^^ these are row names

 
 I assume that the the row.names column is used to link the two files 
together.

If you are in doubt, recommended way is to consult documentation.

?row.names
All data frames have a row names attribute, a character vector of length 
the number of rows with no duplicates nor missing values. 

 
 My turtle data is saved as a *.csv, and I've added a column called 
 row.names, so that it looks like this
 
 row.names,CL,CCL,CW,CCW,CH,CCH
 1,104.4,131.8,89.887,137.4,43.391,89.7
 2,108.79,135.9,87.78,118.1,50.72,71.2
 3,114.12,126.1,89.33,132.8,142.39,78.3
 4,102.87,128.2,84.2,125,45.42,72.4
 5,84.6,104.8,72.61,111.8,41.1,57.3
 
 I've called this file turtles_dca.csv. I've also created a file called 

 turtles_dca_env.csv that looks like this
 
 row.names,Species,Sex,Distribution,Concatenated,Species_overlap
 1,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
 2,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
 3,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
 4,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
 5,Terrapene_ornata,Female,overlap,TO_F_Overlap,TO_Overlap
 
 However, when I read the data into R using this command
 
 turtles.env = read.csv(turtles_dca_env.csv, header = TRUE)
 
 
 and then using the str() command I get 
 
 
  str(turtles)
 'data.frame':   67 obs. of  7 variables:
  $ row.names: int  1 2 3 4 5 6 7 8 9 10 ...
  $ CL   : num  104.4 108.8 114.1 102.9 84.6 ...
  $ CCL  : num  132 136 126 128 105 ...
  $ CW   : num  89.9 87.8 89.3 84.2 72.6 ...
  $ CCW  : num  137 118 133 125 112 ...
  $ CH   : num  43.4 50.7 142.4 45.4 41.1 ...
  $ CCH  : num  89.7 71.2 78.3 72.4 57.3 73.4 67 57 68.8 68 ...
 
 When I run decorana() on this dataset, it appears that the column 
 row.names is included in the analysis, which isn't what I'm looking 
for. 

Then why you added this column to your data?

 
 If I go ahead and delete the column row.names from my data frames 
(i.e. 
 removing it from turtles and turtles.env), I don't believe that the 
 analysis is performed correctly. The two species differ significantly in 

 most of their measurements, but the ordihull() and ordispider() commands 

 show them overlapping almost completely.
 
 I think that I'm missing something pretty basic about inputting and 
 formatting this data for this analysis. Can anyone offer a suggestion on 

 where I'm going astray? I can send a copy of the data if anyone wants to 
look at it.

I am not familiar with functions you use. However you probably want to 
link those 2 files together. If they both are in the same order you can 
just do

turtles.complet - cbind(turtles, turtles.env)

Or if they are in different order you need to find some common column(s) 
and 

?merge

those two files.

Regards 
Petr


 
 Best wishes,
 Chris
 University of Central Oklahoma
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[R] Recode Variable

2012-04-12 Thread David Studer

Hello everybody,

I know this is pretty basic stuff, but could anyone explain me how to
recode a single value of a variable
into a missing value?

I used to do it like this:

myData[myData$var1==5;var1]-NA # recode value 5 into NA

But the column var1 already contains NAs, which
results in the following error message:

missing values are not allowed in subscripted assignments of data frames

Thank you very much for any advice!

David

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Re: [R] Encoding of Sweave file error message

2012-04-12 Thread Rainer Schuermann

I also had the same problem.

Being on Linux, I prefer Walmes' command line method but I found that putting
\usepackage[utf8x]{inputenc}
as the first instruction in the master .Rnw file also does the trick. No need 
to change anything after that in the file, at least not for me!

Rgds,
Rainer


On Thursday 12 April 2012 14:13:06 Duncan Mackay wrote:
 
 At 12:03 12/04/2012, you wrote:
 I had the same problem! So, as I'm a linux user, 
 I prefer use linux terminal. On terminal I type this to compile
 
 R CMD Sweave --encoding=utf-8 myfile.Rnw
 
 and the compilation is successful. Try to set the encoding option in 
 Sweave().
 
 Bests.
 Walmes.
 
 ==
 Walmes Marques Zeviani
 LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
 Departamento de Estatística - Universidade Federal do Paraná
 fone: (+55) 41 3361 3573
 VoIP: (3361 3600) 1053 1173
 e-mail: mailto:wal...@ufpr.brwal...@ufpr.br
 twitter: @walmeszeviani
 homepage: http://www.leg.ufpr.br/%7Ewalmeshttp://www.leg.ufpr.br/~walmes
 linux user number: 531218
 ==
 
 Hi Walmes
 
 Thank you very much. That appears to be the problem.
 When I typed from the DOS terminal
 
 I have exactl ParasiteComb12.Rnw
 
 it compiled the tex file without any error messages.
 
 I have not really got into font encoding and 
 reading the Sweave manual I thought that what I had done would be sufficient.
 
 I found an old note which gave a reference to
 http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4725.html
 http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4889.html
 but that appears to be specific.
 
 The ?Sweave and the Sweave manual appear to be 
 more specific about the latex side.
 
 After having a look at iconvlist()  and bearing 
 in mind Duncan Murdoch's comments about windows I tried
 
 Sweave(D:/Cic/Sweave/Parasite/Comb/12/ParasiteComb12.Rnw, 
 encoding = UTF-8)
 
 from the Rgui command window and compiled without any problems
 When I had a look at the tex file there were a 
 few DOS Alt-248 (degree symbol ) within latex 
 comments which were added last running R2.14 before updating
 
 Removing them and re running without the encoding 
 argument brought things back to normal.
 
 I tried as a test
 \SweaveOpts{encoding=UTF8}
 but that appears not to work
 
 All I have to do now is to put the extra argument 
 into my text editors clip library for Sweave for 
 next time when I cannot solve things.
 Its been a long week !
 
 Regards
 
 Duncan
 
 
 Duncan Mackay
 Department of Agronomy and Soil Science
 University of New England
 ARMIDALE NSW 2351
 Email home: mac...@northnet.com.au
 
 
 
 
 
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Re: [R] Recode Variable

2012-04-12 Thread Tal Galili

Hi David,
You bring up a good question.  I am not sure what is the right way to
solve it.  But here is a simple solution I put together:

x = c(1:10,5)
y = x
x[c(2,3)] - NA

# reproducing the problem:
y[x==5]

na2F - function(x) {
x2 - x
x2[is.na(x)] - F
x2
}
na2F(x==5)

# solved
y[na2F(x==5)]


I'd be happy to see other solutions to it.

With regards,
Tal



Contact
Details:---
Contact me: tal.gal...@gmail.com |  972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-statistics.com (English)
--




On Thu, Apr 12, 2012 at 12:08 PM, David Studer stude...@gmail.com wrote:

 Hello everybody,

 I know this is pretty basic stuff, but could anyone explain me how to
 recode a single value of a variable
 into a missing value?

 I used to do it like this:

 myData[myData$var1==5;var1]-NA # recode value 5 into NA

 But the column var1 already contains NAs, which
 results in the following error message:

 missing values are not allowed in subscripted assignments of data frames

 Thank you very much for any advice!

 David

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 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
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 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


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Re: [R] Recode Variable

2012-04-12 Thread Milan Bouchet-Valat

Le jeudi 12 avril 2012 à 12:29 +0300, Tal Galili a écrit :
 Hi David,
 You bring up a good question.  I am not sure what is the right way to
 solve it.  But here is a simple solution I put together:
 
 x = c(1:10,5)
 y = x
 x[c(2,3)] - NA
 
 # reproducing the problem:
 y[x==5]
 
 na2F - function(x) {
 x2 - x
 x2[is.na(x)] - F
 x2
 }
 na2F(x==5)
 
 # solved
 y[na2F(x==5)]
 
 
 I'd be happy to see other solutions to it.
You can simply use the built-in function which() for this, since it
removes NAs, only returning the position of TRUE elements:
which(c(NA, 1:10 == 5))
[1] 6


My two cents

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Re: [R] Recode Variable

2012-04-12 Thread Milan Bouchet-Valat

Le jeudi 12 avril 2012 à 11:08 +0200, David Studer a écrit :
 Hello everybody,
 
 I know this is pretty basic stuff, but could anyone explain me how to
 recode a single value of a variable
 into a missing value?
 
 I used to do it like this:
 
 myData[myData$var1==5;var1]-NA # recode value 5 into NA
 
 But the column var1 already contains NAs, which
 results in the following error message:
 
 missing values are not allowed in subscripted assignments of data frames
 
 Thank you very much for any advice!
You can just do this:
myData - data.frame(var1=1:10)
myData$var1[2]-NA
myData[myData$var1 == 5, var1] - NA # Fails
myData$var1[myData$var1 == 5] - NA # Works
myData
   var1
1 1
2NA
3 3
4 4
5NA
6 6
7 7
8 8
9 9
10   10


Regards

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Re: [R] Schedule R script using cron




On 12.04.2012 03:51, winie wrote:

I am trying to schedule my R script using cron, but it is not working. It
seems R can not find packages in cron. Anyone can help me? Thanks.

The following is my bash script

# source  my porfile
. /home/winie/.profile
# script.R will load packages
R CMD BATCH /home/script.R


Maybe it does not call the R version your expect? Or you have not set 
the pat to the library given the packages are not installed in R's main 
library in R_HOME?


Uwe Ligges




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Re: [R] loess function take




On 12.04.2012 05:49, arunkumar wrote:

Hi

The function loess takes very long time if the dataset is very huge
I have around 100 records
and used only one independent variable. still it takes very long time

Any suggestion to reduce the time



Use another method that is computationally less expensive for that many 
observations.


Uwe Ligges



-
Thanks in Advance
 Arun
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[R] r software resource persons India (hyd)

2012-04-12 Thread Sridhar Gutam

Looking for r-software resource persons for the Sensitization and Capacity
Building Workshop on Free Software and Knowledge Initiatives in
Agricultural Research for Development to be held in the month of July 2012
at Hyderabad. https://sites.google.com/site/fskiard/
__
Sridhar Gutam PhD, ARS, Patent Laws (NALSAR), IP  Biotech. (WIPO)
Senior Scientist (Plant Physiology)
Central Institute for Subtropical Horticulture http://www.cishlko.org
Rehmankhera, Kakori Post
Lucknow 227107, Uttar Pradesh, India
Phone: +91-522-2841022/23/24; Fax: +91-522-2841025
Mobile:+91-9005760036/8005346136
https://www.facebook.com/gutamsridhar
http://www.linkedin.com/in/sridhargutam
http://twitter.com/gutam2000http://works.bepress.com/sridhar_gutam/rss.html

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Re: [R] Recode Variable

2012-04-12 Thread Rainer Schuermann

1. Some data structured the way you are using would have been helpful.
I used Tal Galil's play data and set up a dataframe with the variable names you 
are using:
structure(list(var1 = c(1, NA, NA, 4, 5, 6, 7, 8, 9, 10, 5), 
var2 = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 5)), .Names = c(var1, 
var2), row.names = c(NA, -11L), class = data.frame)
 myData
   var1 var2
1 11
2NA2
3NA3
4 44
5 55
6 66
7 77
8 88
9 99
10   10   10
1155

2. The error message I get from your line of code is
 myData[myData$var1==5;var1]-NA
Error: unexpected ';' in myData[myData$var1==5;
Probably the semikolon is a typo?

3. If I understand your question correctly, the easiest answer I can find is 
ifelse():
 myData$var1 - ifelse( myData$var1 == 5, NA, myData$var1 )
 myData
   var1 var2
1 11
2NA2
3NA3
4 44
5NA5
6 66
7 77
8 88
9 99
10   10   10
11   NA5

Rgds,
Rainer


On Thursday 12 April 2012 11:08:45 David Studer wrote:
 Hello everybody,
 
 I know this is pretty basic stuff, but could anyone explain me how to
 recode a single value of a variable
 into a missing value?
 
 I used to do it like this:
 
 myData[myData$var1==5;var1]-NA # recode value 5 into NA
 
 But the column var1 already contains NAs, which
 results in the following error message:
 
 missing values are not allowed in subscripted assignments of data frames
 
 Thank you very much for any advice!
 
 David
 
   [[alternative HTML version deleted]]
 
 __
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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[R] Seeking help with LOGIT model

Dear all, I am fitting a LOGIT model on this Data...

Data - structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1,
0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1,
0, 1, 1, 0, 1, 0, 47, 58, 82, 100, 222, 164, 161, 70, 219, 81,
209, 182, 185, 104, 126, 192, 95, 245, 97, 177, 125, 56, 85,
199, 298, 145, 78, 144, 178, 146, 132, 98, 120, 148, 123, 282,
79, 34, 104, 91, 199, 101, 109, 117, 1.1, 0.92, 1.72, 2.18, 1.75,
2.26, 2.07, 1.43, 1.92, 1.82, 2.34, 2.12, 1.81, 1.35, 1.26, 2.07,
2.04, 1.55, 1.89, 1.68, 0.76, 1.96, 1.29, 1.81, 1.72, 2.39, 1.68,
2.29, 2.34, 2.21, 1.42, 1.97, 2.12, 1.9, 1.15, 1.7, 1.24, 1.55,
2.04, 1.59, 2.07, 2, 1.84, 2.04, 51.2, 48.5, 50.8, 54.4, 52.4,
56.7, 54.6, 52.7, 52.3, 53, 55.4, 53.5, 51.6, 48.5, 49.3, 53.9,
55.7, 51.2, 54, 52.2, 51.1, 54, 55, 52.9, 53.7, 55.8, 50.4, 58.8,
54.5, 53.5, 48.8, 54.5, 52.1, 56, 56.2, 53.3, 50.9, 53.2, 51.7,
54.3, 53.7, 54.7, 47, 56.9, 0.321, 0.224, 0.127, 0.063, 0.021,
0.027, 0.139, 0.218, 0.008, 0.012, 0.076, 0.299, 0.04, 0.069,
0.33, 0.017, 0.166, 0.003, 0.01, 0.076, 0.454, 0.032, 0.266,
0.018, 0.038, 0.067, 0.075, 0.064, 0.065, 0.065, 0.09, 0.016,
0.061, 0.019, 0.389, 0.037, 0.161, 0.127, 0.017, 0.222, 0.026,
0.012, 0.057, 0.022, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1,
1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1,
0, 1, 1, 0, 1, 0, 0, 1, 0), .Dim = c(44L, 6L), .Dimnames = list(
c(Obs 1, Obs 2, Obs 3, Obs 4, Obs 5, Obs 6, Obs 7,
Obs 8, Obs 9, Obs 10, Obs 11, Obs 12, Obs 13,
Obs 14, Obs 15, Obs 16, Obs 17, Obs 18, Obs 19,
Obs 20, Obs 21, Obs 22, Obs 23, Obs 24, Obs 25,
Obs 26, Obs 27, Obs 28, Obs 29, Obs 30, Obs 31,
Obs 32, Obs 33, Obs 34, Obs 35, Obs 36, Obs 37,
Obs 38, Obs 39, Obs 40, Obs 41, Obs 42, Obs 43,
Obs 44), c(Y, X 1, X 2, X 3, X 4, X 5)))


glm(Data[,1] ~ Data[,-1], binomial(link = logit))

Call:  glm(formula = Data[, 1] ~ Data[, -1], family = binomial(link = logit))

Coefficients:
  (Intercept)  Data[, -1]X 1  Data[, -1]X 2  Data[, -1]X 3  Data[,
-1]X 4  Data[, -1]X 5
 10.993260.01943   10.61013   -0.66763
70.98785   17.33126

Degrees of Freedom: 43 Total (i.e. Null);  38 Residual
Null Deviance:  44.58
Residual Deviance: 17.46AIC: 29.46
Warning message:
glm.fit: fitted probabilities numerically 0 or 1 occurred


However I am getting a warning mesage as fitted probabilities
numerically 0 or 1 occurred. Here my question is, have I made any
mistakes with my above implementation? Is it just because, I have too
less number of '0' in my response Variable?

Thanks for your help.

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[R] Reading SPSS: underlying numerical codes

2012-04-12 Thread Marion Wenty

Dear people,

I have got a question concerning the underlying numerical codes when
reading an SPSS file into R.

I used the package foreign and when I look at a variable I get the verbal
codes.

I would like to know how it is possible to get the underlying numerical
codes as output, which are the same as in my SPSS file.

Thank you very much in advance for your help!

Marion

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Re: [R] Schedule R script using cron

2012-04-12 Thread Martin Maechler

 winie  winieb...@gmail.com
 on Wed, 11 Apr 2012 18:51:28 -0700 writes:

 I am trying to schedule my R script using cron, but it is not
 working. It seems R can not find packages in cron. Anyone can help me?
 Thanks.

 The following is my bash script

 # source  my porfile
 . /home/winie/.profile
 # script.R will load packages
 R CMD BATCH /home/script.R 

This has almost nothing to with R, but with running scripts in
cron. On the systems, I've been using, the default shell cron uses is
very simple, e.g.,  PATH = /usr/bin:/bin ,
so I assume that's why you source your (bash ?) profile,
 . /home/winie/.profile
above.
But that may not be sufficient; there are other settings,
missing in the simple cron environment, that your .profile
does not fix up, such as
LD_LIBRARY_PATH, R_LIBS, R_PROFILE, ...
I would add  a line to your bash script
  env  /tmp/cron_env_$$
after the  . /home/winie/.profile line,
and see how that (cron_env_... file) differs from what you
get when you type 'env' in a regular interactive shell
where (I assume) your  'R CMD BATCH ...' works correctly.

Hoping that helps,
Martin

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Re: [R] Seeking help with LOGIT model

2012-04-12 Thread ken knoblauch

Christofer Bogaso bogaso.christofer at gmail.com writes:
 Dear all, I am fitting a LOGIT model on this Data...
  snip ---
 glm(Data[,1] ~ Data[,-1], binomial(link = logit))
 
 Call:  glm(formula = Data[, 1] ~ Data[, -1], family = binomial(link = logit))
 
 Coefficients:
   (Intercept)  Data[, -1]X 1  Data[, -1]X 2  Data[, -1]X 3  Data[,
 -1]X 4  Data[, -1]X 5
  10.993260.01943   10.61013   -0.66763
 70.98785   17.33126
 
 Degrees of Freedom: 43 Total (i.e. Null);  38 Residual
 Null Deviance:  44.58
 Residual Deviance: 17.46AIC: 29.46
 Warning message:
 glm.fit: fitted probabilities numerically 0 or 1 occurred
 
 However I am getting a warning mesage as fitted probabilities
 numerically 0 or 1 occurred. Here my question is, 
have I made any
 mistakes with my above implementation? I
s it just because, I have too
 less number of '0' in my response Variable?
 
Look at the output of summary, especially the standard errors.  
You seem to be getting complete
separation on X5 and X4 doesn,'t look so hot either.

Ken

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Re: [R] strsplit help

2012-04-12 Thread alison waller

Thanks - I checked through and it looks as if all of the geneids are 
formatted similarily so I don't know which one would be causing an error.
Interestingly, your sapply method works on the same data.  So I'm happy 
although still confused, because the strsplit method worked the other 
day with a similarly generated dataset.

I dumped my entire dataframe below.  Incase anyone wants to investigate.

Alison

Rumino_Reps_agreeWalign$geneid.prefix - sapply(gene.list, [, 1)
Rumino_Reps_agreeWalign$geneid.suffix - sapply(gene.list, [, 2)
  dput(Rumino_Reps_agreeWalign)
structure(list(geneid = c(657313.locus_tag:RTO_08940, 457412.251848018,
657314.locus_tag:CK5_20630, 657323.locus_tag:CK1_33060, 
657313.locus_tag:RTO_09690,
471875.197297106, 411470.DS231493.G14, 411459.149830627,
657313.locus_tag:RTO_09720, 411460.145845997, 411459.149831369,
657321.locus_tag:RBR_01830, 411460.145846414, 457412.251848805,
657321.locus_tag:RBR_08030, 471875.197296907, 457412.251847995,
657314.locus_tag:CK5_20840, 411460.145846423, 
657314.locus_tag:CK5_25030,
457412.251847990, 471875.197297117, 471875.197299322, 
411459.149831093,
411459.149831815, 411460.145846434, 213810.locus_tag:RUM_09700,
657314.locus_tag:CK5_09460, 657323.locus_tag:CK1_18840, 
471875.197297108,
411460.145846680, 411459.149831368, 657314.locus_tag:CK5_19120,
657321.locus_tag:RBR_09560, 411460.145846435, 
657323.locus_tag:CK1_11530,
457412.251850723, 213810.locus_tag:RUM_12960, 
213810.locus_tag:RUM_14740,
213810.locus_tag:RUM_07030, 471875.197296936, 411459.149831092,
471875.197297110, 471875.197298135, 411460.145846430, 
657314.locus_tag:CK5_20370,
657313.locus_tag:RTO_09790, 657323.locus_tag:CK1_33050, 
411460.145846407,
457412.251849909, 411460.145846340, 657313.locus_tag:RTO_14810,
457412.251848010, 457412.251850599, 657323.locus_tag:CK1_33200,
657323.locus_tag:CK1_33190, 213810.locus_tag:RUM_03050, 
657314.locus_tag:CK5_09880,
213810.locus_tag:RUM_15180, 657313.locus_tag:RTO_14610, 
657313.locus_tag:RTO_23930,
411459.149830473, 657313.locus_tag:RTO_18090, 
657323.locus_tag:CK1_27940,
657314.locus_tag:CK5_20720, 411459.149831855, 471875.197297691,
411459.149833320, 457412.251849358, 657321.locus_tag:RBR_13130,
411459.149831077, 471875.197297272, 657314.locus_tag:CK5_09370,
457412.251847994, 411459.149831080, 657314.locus_tag:CK5_20730,
457412.251850579, 213810.locus_tag:RUM_14870, 
657321.locus_tag:RBR_01750,
657313.locus_tag:RTO_09660, 657314.locus_tag:CK5_28910, 
411460.145846907,
657313.locus_tag:RTO_09860, 457412.251847996, 
657323.locus_tag:CK1_38480,
411460.145846417, 471875.197297592, 411459.149831814, 
457412.251848016,
411459.149831804, 657323.locus_tag:CK1_32880, 
657321.locus_tag:RBR_08130,
411460.145846429, 657313.locus_tag:RTO_09880, 
213810.locus_tag:RUM_03410,
657313.locus_tag:RTO_09740, 657313.locus_tag:RTO_09840, 
457412.251848009,
657323.locus_tag:CK1_33090, 657323.locus_tag:CK1_25000, 
411459.149831095,
411459.149830934, 457412.251847970, 457412.251848000, 
657314.locus_tag:CK5_20680,
411459.149831088, 657323.locus_tag:CK1_19350, 
657321.locus_tag:RBR_08670,
471875.197299547, 411459.149831081, 657323.locus_tag:CK1_32550,
411459.149831091, 657313.locus_tag:RTO_24580, 457412.251848004,
471875.197297195, 411460.145846602, 657321.locus_tag:RBR_06200,
213810.locus_tag:RUM_19570, 411460.145846361, 411459.149833804,
657323.locus_tag:CK1_32930, 471875.197296906, 411459.149831078,
657321.locus_tag:RBR_09900, 411460.145846496, 
657321.locus_tag:RBR_08260,
411459.149833021, 657313.locus_tag:RTO_02600, 
657323.locus_tag:CK1_33030,
657313.locus_tag:RTO_09750, 213810.locus_tag:RUM_14790, 
457412.251848017,
457412.251848806, 457412.251847640, 657314.locus_tag:CK5_20620,
411459.149830474, 657323.locus_tag:CK1_11750, 
213810.locus_tag:RUM_09690,
457412.251847999, 657321.locus_tag:RBR_05870, 411460.145846409,
657313.locus_tag:RTO_16220, 657321.locus_tag:RBR_10630, 
411459.149833026,
457412.251847997, 657313.locus_tag:RTO_09650, 471875.197297129,
471875.197297112, 213810.locus_tag:RUM_14720, 457412.251847991,
657313.locus_tag:RTO_09730, 471875.197297132, 
657313.locus_tag:RTO_14650,
411470.DS231491.G186, 457412.251849520, 657323.locus_tag:CK1_04710,
657323.locus_tag:CK1_04510, 411460.145846182, 411460.145846883,
657321.locus_tag:RBR_08040, 411459.149833983, 457412.251849519,
471875.197297124, 457412.251849906, 657321.locus_tag:RBR_08010,
657321.locus_tag:RBR_03380, 657323.locus_tag:CK1_20230, 
471875.197297115,
657323.locus_tag:CK1_13100, 657323.locus_tag:CK1_32950, 
411460.145846428,
471875.197297120, 213810.locus_tag:RUM_13040, 
657314.locus_tag:CK5_25080,
411459.149831096, 411459.149831090, 411459.14981, 
411459.149831370,
657313.locus_tag:RTO_26330, 411459.149833340, 
657314.locus_tag:CK5_20590,
411460.145846458, 471875.197297290, 657313.locus_tag:RTO_09850,
213810.locus_tag:RUM_12130, 657323.locus_tag:CK1_32910, 
213810.locus_tag:RUM_09770,
657313.locus_tag:RTO_09640, 657313.locus_tag:RTO_09830, 
457412.251849013,
411460.145847544,

[R] How insert data to a column in existing csv file?

2012-04-12 Thread Yellow

I was working with some excel files with a lot of data. 
And by hand it is impossible to handle them. 
So they are now converted to .csv. 

With headers above the columns, like:  
Data1, Data2, Data3 

But now I needed to calculate the log2 value of Data1 and place the result
under Data2. 
I can't find how to do that. 
Does anyone else know? 

I have the log2 values, but how do I get then inside the .csv file under
Data2? 

I already tried write.table(), buy that wasn't it. 
And I am kinda stuck on this now. 


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Re: [R] How insert data to a column in existing csv file?

2012-04-12 Thread ramonovelar

Hi,
You can use write.table with Append = TRUE to keep on writing in the same
csv file, but I don't know how to write in an specific cell of your csv
file. 
 http://stat.ethz.ch/R-manual/R-devel/library/utils/html/write.table.html

write.table (data, file = example.csv, sep = ;, col.names = NA, append =
TRUE, dec =,)

I think the best thing to do once you have imported your data into R is to
create a new csv file and write in it the table you need.

Hope it helps, R

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[R] General question on the message with non zero exit status

2012-04-12 Thread Chel Hee Lee

I have a general question how to understand the message with non-zero exit
status when new package is installed. Based on my experience, this message
implies a package dependence. Am I correct to understand this message? Are
there anyone who can provide some reference or explain details about the
message with non zero exit status?

I very appreciate for your kindness in advance. 


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Re: [R] Recode Variable

2012-04-12 Thread S Ellison



 myData[myData$var1==5;var1]-NA # recode value 5 into NA
try 
myData[!is.na(myData$var1)  myData$var1==5;var1]-NA
or, more simply,
myData$var1[myData$var1==5]-NA

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[R] Help in creating a matrix

2012-04-12 Thread arunkumar1111

Hi

I have dataset with n variables, say n =3  x y z

the formula should be form = x+y+z+x*x +x*y+x*z +y*y + y*z+z*z

my code has to for  loop 

Is there any way  to reduce two loops

  for (i in 1:n)
   {
  for (j in i:n)
  {
dat= cbind(dat,dat[,i]*dat[,j])
  }  
   }






-
Thanks in Advance
Arun
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[R] Support for R in highlight.js

2012-04-12 Thread Ivan Sagalaev


Hello,

I'm the maintainer of a syntax highlighting tool highlight.js[1]. 
Recently the Kaggle project has announced they wanted to sponsor the 
development of the R highlighting definition for it[2]. I wanted to drop 
a line about it here since I suspect this list has much more R 
programmers on it than our small discussion group :-).


So if you're interested and don't mind touching a little bit of 
JavaScript — please reply to the announcement or personally to Adam 
Kennedy adam.kenn...@kaggle.com who's behind it from the Kaggle side.


[1]: http://softwaremaniacs.org/soft/highlight/en/
[2]: https://groups.google.com/d/topic/highlightjs/-ogtOaK-TQY/discussion

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Re: [R] Saving multiple plots using tiff function

2012-04-12 Thread John S

Dear R users,

I still did not receive an answer to my question and went through the
archive with no luck.

So what does tiff(filename =Rplot%03d.tif) mean ? Why the following code
does produce two files?



tiff(filename =Rplot%03d.tif,width=24,height=20,units=cm,res=300,
pointsize=10, compression = lzw)

plot(1)

mtext(Fig 1,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

plot(2)

mtext(Fig 2,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

plot(3)

mtext(Fig 3,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

dev.off()



Your help is appreciated,

John


On Fri, Apr 6, 2012 at 2:26 PM, John S john.smith...@gmail.com wrote:

 Sorry forgot to mention that I am using windows 7 and R session info

 R version 2.15.0 (2012-03-30)
 Platform: i386-pc-mingw32/i386 (32-bit

 Thanks,
 John



 On Fri, Apr 6, 2012 at 2:17 PM, John S john.smith...@gmail.com wrote:

 Dear R experts,

 I am trying to save three plots using tiff graphics devices; however the
 following code only produces two files (Rplot002.tif and Rplot003.tif)
 showing figures 1 and 3. Here is a simplified ex code



 tiff(filename =Rplot%03d.tif,width=24,height=20,units=cm,res=300,
 pointsize=10, compression = lzw)

 plot(1)

 mtext(Fig 1,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

 plot(2)

 mtext(Fig 2,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

 plot(3)

 mtext(Fig 3,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

 dev.off()



 Using pdf () produces the correct 3 figures but I want to use tiff images
 .Any clues why this occurs?

 I am opening a tiff graphics device and writing plots to files in a loop
 so I need to have a single call to tiff().

 Thanks,
 John





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Re: [R] Seeking help with LOGIT model

Thanks Ken for your reply. No doubt your english is quite tough!! I
understand something is not normal with the 5th explanatory variable
(se:2872.17069!) However could not understand what you mean by You
seem to be getting complete separation on X5 ?

Can you please be more elaborate?

Thanks,

On Thu, Apr 12, 2012 at 4:06 PM, ken knoblauch ken.knobla...@inserm.fr wrote:
 Christofer Bogaso bogaso.christofer at gmail.com writes:
 Dear all, I am fitting a LOGIT model on this Data...
   snip ---
 glm(Data[,1] ~ Data[,-1], binomial(link = logit))

 Call:  glm(formula = Data[, 1] ~ Data[, -1], family = binomial(link = logit))

 Coefficients:
   (Intercept)  Data[, -1]X 1  Data[, -1]X 2  Data[, -1]X 3  Data[,
 -1]X 4  Data[, -1]X 5
      10.99326        0.01943       10.61013       -0.66763
 70.98785       17.33126

 Degrees of Freedom: 43 Total (i.e. Null);  38 Residual
 Null Deviance:      44.58
 Residual Deviance: 17.46        AIC: 29.46
 Warning message:
 glm.fit: fitted probabilities numerically 0 or 1 occurred

 However I am getting a warning mesage as fitted probabilities
 numerically 0 or 1 occurred. Here my question is,
 have I made any
 mistakes with my above implementation? I
 s it just because, I have too
 less number of '0' in my response Variable?

 Look at the output of summary, especially the standard errors.
 You seem to be getting complete
 separation on X5 and X4 doesn,'t look so hot either.

 Ken

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Re: [R] Reading SPSS: underlying numerical codes

2012-04-12 Thread Ista Zahn

Hi Marion,

Did you look at the help file? Did you try use.value.labels = FALSE?

Best,
Ista

On Thu, Apr 12, 2012 at 6:28 AM, Marion Wenty marion.we...@gmail.com wrote:
 Dear people,

 I have got a question concerning the underlying numerical codes when
 reading an SPSS file into R.

 I used the package foreign and when I look at a variable I get the verbal
 codes.

 I would like to know how it is possible to get the underlying numerical
 codes as output, which are the same as in my SPSS file.

 Thank you very much in advance for your help!

 Marion

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[R] How to calculate the McFadden R-square for LOGIT model?

Dear all, can somebody please help me how to calculate McFadden
R-square for a LOGIT model? Corresponding definition can be found
here:

http://publib.boulder.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Falg_plum_statistics_rsq_mcfadden.htm


Here is my data:

Data - structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1,
0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1,
0, 1, 1, 0, 1, 0, 47, 58, 82, 100, 222, 164, 161, 70, 219, 81,
209, 182, 185, 104, 126, 192, 95, 245, 97, 177, 125, 56, 85,
199, 298, 145, 78, 144, 178, 146, 132, 98, 120, 148, 123, 282,
79, 34, 104, 91, 199, 101, 109, 117, 1.1, 0.92, 1.72, 2.18, 1.75,
2.26, 2.07, 1.43, 1.92, 1.82, 2.34, 2.12, 1.81, 1.35, 1.26, 2.07,
2.04, 1.55, 1.89, 1.68, 0.76, 1.96, 1.29, 1.81, 1.72, 2.39, 1.68,
2.29, 2.34, 2.21, 1.42, 1.97, 2.12, 1.9, 1.15, 1.7, 1.24, 1.55,
2.04, 1.59, 2.07, 2, 1.84, 2.04, 51.2, 48.5, 50.8, 54.4, 52.4,
56.7, 54.6, 52.7, 52.3, 53, 55.4, 53.5, 51.6, 48.5, 49.3, 53.9,
55.7, 51.2, 54, 52.2, 51.1, 54, 55, 52.9, 53.7, 55.8, 50.4, 58.8,
54.5, 53.5, 48.8, 54.5, 52.1, 56, 56.2, 53.3, 50.9, 53.2, 51.7,
54.3, 53.7, 54.7, 47, 56.9, 0.321, 0.224, 0.127, 0.063, 0.021,
0.027, 0.139, 0.218, 0.008, 0.012, 0.076, 0.299, 0.04, 0.069,
0.33, 0.017, 0.166, 0.003, 0.01, 0.076, 0.454, 0.032, 0.266,
0.018, 0.038, 0.067, 0.075, 0.064, 0.065, 0.065, 0.09, 0.016,
0.061, 0.019, 0.389, 0.037, 0.161, 0.127, 0.017, 0.222, 0.026,
0.012, 0.057, 0.022, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1,
1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1,
0, 1, 1, 0, 1, 0, 0, 1, 0), .Dim = c(44L, 6L), .Dimnames = list(
c(Obs 1, Obs 2, Obs 3, Obs 4, Obs 5, Obs 6, Obs 7,
Obs 8, Obs 9, Obs 10, Obs 11, Obs 12, Obs 13,
Obs 14, Obs 15, Obs 16, Obs 17, Obs 18, Obs 19,
Obs 20, Obs 21, Obs 22, Obs 23, Obs 24, Obs 25,
Obs 26, Obs 27, Obs 28, Obs 29, Obs 30, Obs 31,
Obs 32, Obs 33, Obs 34, Obs 35, Obs 36, Obs 37,
Obs 38, Obs 39, Obs 40, Obs 41, Obs 42, Obs 43,
Obs 44), c(Y, X 1, X 2, X 3, X 4, X 5)))


AND, my model is:

glm(Data[,1] ~ Data[,-1], binomial(link = logit))

Thanks,

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Re: [R] Saving multiple plots using tiff function

2012-04-12 Thread Berend Hasselman


On 12-04-2012, at 13:07, John S wrote:

 Dear R users,
 
 I still did not receive an answer to my question and went through the
 archive with no luck.
 
 So what does tiff(filename =Rplot%03d.tif) mean ?


Just read the documentation for tiff: ?tiff

 Why the following code
 does produce two files?
 

It produces no files for me.
Only an error message.

 
 tiff(filename =Rplot%03d.tif,width=24,height=20,units=cm,res=300,
 pointsize=10, compression = lzw)
 
 plot(1)
 
 mtext(Fig 1,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)
 
 plot(2)
 
 mtext(Fig 2,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)
 
 plot(3)
 
 mtext(Fig 3,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)
 
 dev.off()
 

You must specify the antialias argument.
Which I did: I set it to none and got 3 .tif (plot) files.
So I don't know what's wrong with your stuff.

Berend

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Re: [R] Seeking help with LOGIT model

2012-04-12 Thread Ken Knoblauch


You should look up the Hauck-Donne phenomenon, which shows that
with binomial GLMs, the standard error can grow faster than
the effect size.  Complete separation results, for example,
when one predictor (or a combination of several predictors)
perfectly predicts the response.  Something like this seems
to be happening for variables 4 and 5.  You could try the
brglm function from the package of the same name, which
uses bias correction.  Compare (after coercing your Data to
a data frame):

summary(glm(Y ~ ., binomial, Data))

Call:
glm(formula = Y ~ ., family = binomial, data = Data)

Deviance Residuals:
 Min1QMedian3Q   Max
-2.00979   0.0   0.6   0.27987   1.82302

Coefficients:
  Estimate Std. Error z value Pr(|z|)
(Intercept)   10.99326   20.77336   0.529   0.5967
`X 1`  0.019430.01040   1.868   0.0617 .
`X 2` 10.610135.65409   1.877   0.0606 .
`X 3` -0.667630.47668  -1.401   0.1613
`X 4` 70.98785   36.41181   1.950   0.0512 .
`X 5` 17.33126 2872.17069   0.006   0.9952


summary(brglm(Y ~ ., binomial, Data))

Call:
brglm(formula = Y ~ ., family = binomial, data = Data)


Coefficients:
 Estimate Std. Error z value Pr(|z|)
(Intercept) 12.017791  14.337183   0.838   0.4019
`X 1`0.014898   0.008263   1.803   0.0714 .
`X 2`8.307941   4.010792   2.071   0.0383 *
`X 3`   -0.576309   0.352097  -1.637   0.1017
`X 4`   35.627644  16.638766   2.141   0.0323 *
`X 5`2.134544   2.570756   0.830   0.4064


Good luck.

Ken



Quoting Christofer Bogaso bogaso.christo...@gmail.com:


Thanks Ken for your reply. No doubt your english is quite tough!! I
understand something is not normal with the 5th explanatory variable
(se:2872.17069!) However could not understand what you mean by You
seem to be getting complete separation on X5 ?

Can you please be more elaborate?

Thanks,

On Thu, Apr 12, 2012 at 4:06 PM, ken knoblauch   
ken.knobla...@inserm.fr wrote:

Christofer Bogaso bogaso.christofer at gmail.com writes:

Dear all, I am fitting a LOGIT model on this Data...

  snip ---

glm(Data[,1] ~ Data[,-1], binomial(link = logit))

Call:  glm(formula = Data[, 1] ~ Data[, -1], family =   
binomial(link = logit))


Coefficients:
  (Intercept)  Data[, -1]X 1  Data[, -1]X 2  Data[, -1]X 3  Data[,
-1]X 4  Data[, -1]X 5
     10.99326        0.01943       10.61013       -0.66763
70.98785       17.33126

Degrees of Freedom: 43 Total (i.e. Null);  38 Residual
Null Deviance:      44.58
Residual Deviance: 17.46        AIC: 29.46
Warning message:
glm.fit: fitted probabilities numerically 0 or 1 occurred

However I am getting a warning mesage as fitted probabilities
numerically 0 or 1 occurred. Here my question is,

have I made any

mistakes with my above implementation? I

s it just because, I have too

less number of '0' in my response Variable?


Look at the output of summary, especially the standard errors.
You seem to be getting complete
separation on X5 and X4 doesn,'t look so hot either.

Ken

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Re: [R] deferred call

2012-04-12 Thread Whit Armstrong

Bert and Gabor,

Thanks for clarifying. Much appreciated.

One more question.  Do either of you know the location of the code
that does the lookup of the default arguments?

I would like to be able to capture the implicit dependency of the
function on the default arguments.

Hence, I would write something like:

capture.dag - function(fun) {
ans - list()
args - formals(fun)
for(nm in names(args)) {
ans[[ nm ]] - lookup.the.object(args[[nm]])
}

ans
}

However, it seems that this logic is already implemented in the core
of R, and it would be great to re-use it.

Thanks,
Whit


On Thu, Apr 12, 2012 at 1:00 AM, Bert Gunter gunter.ber...@gene.com wrote:
 On Wed, Apr 11, 2012 at 8:12 PM, Gabor Grothendieck
 ggrothendi...@gmail.com wrote:
 On Wed, Apr 11, 2012 at 10:17 PM, Whit Armstrong
 armstrong.w...@gmail.com wrote:
 I must admit I'm a little ashamed to have been using R for so long,
 and still lack a sound understanding of deferred calls, eval, deparse,
 substitute, and friends.

 I'm attempting to make a deferred call to a function which has default
 arguments in the following way:

 call.foo - function(f) {
    x - f()
 }

 x - 1:10
 f - function(x=x) { x^2 }
 call.foo(f)

 However, I'm getting the error:
 Error in x^2 : 'x' is missing

 Is there a common R idiom for calling 'formals' on the function, and
 then grabbing the named default arguments from the enclosing frame?

 I naively thought that since function 'f' was defined w/ a default
 argument of 'x' and x is defined in the same envir as the function
 itself, that the call would succeed.


 f - function(x=x) x^2 is an endless recursion.  Try

 To amplify just a bit on Gabor's comment, section 4.3.3 of the R
 language definition explicitly states:

 One of the most important things to know about the evaluation of
 arguments to a function is
 that supplied arguments and default arguments are treated differently.
 The supplied arguments
 to a function are evaluated in the evaluation frame of the calling
 function. The default arguments
 to a function are evaluated in the evaluation frame of the function.

 So foo - function (x = x) {...}
 tries to define foo with the default argument x, which is evaluated in
 the ** environment of the function ** not in the caller's environment,
 where it is 1:10.  So if x ever needs to be evaluated within foo
 (i.e., its promise is forced), then it looks for the value of the rhs
 of the x=x  assignment within foo, which is (the promise for) x,
 again, within foo, which is x again,...

 HTH

 -- Bert


  f - function(x.=x) { x^2 }

 (note the dot)

 --
 Statistics  Software Consulting
 GKX Group, GKX Associates Inc.
 tel: 1-877-GKX-GROUP
 email: ggrothendieck at gmail.com

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 Internal Contact Info:
 Phone: 467-7374
 Website:
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Re: [R] Saving multiple plots using tiff function

2012-04-12 Thread John S

Thanks Berend for your answer!

I read the documentation but I dont understand filename =Rplot%03d.tif  ?

Do you mind sending me what you tried?


On Thu, Apr 12, 2012 at 7:34 AM, Berend Hasselman b...@xs4all.nl wrote:


 On 12-04-2012, at 13:07, John S wrote:

  Dear R users,
 
  I still did not receive an answer to my question and went through the
  archive with no luck.
 
  So what does tiff(filename =Rplot%03d.tif) mean ?


 Just read the documentation for tiff: ?tiff

  Why the following code
  does produce two files?
 

 It produces no files for me.
 Only an error message.

 
  tiff(filename =Rplot%03d.tif,width=24,height=20,units=cm,res=300,
  pointsize=10, compression = lzw)
 
  plot(1)
 
  mtext(Fig 1,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)
 
  plot(2)
 
  mtext(Fig 2,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)
 
  plot(3)
 
  mtext(Fig 3,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)
 
  dev.off()
 

 You must specify the antialias argument.
 Which I did: I set it to none and got 3 .tif (plot) files.
 So I don't know what's wrong with your stuff.

 Berend



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Re: [R] Saving multiple plots using tiff function

2012-04-12 Thread S Ellison


 So what does tiff(filename =Rplot%03d.tif) mean ?

Just read the documentation for tiff: ?tiff

A look at ?sprintf might also be useful if you're unfamiliar with the C format 
specification. %03d is the format spec for a 3-digit decimal number with 
leading zeroes.
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Re: [R] Saving multiple plots using tiff function




On 12.04.2012 13:49, John S wrote:

Thanks Berend for your answer!

I read the documentation but I don’t understand filename =Rplot%03d.tif  ?

Do you mind sending me what you tried?



This is a bug in R. I'll take a look.

Best,
Uwe Ligges





On Thu, Apr 12, 2012 at 7:34 AM, Berend Hasselmanb...@xs4all.nl  wrote:



On 12-04-2012, at 13:07, John S wrote:


Dear R users,

I still did not receive an answer to my question and went through the
archive with no luck.

So what does tiff(filename =Rplot%03d.tif) mean ?



Just read the documentation for tiff: ?tiff


Why the following code
does produce two files?



It produces no files for me.
Only an error message.



tiff(filename =Rplot%03d.tif,width=24,height=20,units=cm,res=300,
pointsize=10, compression = lzw)

plot(1)

mtext(Fig 1,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

plot(2)

mtext(Fig 2,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

plot(3)

mtext(Fig 3,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

dev.off()



You must specify the antialias argument.
Which I did: I set it to none and got 3 .tif (plot) files.
So I don't know what's wrong with your stuff.

Berend




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Re: [R] Reading SPSS: underlying numerical codes

2012-04-12 Thread Marion Wenty

Hi Ista,

thank you for your reply!

Yes, I looked at the help sheet but didn't use this command because I would
still like the categorial variables to be converted into factors and have
the value labels from SPSS imported into R as levels.

With the

use.value.labels = FALSE?

command I do get the same underlying codes as in SPSS but I loose the
information about the levels, I think.

Does anyone know a way to preserve both?

Thank you very much for your help in advance?

Marion


2012/4/12 Ista Zahn istaz...@gmail.com

 Hi Marion,

 Did you look at the help file? Did you try use.value.labels = FALSE?

 Best,
 Ista

 On Thu, Apr 12, 2012 at 6:28 AM, Marion Wenty marion.we...@gmail.com
 wrote:
  Dear people,
 
  I have got a question concerning the underlying numerical codes when
  reading an SPSS file into R.
 
  I used the package foreign and when I look at a variable I get the verbal
  codes.
 
  I would like to know how it is possible to get the underlying numerical
  codes as output, which are the same as in my SPSS file.
 
  Thank you very much in advance for your help!
 
  Marion
 
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Re: [R] General question on the message with non zero exit status




On 12.04.2012 12:05, Chel Hee Lee wrote:

I have a general question how to understand the message with non-zero exit
status when new package is installed. Based on my experience, this message
implies a package dependence. Am I correct to understand this message? Are
there anyone who can provide some reference or explain details about the
message with non zero exit status?


A process typically indicates success by an exit status 0 and csan flag 
different kinds of errors by other exit codes. This is so far unrelated 
to R.
The INSTALL script evaluates the exit status and tells you that 
something went wrong according to that status, for more information, you 
will need to look at the (text) output of the INSTALL run.


Uwe Ligges





I very appreciate for your kindness in advance.


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[R] Using dcast with multiple functions to aggregate

2012-04-12 Thread Jokel Meyer

Dear R communitiy,

I am trying to use multiple functions for aggregation within a function
call for dcast. However this seems to result in an error. Also I have not
managed to make dcast() work with fun.aggregate=sd. Please find attached
some example code using the ChickWeight data.

Many thanks for your help!
Jokel


#Chick weight example

names(ChickWeight) - tolower(names(ChickWeight))


sd(ChickWeight$weight) # works fine

mean(ChickWeight$weight) # works fine

length(ChickWeight$weight) # works fine


chick_m - melt(ChickWeight, id=2:4, na.rm=TRUE)

dcast(chick_m, time~variable, mean) # works fine

dcast(chick_m, time~variable, length) # works fine


dcast(chick_m, time~variable, fun.aggregate=sd) # gives an error

dcast(chick_m, time~variable, c(mean, length)) # gives an error

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Re: [R] How to calculate the McFadden R-square for LOGIT model?

Please ignore this mail. I got a solution by using 'pscl' package!

On Thu, Apr 12, 2012 at 4:56 PM, Christofer Bogaso
bogaso.christo...@gmail.com wrote:
 Dear all, can somebody please help me how to calculate McFadden
 R-square for a LOGIT model? Corresponding definition can be found
 here:

 http://publib.boulder.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Falg_plum_statistics_rsq_mcfadden.htm


 Here is my data:

 Data - structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1,
 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1,
 0, 1, 1, 0, 1, 0, 47, 58, 82, 100, 222, 164, 161, 70, 219, 81,
 209, 182, 185, 104, 126, 192, 95, 245, 97, 177, 125, 56, 85,
 199, 298, 145, 78, 144, 178, 146, 132, 98, 120, 148, 123, 282,
 79, 34, 104, 91, 199, 101, 109, 117, 1.1, 0.92, 1.72, 2.18, 1.75,
 2.26, 2.07, 1.43, 1.92, 1.82, 2.34, 2.12, 1.81, 1.35, 1.26, 2.07,
 2.04, 1.55, 1.89, 1.68, 0.76, 1.96, 1.29, 1.81, 1.72, 2.39, 1.68,
 2.29, 2.34, 2.21, 1.42, 1.97, 2.12, 1.9, 1.15, 1.7, 1.24, 1.55,
 2.04, 1.59, 2.07, 2, 1.84, 2.04, 51.2, 48.5, 50.8, 54.4, 52.4,
 56.7, 54.6, 52.7, 52.3, 53, 55.4, 53.5, 51.6, 48.5, 49.3, 53.9,
 55.7, 51.2, 54, 52.2, 51.1, 54, 55, 52.9, 53.7, 55.8, 50.4, 58.8,
 54.5, 53.5, 48.8, 54.5, 52.1, 56, 56.2, 53.3, 50.9, 53.2, 51.7,
 54.3, 53.7, 54.7, 47, 56.9, 0.321, 0.224, 0.127, 0.063, 0.021,
 0.027, 0.139, 0.218, 0.008, 0.012, 0.076, 0.299, 0.04, 0.069,
 0.33, 0.017, 0.166, 0.003, 0.01, 0.076, 0.454, 0.032, 0.266,
 0.018, 0.038, 0.067, 0.075, 0.064, 0.065, 0.065, 0.09, 0.016,
 0.061, 0.019, 0.389, 0.037, 0.161, 0.127, 0.017, 0.222, 0.026,
 0.012, 0.057, 0.022, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1,
 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1,
 0, 1, 1, 0, 1, 0, 0, 1, 0), .Dim = c(44L, 6L), .Dimnames = list(
    c(Obs 1, Obs 2, Obs 3, Obs 4, Obs 5, Obs 6, Obs 7,
    Obs 8, Obs 9, Obs 10, Obs 11, Obs 12, Obs 13,
    Obs 14, Obs 15, Obs 16, Obs 17, Obs 18, Obs 19,
    Obs 20, Obs 21, Obs 22, Obs 23, Obs 24, Obs 25,
    Obs 26, Obs 27, Obs 28, Obs 29, Obs 30, Obs 31,
    Obs 32, Obs 33, Obs 34, Obs 35, Obs 36, Obs 37,
    Obs 38, Obs 39, Obs 40, Obs 41, Obs 42, Obs 43,
    Obs 44), c(Y, X 1, X 2, X 3, X 4, X 5)))


 AND, my model is:

 glm(Data[,1] ~ Data[,-1], binomial(link = logit))

 Thanks,

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Re: [R] How to calculate the McFadden R-square for LOGIT model?

2012-04-12 Thread Ben Bolker

Christofer Bogaso bogaso.christofer at gmail.com writes:

 
 Dear all, can somebody please help me how to calculate McFadden
 R-square for a LOGIT model?
  
  [snip]

library(sos)
findFn(McFadden)

  brings you to:

http://finzi.psych.upenn.edu/R/library/pscl/html/pR2.html

  i.e. install the sos package; use it to search 
  install the pscl package
  use the pR2() function

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Re: [R] How insert data to a column in existing csv file?

2012-04-12 Thread David Winsemius



On Apr 12, 2012, at 5:18 AM, Yellow wrote:


I was working with some excel files with a lot of data.
And by hand it is impossible to handle them.
So they are now converted to .csv.

With headers above the columns, like:
Data1, Data2, Data3

But now I needed to calculate the log2 value of Data1 and place the  
result

under Data2.
I can't find how to do that.


First you need to explain more clearly what you mean by place the  
result
under Data2. Is this a display concern? Or are you trying to  
interleave rows of original data and logged data using a column  
organization? Why only Data2? What should go in the rows for Data1 and  
Data3? ? What is the goal of this effort?




Does anyone else know?

I have the log2 values, but how do I get then inside the .csv file  
under

Data2?


Post some sample code that constructs the data.frames and the code you  
used.




I already tried write.table(), buy that wasn't it.
And I am kinda stuck on this now.



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[R] Centering (e.g. on prcomp)

2012-04-12 Thread Jessica Streicher

Hi!

I'm doing a PCA on some testdata (only 2 features) currently to see what 
happens. I read a lot of times one should center ones data, so i left the 
option on.

But now i am scratching my head on how to correctly transform new data to be 
comparable to the data used in the pca.

pca$x are the points (in PC system) the function returns
origpoints%*%pca$rotation

is not quite the same, because it is missing the centering

for the original data i can of course do scale(origpoints,scaled=F) beforehand, 
and then the results will be the same, but for new data that option isn't 
available. So how would i properly transform it?

greetings
Jessica
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[R] R error message

2012-04-12 Thread Harriet Lucy Stubbs



Hi,

I'm trying to do an exploratory factor analysis for a uni assignment  
but I keep getting this error message coming up


[1] One of your variables is a constant. Constants are disallowed as  
part of a scale.


when I turn the data into a matrix and look at the stats. I've been  
told that this means one of the variables doesn't vary much any more,  
but I am really stuck on how to sort this out. The code I have used is



summary(prefdata)
prefdata[prefdata5]=NA
summary(prefdata)
prefdata2=as.matrix(prefdata[3:22])
stats=paf(prefdata2)
[1] One of your variables is a constant. Constants are disallowed as  
part of a scale.


Any help would be greatly appreciated, a few of us are stuck with this  
and we're going out of our minds trying to figure out how to fix it!


Thank you so much,

Harriet  the MSc students at Edinburgh






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Re: [R] Help in creating a matrix

2012-04-12 Thread S Ellison

I have dataset with n variables, say n =3  x y z
the formula should be form = x+y+z+x*x +x*y+x*z +y*y + y*z+z*z
my code has to for  loop
Is there any way  to reduce two loops
  for (i in 1:n)
  {
  for (j in i:n)
 {
dat= cbind(dat,dat[,i]*dat[,j])
  }
   }


Yes; use outer

But 
- Why only two levels of looping for three variables?
- What have i, j and dat to do with the formula? 
- Why doesnt the formula appear anywhere in the loop?


-
Thanks in Advance
Arun
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[R] Multivariate multilevel mixed effects model: interaction

2012-04-12 Thread Eiko Fried

Hello.

I am running a multivariate multilevel mixed effects model, and am trying
to understand what the interaction term tells me.
A very simplified version of the model looks like this:

model - lmer (phq ~ -1 + as.factor(index_phq) * Neuro + ( -1 +
as.factor(index_phq)|UserID), data=data)

The phq variable is a categorical depression score on 9 depression items
(classified by the variable index_phq), and Neuroticism is a covariate
(random effect = the subjects of my study, they should be allowed to vary
in slope/intercept).


The output looks like this:

Fixed effects:
EstimateStd.Error t-value
as.factor(index_phq)10.0185335  0.0466784   0.397
as.factor(index_phq)2   -0.0327630  0.0453493  -0.722
as.factor(index_phq)30.2210580  0.0612363   3.610
as.factor(index_phq)40.6240455  0.0582654  10.710
as.factor(index_phq)50.1121727  0.0622298   1.803
as.factor(index_phq)6   -0.1797495  0.0484940  -3.707
as.factor(index_phq)7   -0.0907630  0.0488517  -1.858
as.factor(index_phq)8   -0.0854370  0.0384632  -2.221
as.factor(index_phq)9   -0.0621792  0.0319729  -1.945
Neuro  0.0218704  0.0019690  11.107
as.factor(index_phq)2:Neuro  0.0026006  0.0018268   1.424
as.factor(index_phq)3:Neuro  0.0012185  0.0025774   0.473
as.factor(index_phq)4:Neuro  0.0009458  0.0023336   0.405
as.factor(index_phq)5:Neuro  0.0061280  0.0025547   2.399
as.factor(index_phq)6:Neuro  0.0070453  0.0018788   3.750
as.factor(index_phq)7:Neuro -0.0008890  0.0020755  -0.428
as.factor(index_phq)8:Neuro -0.0092411  0.0020197  -4.575
as.factor(index_phq)9:Neuro -0.0159498  0.0021470  -7.429

Looking only at the interaction effects, do I understand correctly that ...
1) Neuroticism has a significant effect on all PHQ items, because the
effect is significant on phq1 (t-value=11.107), and the other t-values are
at a maximum -7.429 lower than the t-value of 11.107, meaning they are
still significant because they are still all above t~2?
2) The strongest effect is on PHQ6, which is significantly higher than the
effect from Neuro on PHQ1?
3) The weakest effect is on PHQ9, which is significantly lower than the
effect from Neuro on PHQ1?


Thank you
Eiko

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[R] pyramid.plot in plotrix, axis labelling

2012-04-12 Thread Gavin Rudge

Hi, I've been looking at ways to make pyramid plots in R.  I like the 
pyramid.plot method in plotrix as it seems the simplest to use and building 
them in ggplot looks a bit more code intensive than I'd like, being as I'm new 
to R.  This package does pretty much what I need it to do, however I can't seem 
to scale the x axis labels.  The other labels scale fine with labelcex.

I guess the preferred method is to remove them and re-build them as you might 
in the base package, but I have no idea how to refer to them as there are two 
of them.

I have enclosed some sample data lifted from another example.  I've scaled down 
the other labels using labelcex whch leaves the disparity in sizes that I'm 
trying to remove.  I'd like something like this but with the x axis lables the 
same size as the y.


 mpop=c(50,75,80,100,110,90,85,60,40,20)
 fpop=c(50,75,80,100,110,90,85,60,50,30)
 coh=c(0-9,10-19,20-29,30-39,40-49,50-59,60-69,70-79,80-89,90-99)
 pyramid.plot(mpop,fpop,labels=coh,gap=15,labelcex=0.7,top.labels=c(males,age
  group,females),lxcol=red,rxcol=blue, 
 laxlab=c(0,50,100,150),raxlab=c(0,50,100,150))



Any suggestions gratefully recieved.



Gavin.

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Re: [R] Encoding of Sweave file error message

2012-04-12 Thread Duncan Murdoch


On 12-04-12 12:13 AM, Duncan Mackay wrote:



At 12:03 12/04/2012, you wrote:

I had the same problem! So, as I'm a linux user,
I prefer use linux terminal. On terminal I type this to compile

R CMD Sweave --encoding=utf-8 myfile.Rnw

and the compilation is successful. Try to set the encoding option in Sweave().

Bests.
Walmes.

==
Walmes Marques Zeviani
LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
Departamento de Estatística - Universidade Federal do Paraná
fone: (+55) 41 3361 3573
VoIP: (3361 3600) 1053 1173
e-mail:mailto:wal...@ufpr.brwal...@ufpr.br
twitter: @walmeszeviani
homepage:http://www.leg.ufpr.br/%7Ewalmeshttp://www.leg.ufpr.br/~walmes
linux user number: 531218
==


Hi Walmes

Thank you very much. That appears to be the problem.
When I typed from the DOS terminal

R CMD Sweave --encoding=utf-8 ParasiteComb12.Rnw

it compiled the tex file without any error messages.

I have not really got into font encoding and
reading the Sweave manual I thought that what I had done would be sufficient.

I found an old note which gave a reference to
http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4725.html
http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4889.html
but that appears to be specific.

The ?Sweave and the Sweave manual appear to be
more specific about the latex side.

After having a look at iconvlist()  and bearing
in mind Duncan Murdoch's comments about windows I tried

Sweave(D:/Cic/Sweave/Parasite/Comb/12/ParasiteComb12.Rnw,
encoding = UTF-8)

from the Rgui command window and compiled without any problems
When I had a look at the tex file there were a
few DOS Alt-248 (degree symbol ) within latex
comments which were added last running R2.14 before updating


That doesn't sound like UTF-8 encoding, it sounds like Latin-1.  So 
declaring it to be UTF-8 will eventually cause you some problems, when 
you put some of those characters in a place that LaTeX processes.  You 
can avoid the problem by putting this line in your Rnw file:


\usepackage[latin1]{inputenc}

as the ?Sweave help page says.  Or, just delete those non-ASCII 
characters.  There's a function in the tools package to detect them: 
see ?tools::showNonASCII.


Duncan Murdoch




Removing them and re running without the encoding
argument brought things back to normal.

I tried as a test
\SweaveOpts{encoding=UTF8}
but that appears not to work

All I have to do now is to put the extra argument
into my text editors clip library for Sweave for
next time when I cannot solve things.
Its been a long week !

Regards

Duncan


Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au





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Re: [R] Centering (e.g. on prcomp)

2012-04-12 Thread Jessica Streicher

Ah.. forget it, something must have gone wrong while i was testing (probably 
messed up some apply()). Seems you can just subtract the returned means - i 
hope at least.


Am 12.04.2012 um 14:30 schrieb Jessica Streicher:

 Hi!
 
 I'm doing a PCA on some testdata (only 2 features) currently to see what 
 happens. I read a lot of times one should center ones data, so i left the 
 option on.
 
 But now i am scratching my head on how to correctly transform new data to be 
 comparable to the data used in the pca.
 
 pca$x are the points (in PC system) the function returns
 origpoints%*%pca$rotation
 
 is not quite the same, because it is missing the centering
 
 for the original data i can of course do scale(origpoints,scaled=F) 
 beforehand, and then the results will be the same, but for new data that 
 option isn't available. So how would i properly transform it?
 
 greetings
 Jessica
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Re: [R] Encoding of Sweave file error message

2012-04-12 Thread Duncan Mackay


Hi Duncan

Thank you for the tips

I tried

\usepackage[latin1]{inputenc}

but it still bailed up.

tried showNonASCII on the file with the ° typed 
as Alt-248 (used to doing as DOS value)

becomes Alt-176 in ASCII

% 1° line
resulted in
483: % 1b0 line

The showNonASCII is a nifty function

Duncan


At 22:32 12/04/2012, you wrote:

On 12-04-12 12:13 AM, Duncan Mackay wrote:



At 12:03 12/04/2012, you wrote:

I had the same problem! So, as I'm a linux user,
I prefer use linux terminal. On terminal I type this to compile

R CMD Sweave --encoding=utf-8 myfile.Rnw

and the compilation is successful. Try to set 
the encoding option in Sweave().


Bests.
Walmes.

==
Walmes Marques Zeviani
LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
Departamento de Estatística - Universidade Federal do Paraná
fone: (+55) 41 3361 3573
VoIP: (3361 3600) 1053 1173
e-mail:mailto:wal...@ufpr.brwal...@ufpr.br
twitter: @walmeszeviani
homepage:http://www.leg.ufpr.br/%7Ewalmeshttp://www.leg.ufpr.br/~walmes
linux user number: 531218
==


Hi Walmes

Thank you very much. That appears to be the problem.
When I typed from the DOS terminal

R CMD Sweave --encoding=utf-8 ParasiteComb12.Rnw

it compiled the tex file without any error messages.

I have not really got into font encoding and
reading the Sweave manual I thought that what I had done would be sufficient.

I found an old note which gave a reference to
http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4725.html
http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4889.html
but that appears to be specific.

The ?Sweave and the Sweave manual appear to be
more specific about the latex side.

After having a look at iconvlist()  and bearing
in mind Duncan Murdoch's comments about windows I tried

Sweave(D:/Cic/Sweave/Parasite/Comb/12/ParasiteComb12.Rnw,
encoding = UTF-8)

from the Rgui command window and compiled without any problems
When I had a look at the tex file there were a
few DOS Alt-248 (degree symbol ) within latex
comments which were added last running R2.14 before updating


That doesn't sound like UTF-8 encoding, it 
sounds like Latin-1.  So declaring it to be 
UTF-8 will eventually cause you some problems, 
when you put some of those characters in a place 
that LaTeX processes.  You can avoid the problem 
by putting this line in your Rnw file:


\usepackage[latin1]{inputenc}

as the ?Sweave help page says.  Or, just delete 
those non-ASCII characters.  There's a function 
in the tools package to detect them: see ?tools::showNonASCII.


Duncan Murdoch




Removing them and re running without the encoding
argument brought things back to normal.

I tried as a test
\SweaveOpts{encoding=UTF8}
but that appears not to work

All I have to do now is to put the extra argument
into my text editors clip library for Sweave for
next time when I cannot solve things.
Its been a long week !

Regards

Duncan


Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au





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Re: [R] Michaelson-Morley Speed of Light Data

2012-04-12 Thread Michael Friendly

The same data, with the proper citations to Michelson(1882) and 
Stigler(1977) are contained in the HistData package as data(Michelson)

See
library(HistData)
example(Michelson)


On 4/11/2012 7:42 AM, Duncan Murdoch wrote:

On 12-04-11 12:43 AM, Křištof Želechovski wrote:

URL: http://finzi.psych.upenn.edu/R/library/datasets/html/morley.html

The classical data of Michaelson and Morley on the speed of light

Can you provide more information about the data? How were they obtained,
etc.? I do not have the book Genstat Primer and the nearest location
where
it is available is University of York which is rather far from my
location.


If you can't find the cited reference, I'd try Google. For instance, it
led me to this page

http://en.wikipedia.org/wiki/File:Michelsonmorley-boxplot.svg

which appears to show five series.

Duncan Murdoch



Note that the data for the Michelson-Morley experiments [1] consist of 6
experiments of 17 runs each, not of 5 series of 20 runs each.

Best regards,
Christopher Yeleighton

___
[1]URL:
http://en.wikisource.org/wiki/On_the_Relative_Motion_of_the_Earth_and_the_Luminiferous_Ether





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--
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Professor, Psychology Dept.
York University  Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

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Re: [R] Encoding of Sweave file error message

2012-04-12 Thread Duncan Mackay


Hi Rainer

Thanks for an alternative. For the record I tried 
your latex solution on my Windows 7


\usepackage[utf8x]{inputenc}

but it failed on the Alt-248

Regards

Duncan


At 19:13 12/04/2012, you wrote:

I also had the same problem.

Being on Linux, I prefer Walmes' command line method but I found that putting
\usepackage[utf8x]{inputenc}
as the first instruction in the master .Rnw file 
also does the trick. No need to change anything 
after that in the file, at least not for me!


Rgds,
Rainer


On Thursday 12 April 2012 14:13:06 Duncan Mackay wrote:

 At 12:03 12/04/2012, you wrote:
 I had the same problem! So, as I'm a linux user,
 I prefer use linux terminal. On terminal I type this to compile
 
 R CMD Sweave --encoding=utf-8 myfile.Rnw
 
 and the compilation is successful. Try to 
set the encoding option in Sweave().

 
 Bests.
 Walmes.
 
 ==
 Walmes Marques Zeviani
 LEG (Laboratório de Estatística e Geoinformação, 25.450418 S, 49.231759 W)
 Departamento de Estatística - Universidade Federal do Paraná
 fone: (+55) 41 3361 3573
 VoIP: (3361 3600) 1053 1173
 e-mail: mailto:wal...@ufpr.brwal...@ufpr.br
 twitter: @walmeszeviani
 homepage: http://www.leg.ufpr.br/%7Ewalmeshttp://www.leg.ufpr.br/~walmes
 linux user number: 531218
 ==

 Hi Walmes

 Thank you very much. That appears to be the problem.
 When I typed from the DOS terminal

 I have exactl ParasiteComb12.Rnw

 it compiled the tex file without any error messages.

 I have not really got into font encoding and
 reading the Sweave manual I thought that what 
I had done would be sufficient.


 I found an old note which gave a reference to
 http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4725.html
 http://tolstoy.newcastle.edu.au/R/e10/help/10/05/4889.html
 but that appears to be specific.

 The ?Sweave and the Sweave manual appear to be
 more specific about the latex side.

 After having a look at iconvlist()  and bearing
 in mind Duncan Murdoch's comments about windows I tried

 Sweave(D:/Cic/Sweave/Parasite/Comb/12/ParasiteComb12.Rnw,
 encoding = UTF-8)

 from the Rgui command window and compiled without any problems
 When I had a look at the tex file there were a
 few DOS Alt-248 (degree symbol ) within latex
 comments which were added last running R2.14 before updating

 Removing them and re running without the encoding
 argument brought things back to normal.

 I tried as a test
 \SweaveOpts{encoding=UTF8}
 but that appears not to work

 All I have to do now is to put the extra argument
 into my text editors clip library for Sweave for
 next time when I cannot solve things.
 Its been a long week !

 Regards

 Duncan


 Duncan Mackay
 Department of Agronomy and Soil Science
 University of New England
 ARMIDALE NSW 2351
 Email home: mac...@northnet.com.au





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Re: [R] Saving multiple plots using tiff function




On 12.04.2012 13:53, Uwe Ligges wrote:



On 12.04.2012 13:49, John S wrote:

Thanks Berend for your answer!

I read the documentation but I don’t understand filename
=Rplot%03d.tif ?

Do you mind sending me what you tried?



This is a bug in R. I'll take a look.



I think I have a fix, will check and commit later today.

Uwe Ligges




Best,
Uwe Ligges





On Thu, Apr 12, 2012 at 7:34 AM, Berend Hasselmanb...@xs4all.nl wrote:



On 12-04-2012, at 13:07, John S wrote:


Dear R users,

I still did not receive an answer to my question and went through the
archive with no luck.

So what does tiff(filename =Rplot%03d.tif) mean ?



Just read the documentation for tiff: ?tiff


Why the following code
does produce two files?



It produces no files for me.
Only an error message.



tiff(filename =Rplot%03d.tif,width=24,height=20,units=cm,res=300,
pointsize=10, compression = lzw)

plot(1)

mtext(Fig 1,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

plot(2)

mtext(Fig 2,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

plot(3)

mtext(Fig 3,side=3,line=4,adj=0.50,padj=2,col=black,cex=1)

dev.off()



You must specify the antialias argument.
Which I did: I set it to none and got 3 .tif (plot) files.
So I don't know what's wrong with your stuff.

Berend




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Re: [R] Survreg output - interpretation

2012-04-12 Thread Terry Therneau


--- begin included message ---
Hello R users,
I am analizing survival data (mostly uncensored) and want to extract the
most out of it.
Since I have more than one factor, I?ve read that the survival regression
can help to test the interactions between factors, and then decide how to do
the comparisons using the Log-rank test (survdiff).
1- if I chose the Weibull distribution, does the output inform the goodness
of fit to it? perhaps in this part of the output...

Weibull distribution
Loglik(model)= -1302.8   Loglik(intercept only)= -1311
Chisq= 16.49 on 11 degrees of freedom, p= 0.12
Number of Newton-Raphson Iterations: 7
n= 873

2- one of my factors is gender (2 levels). With survreg, it appears as
significant, but if I compare them with log-rank it turns not significant.
Are they comparing different things? or is it a test power issue?

--- end inclusion ---

1. To understand goodness of fit you need to look at the residuals in 
multiple ways.  (The same answer applies to ordinary linear regression.)


2. You have not given us enough information to answer the questions.  If 
the data is p=.049 vs p=.051, the the answers are in agreement even 
though the artificial label of significant changes.  The logrank test 
and survreg are not the same model.  If the data is p=.02 vs p=.8, then 
you have an error in the code.


Terry Therneau

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[R] selective labels display on histogram

2012-04-12 Thread carol white

Hello,
Is it possible to selectively display labels on a histogram?

Thanks

Carol

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Re: [R] number of warnings

2012-04-12 Thread helin_susam

Any help ?

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[R] Problem with lmer and fixef

2012-04-12 Thread swertie

Hello,
I am trying to do contrasts after applying a binomial mixed effect model
with the function lmer. I have to extract the fix effect values, but as I
write fixef(model), I get this error message:  

Error in UseMethod(fixef) : 
no method for 'fixef' with objects of class mer 

Has anybody some ideas why? And how can I then post-hoc testing my data if I
cannot do the contrasts?

Thank you very much

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[R] Curve fitting, probably splines

2012-04-12 Thread Michael Haenlein

Dear all,

This is probably more related to statistics than to [R] but I hope someone
can give me an idea how to solve it nevertheless:

Assume I have a variable y that is a function of x: y=f(x). I know the
average value of y for different intervals of x. For example, I know that
in the interval[0;x1] the average y is y1, in the interval [x1;x2] the
average y is y2 and so forth.

I would like to find a line of minimum curvature so that the average values
of y in each interval correspond to y1, y2, ...

My idea was to use (cubic) splines. But the problem I have seems somewhat
different to what is usually done with splines. As far as I understand it,
splines help to find a curve that passes a set of given points. But I don't
have any points, I only have average values of y per interval.

If you have any suggestions on how to solve this, I'd love to hear them.

Thanks very much in advance,

Michael

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Re: [R] number of warnings

Hi
 
 Any help ?

Call 999

Regards
Petr

 
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 View this message in context: http://r.789695.n4.nabble.com/number-of-
 warnings-tp4550325p4551760.html
 Sent from the R help mailing list archive at Nabble.com.
 
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Re: [R] selective labels display on histogram

Hi

 
 Hello,
 Is it possible to selectively display labels on a histogram?

What labels?

Like that?

x-rnorm(1)
hist(x)
hist(x, axes=F, xlab=bla, ylab=ble, main=bleble)
axis(1, at=c(-4, -1, 1, 4))

Regards
Petr

 
 Thanks
 
 Carol
 
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Re: [R] R error message

2012-04-12 Thread mlell08

Hi,
 The code I have used is

 summary(prefdata)
 prefdata[prefdata5]=NA
 summary(prefdata)
 prefdata2=as.matrix(prefdata[3:22])
 stats=paf(prefdata2)
 [1] One of your variables is a constant. Constants are disallowed as
 part of
could you provide some data / sample data you used for prefdata and code
that is fully reproducible?

Regards!

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Re: [R] Problem with lmer and fixef

2012-04-12 Thread Ben Bolker

swertie v_coudrain at voila.fr writes:

 I am trying to do contrasts after applying a binomial mixed effect model
 with the function lmer. I have to extract the fix effect values, but as I
 write fixef(model), I get this error message:  
 
 Error in UseMethod(fixef) : 
 no method for 'fixef' with objects of class mer 
 
 Has anybody some ideas why? And how can I then post-hoc testing my data if I
 cannot do the contrasts?
 
 Thank you very much

  The most likely answer is that you have loaded another package that
interferes with the lme4 package, most likely nlme.  For example:

library(lme4) ## CRAN version, or use lme4.0 from r-forge
example(lmer)  ## to generate some fitted values
fixef(fm1) ## works
library(nlme) ## produces warning about masking The following objects ...
fixef(fm1) ## gives your error
detach(package:nlme) 
fixef(fm1)  ## works again

  other possible culprits are the glmmADMB package, or other
packages that depend on (and hence automatically load) nlme.
See sessionInfo() ...

  Questions like this are probably more suited to the r-sig-mixed-models
list.

  Ben Bolker

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Re: [R] Support for R in highlight.js

2012-04-12 Thread Yihui Xie

There are numerous JS libraries for syntax highlighting. I have never
tried highlight.js yet, but I wrote something for SyntaxHighlighter
which might be easily translated to highlight.js:
http://yihui.name/en/2010/09/syntaxhighlighter-brush-for-the-r-language/

Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA



On Thu, Apr 12, 2012 at 2:04 AM, Ivan Sagalaev
man...@softwaremaniacs.org wrote:
 Hello,

 I'm the maintainer of a syntax highlighting tool highlight.js[1]. Recently
 the Kaggle project has announced they wanted to sponsor the development of
 the R highlighting definition for it[2]. I wanted to drop a line about it
 here since I suspect this list has much more R programmers on it than our
 small discussion group :-).

 So if you're interested and don't mind touching a little bit of JavaScript —
 please reply to the announcement or personally to Adam Kennedy
 adam.kenn...@kaggle.com who's behind it from the Kaggle side.

 [1]: http://softwaremaniacs.org/soft/highlight/en/
 [2]: https://groups.google.com/d/topic/highlightjs/-ogtOaK-TQY/discussion

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Re: [R] number of warnings

This is the R-help mailig list, not Nabble, hence quote the original 
message!


Anyway, the answer is: See ?options and its argument nwarnings.

Uwe ligges




On 12.04.2012 14:49, helin_susam wrote:

Any help ?

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Re: [R] Remove superscripts from HTML objects

2012-04-12 Thread mlell08

Hi,

h - htmlpCatsupa/sup/ppDog/p/html
sub(sup.*sup,,h)

see http://en.wikibooks.org/wiki/R_Programming/Text_Processing for more
information.

Regards!

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Re: [R] selective labels display on histogram

2012-04-12 Thread carol white

No, data labels on the histogram bars. labels = T in hist displays all data 
labels.

thanks




 From: Petr PIKAL petr.pi...@precheza.cz

Cc: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch 
Sent: Thursday, April 12, 2012 4:03 PM
Subject: Re: [R] selective labels display on histogram

Hi

 
 Hello,
 Is it possible to selectively display labels on a histogram?

What labels?

Like that?

x-rnorm(1)
hist(x)
hist(x, axes=F, xlab=bla, ylab=ble, main=bleble)
axis(1, at=c(-4, -1, 1, 4))

Regards
Petr

 
 Thanks
 
 Carol
 
    [[alternative HTML version deleted]]
 
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 https://stat.ethz.ch/mailman/listinfo/r-help
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[[alternative HTML version deleted]]

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[R] correlation matrix between data from different files

2012-04-12 Thread jeff6868

Dear users,

I'm quite a new french R-user, and I have a problem about doing a
correlation matrix.
I have temperature data for each weather station of my study area and for
each year (for example, a data file for the weather station N°1 for the year
2009, a data file for the N°2 for the year 2010, ). So I have 70
weather stations with one data file per year since 2005. Each station has 4
temperature sensors.
Each data file has exactly the same structure: datehour, sensor1, sensor2,
sensor3, sensor4. Here's an example:

time sensor1 sensor2 sensor3sensor4
01/01/2008 00:00-0.25 -2.43 -3.25 -2.37
01/01/2008 00:15-0.18 -2.37 -3.18 -2.25
01/01/2008 00:30-0.25 -2.5-3.37 -2.56
01/01/2008 00:45-0.25 -2.37 -3.31 -2.37

I need to do a matrix correlation between each same sensors of the different
stations (one correlation matrix between all the sensors 1 of the 70
stations, another one for sensor 2, ...).
I have to find for each year and each station the best correlation. For
example, which one of the 70 weather stations is the most well correlated
with station 1 for the sensor 1? and with station 2? ... and so one for each
sensor and each station.

Example:

Sensor 1 for the year 2009

Station 1 Station 2 Station 3 [...]
Station 1 1 0.910 0.748
Station 2 0.91010.6
Station 3 0.748 0.6 1
[...]

And the same for year 2005,2006,2007,2008,2009,2010,2011 for each of the 4
sensors.

Have you got any idea how can I do this on R?
Should I first merge all the sensors in one file or could I do it with data
in separate files (like I have for the moment)?
Thank you very much for all your answers!

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Re: [R] How insert data to a column in existing csv file?

2012-04-12 Thread Nordlund, Dan (DSHS/RDA)

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Yellow
 Sent: Thursday, April 12, 2012 2:18 AM
 To: r-help@r-project.org
 Subject: [R] How insert data to a column in existing csv file?

 I was working with some excel files with a lot of data.
 And by hand it is impossible to handle them.
 So they are now converted to .csv.

 With headers above the columns, like:
 Data1, Data2, Data3

 But now I needed to calculate the log2 value of Data1 and place the
 result
 under Data2.
 I can't find how to do that.
 Does anyone else know?

 I have the log2 values, but how do I get then inside the .csv file
 under
 Data2?

 I already tried write.table(), buy that wasn't it.
 And I am kinda stuck on this now.

In the absence of a reproducible example, we can only guess.  My guess is that 
you should read the csv file into a data frame, add or modify your variable(s), 
then write out a new csv file.

Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204

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Re: [R] How insert data to a column in existing csv file?

2012-04-12 Thread jim holtman

I would suggest using the XLConnect package so that you can read/write
the Excel files directly.  You can read in the files to a dataframe,
make your transformations and then write the result back out to the
Excel file.

On Thu, Apr 12, 2012 at 11:29 AM, Nordlund, Dan (DSHS/RDA)
nord...@dshs.wa.gov wrote:
 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Yellow
 Sent: Thursday, April 12, 2012 2:18 AM
 To: r-help@r-project.org
 Subject: [R] How insert data to a column in existing csv file?

 I was working with some excel files with a lot of data.
 And by hand it is impossible to handle them.
 So they are now converted to .csv.

 With headers above the columns, like:
 Data1, Data2, Data3

 But now I needed to calculate the log2 value of Data1 and place the
 result
 under Data2.
 I can't find how to do that.
 Does anyone else know?

 I have the log2 values, but how do I get then inside the .csv file
 under
 Data2?

 I already tried write.table(), buy that wasn't it.
 And I am kinda stuck on this now.



 In the absence of a reproducible example, we can only guess.  My guess is 
 that you should read the csv file into a data frame, add or modify your 
 variable(s), then write out a new csv file.


 Dan

 Daniel J. Nordlund
 Washington State Department of Social and Health Services
 Planning, Performance, and Accountability
 Research and Data Analysis Division
 Olympia, WA 98504-5204



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-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

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Re: [R] selective labels display on histogram