Re: [R] advice/opinion on - vs = in teaching R
On Fri, Jan 15, 2010 at 3:45 AM, Erin Hodgess erinm.hodg...@gmail.comwrote: Hi R People: I'm teaching a statistical computing class using R starting next week (yay!) and I have an opinion type question, please. I'm old school and use - in an assignment. You call that 'old school'?? I still use ' x_1'! Of course ESS turns the underscore into '-' magically. Perhaps these guys should redo their tests with slightly different syntax: http://www.cs.mdx.ac.uk/research/PhDArea/saeed/paper1.pdf Barry -- blog: http://geospaced.blogspot.com/ web: http://www.maths.lancs.ac.uk/~rowlings web: http://www.rowlingson.com/ twitter: http://twitter.com/geospacedman pics: http://www.flickr.com/photos/spacedman [[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] Replacing NAs with 0 for variables with the same ending
Dear all, I'm looking for a way to replace NA's with 0 for a number of variables which share the same ending and which constitute a subset of a data frame. Say, for example, there is data - data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) , ay=c(5,NA,2,NA,0) , by=c(4,2,NA,2,1)) data ax bx ay by 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 I wish to apply something like // // / data[is.na(data)] - 0/ // but not to the entire data frame, rather only to the variables ending with x. There should be something which emulates the use of a wildcard, ie. which makes the operation being carried out for all variables *x. I tried with grep and glob2rx but did not succeed. Many thanks for any hints! Uli Kleinwechter -- Uli Kleinwechter Agricultural and Food Policy Group (420a) Faculty of Agricultural Sciences University of Hohenheim D-70593 Stuttgart Phone: (+49) 711 459-22656 Fax: (+49) 711 459-23752 E-mail: u.kleinwech...@uni-hohenheim.de http://www.uni-hohenheim.de/apo __ 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] advice/opinion on - vs = in teaching R
On Fri, Jan 15, 2010 at 6:57 AM, Ted Harding ted.hard...@manchester.ac.ukwrote: There is at least one context where the distinction must be preserved. Example: pnorm(1.5) # [1] 0.9331928 pnorm(x=1.5) # Error in pnorm(x = 1.5) : unused argument(s) (x = 1.5) pnorm(x-1.5) # [1] 0.9331928 x # [1] 1.5 Ted. I would regard modifying a variable within the parameters of a function call as pretty tasteless. What does: foo(x-2,x) or foo(x,x-3) do that couldn't be done clearer with two lines of code? Remember: 'eschew obfuscation'. Barry -- blog: http://geospaced.blogspot.com/ web: http://www.maths.lancs.ac.uk/~rowlings web: http://www.rowlingson.com/ twitter: http://twitter.com/geospacedman pics: http://www.flickr.com/photos/spacedman [[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] advice/opinion on - vs = in teaching R
On 15-Jan-10 08:14:04, Barry Rowlingson wrote: On Fri, Jan 15, 2010 at 6:57 AM, Ted Harding ted.hard...@manchester.ac.ukwrote: There is at least one context where the distinction must be preserved. Example: pnorm(1.5) # [1] 0.9331928 pnorm(x=1.5) # Error in pnorm(x = 1.5) : unused argument(s) (x = 1.5) pnorm(x-1.5) # [1] 0.9331928 x # [1] 1.5 Ted. I would regard modifying a variable within the parameters of a function call as pretty tasteless. What does: foo(x-2,x) or foo(x,x-3) do that couldn't be done clearer with two lines of code? Remember: 'eschew obfuscation'. Barry Tasteless or not, the language allows it to be done; and therefore discussion of distinctions between ways of doing it is relevant to Erin's question! While I am at it, in addition to the above example, we can have x - 1.234 sqrt(x=4) # [1] 2 x # [1] 1.234 compared with (as in the first example): x - 1.234 sqrt(x-4) # [1] 2 x # [1] 4 There is a passage in ?- (which I don't completely understand) which is also relevant to Erin's query about '=' vs '-': The operators '-' and '=' assign into the environment in which they are evaluated. The operator '-' can be used anywhere, whereas the operator '=' is only allowed at the top level (e.g., in the complete expression typed at the command prompt) or as one of the subexpressions in a braced list of expressions. (I'm not too clear about the scope of one of the subexpressions in a braced list of expressions). Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 15-Jan-10 Time: 09:08:41 -- XFMail -- __ 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] advice/opinion on - vs = in teaching R
On Fri, Jan 15, 2010 at 2:38 PM, Ted Harding
ted.hard...@manchester.ac.uk wrote:
On 15-Jan-10 08:14:04, Barry Rowlingson wrote:
On Fri, Jan 15, 2010 at 6:57 AM, Ted Harding
ted.hard...@manchester.ac.ukwrote:
There is at least one context where the distinction must be
preserved. Example:
pnorm(1.5)
# [1] 0.9331928
pnorm(x=1.5)
# Error in pnorm(x = 1.5) : unused argument(s) (x = 1.5)
pnorm(x-1.5)
# [1] 0.9331928
x
# [1] 1.5
Ted.
I would regard modifying a variable within the parameters of a
function call as pretty tasteless. What does:
foo(x-2,x)
or
foo(x,x-3)
do that couldn't be done clearer with two lines of code?
Remember: 'eschew obfuscation'.
Barry
Tasteless or not, the language allows it to be done; and therefore
discussion of distinctions between ways of doing it is relevant to
Erin's question!
While I am at it, in addition to the above example, we can have
x - 1.234
sqrt(x=4)
# [1] 2
x
# [1] 1.234
compared with (as in the first example):
x - 1.234
sqrt(x-4)
# [1] 2
x
# [1] 4
There is a passage in ?- (which I don't completely understand)
which is also relevant to Erin's query about '=' vs '-':
The operators '-' and '=' assign into the environment in
which they are evaluated. The operator '-' can be used
anywhere, whereas the operator '=' is only allowed at the
top level (e.g., in the complete expression typed at the
command prompt) or as one of the subexpressions in a braced
list of expressions.
(I'm not too clear about the scope of one of the subexpressions
in a braced list of expressions).
For example:
x = xyplot(1~1)
system.time(x = xyplot(1~1))
Error in system.time(x = xyplot(1 ~ 1)) :
unused argument(s) (x = xyplot(1 ~ 1))
system.time({ x = xyplot(1~1) })
user system elapsed
0.008 0.000 0.005
Of course, - would not have had a problem. This is the most common
problem I personally have had using = for assignment (better
readability of - is also a huge plus).
-Deepayan
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Re: [R] Sampling from a Postgres database
One way could be to first select only the unique ID's, sample this and then select only the relevant records: strQuery = SELECT ID from tblFoo; IDs - sqlQuery(channel, strQuery) sample.IDs - sample(IDs,10) strQuery = paste(SELECT ID from tblFoo WHRE ID IN(, sample.IDs, );) IDs - sqlQuery(channel, strQuery) Bart christiaan pauw-2 wrote: Hi Everybody Is there a way in which one can use the RPostgreSQL package to take a sample from a table in Postgres database without having to read the whole table into R regards Christiaan [[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. -- View this message in context: http://n4.nabble.com/Sampling-from-a-Postgres-database-tp1014506p1014638.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] Replacing NAs with 0 for variables with the same ending
On 01/15/2010 07:10 PM, Uli Kleinwechter wrote: Dear all, I'm looking for a way to replace NA's with 0 for a number of variables which share the same ending and which constitute a subset of a data frame. Say, for example, there is data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) , ay=c(5,NA,2,NA,0) , by=c(4,2,NA,2,1)) data ax bx ay by 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 I wish to apply something like // // / data[is.na(data)]- 0/ // but not to the entire data frame, rather only to the variables ending with x. Hi Uli, How about: data[,grep(x,names(data))][is.na(data[,grep(x,names(data))])]-0 Jim __ 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] advice/opinion on - vs = in teaching R
On 15-Jan-10 09:29:16, Deepayan Sarkar wrote:
On Fri, Jan 15, 2010 at 2:38 PM, Ted Harding
ted.hard...@manchester.ac.uk wrote:
On 15-Jan-10 08:14:04, Barry Rowlingson wrote:
On Fri, Jan 15, 2010 at 6:57 AM, Ted Harding
ted.hard...@manchester.ac.ukwrote:
There is at least one context where the distinction must be
preserved. Example:
Â_pnorm(1.5)
Â_# [1] 0.9331928
Â_pnorm(x=1.5)
Â_# Error in pnorm(x = 1.5) : unused argument(s) (x = 1.5)
Â_pnorm(x-1.5)
Â_# [1] 0.9331928
Â_x
Â_# [1] 1.5
Ted.
I would regard modifying a variable within the parameters of a
function call as pretty tasteless. What does:
Â_foo(x-2,x)
or
Â_foo(x,x-3)
do that couldn't be done clearer with two lines of code?
Â_Remember: 'eschew obfuscation'.
Barry
Tasteless or not, the language allows it to be done; and therefore
discussion of distinctions between ways of doing it is relevant to
Erin's question!
While I am at it, in addition to the above example, we can have
Â_x - 1.234
Â_sqrt(x=4)
Â_# [1] 2
Â_x
Â_# [1] 1.234
compared with (as in the first example):
Â_x - 1.234
Â_sqrt(x-4)
Â_# [1] 2
Â_x
Â_# [1] 4
There is a passage in ?- (which I don't completely understand)
which is also relevant to Erin's query about '=' vs '-':
Â_The operators '-' and '=' assign into the environment in
Â_which they are evaluated. Â_The operator '-' can be used
Â_anywhere, whereas the operator '=' is only allowed at the
Â_top level (e.g., in the complete expression typed at the
Â_command prompt) or as one of the subexpressions in a braced
Â_list of expressions.
(I'm not too clear about the scope of one of the subexpressions
in a braced list of expressions).
For example:
x = xyplot(1~1)
system.time(x = xyplot(1~1))
Error in system.time(x = xyplot(1 ~ 1)) :
unused argument(s) (x = xyplot(1 ~ 1))
system.time({ x = xyplot(1~1) })
user system elapsed
0.008 0.000 0.005
Of course, - would not have had a problem. This is the most common
problem I personally have had using = for assignment (better
readability of - is also a huge plus).
-Deepayan
Thanks for spelling out braced list, Deepayan.
And I have to agree with you about the readability of -.
Indeed, as summary advice to Erin, I wouild say use - except
in the specific context of assigning values to named parameters
in functions, to named elements of lists, and the like (where
use of = is mandatory anyway, or you won't get the desired
effect -- see below).
list(x-1.234,y-2.345)
# [[1]]
# [1] 1.234
# [[2]]
# [1] 2.345
list(x=1.234,y=2.345)
# $x
# [1] 1.234
# $y
# [1] 2.345
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 15-Jan-10 Time: 10:01:55
-- XFMail --
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[R] Remove part of string in colname and calculate mean for columns groups
Hi all, I have two question. First, I wonder how to remove a part of the column names in a matrix? I would like to remove the _ACCX or _NAX part below. Is there a method where the _ as well as all characters after i can be removed? dim(exprdata) [1] 88 512 colnames(exprdata[,c(1:20)]) [1] Akita_ACC1 Akita_ACC2 Akita_ACC3 Akita_ACC4 Alc.0_ACC1 Alc.0_ACC2 Alc.0_ACC3 [8] Alc.0_ACC4 Alc.0_ACC5 Bl.1_ACC1 Bl.1_ACC2 Bl.1_ACC3 Bl.1_ACC4 Bla.1_ACC1 [15] Bla.1_ACC2 Bla.1_ACC3 Bla.1_ACC4 Blh.1_ACC1 Blh.1_ACC2 Blh.1_ACC3 Secondly, I would like to calculate the mean of each column group in the matrix, for instance all columns beginning with Akita, and save all new columns as a new matrix. For instance, use: head(exprdata[,c(1:4)]) Akita_ACC1 Akita_ACC2 Akita_ACC3 Akita_ACC4 A15-101 6.668931 NA NA NA A122001-101 10.562564 11.706395 11.608989 8.289093 A128001-101 14.946749 8.112625 8.176438 10.104254 A133001-101 5.186679 6.089870 4.119589 3.168841 A133003-101 NA NA 19.825480 2.587695 A134001-101 3.259402 4.835642 4.679607 4.490254 To get something like: Akita A15-101 6.668931 A122001-101 10.54176 A128001-101 10.10425 A133001-101 3.168841 A133003-101 2.587695 A134001-101 4.490254 However, the column groups are of different sizes (3-10 columns) so I guess I'll need a method based on the column names. Anyone who can help me? Best regards, Joel _ Nya Windows 7 - Hitta en dator som passar dig! Mer information. http://windows.microsoft.com/shop [[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] advice/opinion on - vs = in teaching R
G'day all,
On Fri, 15 Jan 2010 09:08:44 - (GMT)
(Ted Harding) ted.hard...@manchester.ac.uk wrote:
On 15-Jan-10 08:14:04, Barry Rowlingson wrote:
[...]
I would regard modifying a variable within the parameters of a
function call as pretty tasteless. What does:
foo(x-2,x)
or
foo(x,x-3)
do that couldn't be done clearer with two lines of code?
Depending on the definition of foo() more than two lines might be
necessary to clarify what this code is actually supposed to do. :)
Remember: 'eschew obfuscation'.
Absolutely.
Tasteless or not, the language allows it to be done; and therefore
discussion of distinctions between ways of doing it is relevant to
Erin's question!
And a full discussion of these examples would include to warn about the
side effects of lazy evaluation:
R rm(list=ls(all=TRUE))
R foo - function(x, y){
+ if(x 0 ) x else x + y}
R foo(2, x - 10)
[1] 2
R x
Error: object 'x' not found
R foo(-2, x - 10)
[1] 8
R x
[1] 10
Having said this, I often use plot(fm - lm(y ~ . , somedata)).
And, yes, students have complained that the code I gave them was not
working, that they got a strange error message and they promised that
they had typed exactly what I had written on the lab sheet. On
checking, they had, of course, typed plot(fm = lm(y ~ . , somedata))
Cheers,
Berwin
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[R] Best method
Hi,
I would like to ask for advice about best statistics method for
my problem.
I was done questionnaire about headache.
My data are:
Y - frequency of symptoms occur - times per month in range 0..30
(where 30 is daily and zero for never)
and independent variables:
X1 - sex - category {M,F}
X2 - age - linear value
X3 - type of work {administrative, manual, ...}
...
Which model is the best for my problem: to describe weight of
factors in equation chance_to_present_symptom ~ variables:
Y~X1+X2+X3
Y is not linear value with normal distribution.
Y describe something like chance of to have symptom.
I can't use linear regression, but something like logistic regression.
Logistic is only for two (or more) Y value which is categorised not
linear.
Thank for any advice.
-vladimir-
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[R] the sample() function
hello R-Wizards! again i'm invoking your presence!! since all the fuss about the paradoxes on a computer algorithm generating caos or un-determinancy, i recently grew quite curious about the mechanism underlying the procedure of NUMBER RADOMIZATION. could anyone of you, masters, attach me the algorithm (or source code? is it right?) behind the *sample()* function, so i can inspect in detail the mechanism of this so gossiped radomization? thank you, sincerely federico bonofiglio, student of statistics at milano bicocca university, italia [[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] HTML translation problem in R-2.10.1
Hi everyone, The problem was the result of my historical misbehavior of embedding links within certain font enhancements. This used to work, but no longer. Any of you package maintainers who find that your links are suddenly becoming literal text on the HTML help pages are likely to have the same problem. Solution - remove any \samp tags around the links. Thanks to Duncan who provided the necessary info. New versions of the clinsig, crank, plotrix and prettyR packages will appear shortly. Jim __ 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] Connecting R with MS SQL server 2005
If anybody can provide me a link it will be very much helpful -- View this message in context: http://n4.nabble.com/Connecting-R-with-MS-SQL-server-2005-tp1014643p1014669.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] Replacing NAs with 0 for variables with the same ending
Hi, this works aswell: for(i in 1:ncol(data)) data[is.na(data[,i]),i] - 0 i am sure there is way doing it with a member of the apply family, maybe someone else has an idea. Johannes On Fri, Jan 15, 2010 at 9:51 PM, Jim Lemon j...@bitwrit.com.au wrote: On 01/15/2010 07:10 PM, Uli Kleinwechter wrote: Dear all, I'm looking for a way to replace NA's with 0 for a number of variables which share the same ending and which constitute a subset of a data frame. Say, for example, there is data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) , ay=c(5,NA,2,NA,0) , by=c(4,2,NA,2,1)) data ax bx ay by 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 I wish to apply something like // // / data[is.na(data)]- 0/ // but not to the entire data frame, rather only to the variables ending with x. Hi Uli, How about: data[,grep(x,names(data))][is.na(data[,grep(x,names(data))])]-0 Jim __ 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] memDecompress and zlib compressed base64 encoded string
Prof Brian Ripley wrote: I have zlib compressed strings (example is attached) What is that file? Not gzip compression: gannet% file compressed.txt compressed.txt: ASCII text, with very long lines since gzip uses a magic header that 'file' knows about. And even if the header was stripped, such files are 8-bit and yours is ASCII. Try x - 'Johannes Graumann' xx - charToRaw(x) xxx - memCompress(xx, g) rawToChar(xxx) [1] x\x9c\xf3\xca\xcfH\xcc\xcbK-Vp/J,\xcd\0052\001:\n\006\x90 to see what a real gzipped string looks like. and would like to decompress them using memDecompress ... I try this: connection - file(compressed.txt,r) compressed - readLines(connection) I am dealing with mass spectrometric data in a XML file format (mzXML). The biggest part of the contained data is actual mass spectra that are base64 encoded and optionally compressed using http://zlib.net (saving quite some storage space). When they are compressed I just get an XML node that looks like this peaksCONTENT OF THE ORIGINAL ATTACHMENT HERE/peaks I would like to be able to decompress that string and thought that memDecompress was the right tool to do so ... You have not told us the 'at a minimum' information requested in the posting guide. But you should not expect that to read a binary file, especially not in a MBCS locale. We have readBin for that purpose. I'm actually reading this in as a string from the XML file ... memDecompress(as.raw(compressed),type=g) I don't think you know what as.raw does: it does not convert bytes in a character string to raw (for which you need charToRaw). It is always a good idea to look at each stage of your computation: as.raw(compressed) [1] 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 [26] 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 Yup, that was plain stupid and trying to make memDecompress run at all (since handing it the character string also resulted in an error. sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 [9] LC_ADDRESS=en_US.UTF-8LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rkward_0.5.1 loaded via a namespace (and not attached): [1] tools_2.10.1 Thanks for any further hints, Joh __ 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] estimating rho of Poisson distributed data
Mean and variance of Poisson distributed data are specified by \rho. How can I estimate \rho for a set of measurements in R? Many thanks! Titus __ 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] advice/opinion on - vs = in teaching R
Barry Rowlingson wrote: On Fri, Jan 15, 2010 at 3:45 AM, Erin Hodgess erinm.hodg...@gmail.comwrote: Hi R People: I'm teaching a statistical computing class using R starting next week (yay!) and I have an opinion type question, please. I'm old school and use - in an assignment. You call that 'old school'?? I still use ' x_1'! Of course ESS turns the underscore into '-' magically. Perhaps these guys should redo their tests with slightly different syntax: http://www.cs.mdx.ac.uk/research/PhDArea/saeed/paper1.pdf Barry I do like their experimental design: In a bizarre event which one of the authors insists was planned, and the other maintains was a really stupid idea that just happened to work, the test was first administered to about 30 students on a (Like in the sense of being amused, of course) -p -- 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] Latent Profile Analysis Package?
Jon, There are packages that fit mixtures of multivariate normals (mclust) and in flexmix one can also model multiple measures (with local independence assumption). hth, Ingmar On Fri, Jan 15, 2010 at 11:08 AM, Jon Toledo tintin...@hotmail.com wrote: Iæe several packages for latent class analysis, but I was wondering if there is a package for continuos variables, which allows latent prfile analysis. Thanks for your help in advance, J Toledo _ cial-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_1:092 [[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] Can I save R graphs as a R objects
vikrant wrote: Can I save R graphs as a R objects ? IF yes then if I click this R object can I edit my chart as in Excel. Please suggest your views When you use the graphics functions from the lattice package (e.g. xyplot) you can save them to a file (see ?save) because it creates an object that represents the graph. When using the standard plot system I think this is not possible. But if you have the original data and an R script to make the graph, you don't need to save the graph explicitly. When processing the data for the graph takes a long time, you can run the script to just before making the graph and save all the appropriate objects to disk. Next time you only need to load your data (see ?load) and make the plot. cheers, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] Barplots in R
Hi! Let's suppose the values for the x axis are stored in 'values'. barplot(values, col=c(rep(Red,3),rep(1,length(values)-8),rep(Blue,5))) HTH, Kimmo vikrant kirjoitti: Suppose I need to draw a Grouped bar plot with 100 values on the X axis. Now my question is If I need to highlight suppose first three values by some color say 'red' and also I need to highlight last 5 datavalues by some color say 'blue' and the rest of the data in between I need not display. Is it possible? If yes How? Could anyone explain __ 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] Connecting R with MS SQL server 2005
vikrant wrote: Is it possible to connect R with Ms SQL Server 2005 ? If Yes how to connect it and can you please provide some tutorial for it? It's easiest using RODBC. Using Control Panel/Administrator/Data Sources (Free translation from German, might be slightly off), create a source using the SQL Server Native Client; you might have to install that client from the MS site, if it is not there. Then, connect to that source and issue a SELECT... Dieter -- View this message in context: http://n4.nabble.com/Connecting-R-with-MS-SQL-server-2005-tp1014643p1014705.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] Can I save R graphs as a R objects
You can use the recordPlot function from base package also On Fri, Jan 15, 2010 at 7:26 AM, vikrant vikrant.shi...@tcs.com wrote: Can I save R graphs as a R objects ? IF yes then if I click this R object can I edit my chart as in Excel. Please suggest your views -- View this message in context: http://n4.nabble.com/Can-I-save-R-graphs-as-a-R-objects-tp1014621p1014621.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Connecting R with MS SQL server 2005
On 15.01.2010 11:23, vikrant wrote: If anybody can provide me a link it will be very much helpful See package RODBC. Uwe Ligges __ 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] Can I save R graphs as a R objects
On Fri, Jan 15, 2010 at 11:26 AM, vikrant vikrant.shi...@tcs.com wrote: Can I save R graphs as a R objects ? I have seen that feature in the rkward GUI (which is by the way the BEST GUI I have seen for a long time!), but I haven't played with that feature a lot, so I can not comment on your second question. By the way: rkward has SOME editing functionality for graphs, after they are created (GUI type) Cheers, Rainer IF yes then if I click this R object can I edit my chart as in Excel. Please suggest your views -- View this message in context: http://n4.nabble.com/Can-I-save-R-graphs-as-a-R-objects-tp1014621p1014621.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. -- NEW GERMAN FAX NUMBER!!! Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)321 2125 2244 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.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.
Re: [R] select: bad file descriptor in the multicore package
On 13.01.2010 05:43, Hao Cen wrote: Hi, I wonder anyone knows what causes the error message select: bad file descriptor in the multicore package. This error sometimes occurs and sometimes doesn't. I couldn't find any documentation on this error about this package. As the R-help footer tells us: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Please try to give relevant information or start debugging yourself. Uwe Ligges thanks Jeff __ 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] Remove part of string in colname and calculate mean for columns groups
Joel Fürstenberg-Hägg wrote: I have two question. First, I wonder how to remove a part of the column names in a matrix? I would like to remove the _ACCX or _NAX part below. Is there a method where the _ as well as all characters after i can be removed? Secondly, I would like to calculate the mean of each column group in the matrix, for instance all columns beginning with Akita, and save all new columns as a new matrix. If you do that in the example you gave, duplicate column names would be the result, but let's assume that was a typo. # Simplify names data = data.frame(Akita.0_ACC1=1:2,Akita.1_ACC2=2:3,Alc.0_ACC1=3:4) names(data) = sub(_.*,,names(data)) # Make a new data frame with the Akitas only dataAkita = data[,grep(Akita,names(data))] To do the averaging, check the examples in package plyr. Dieter -- View this message in context: http://n4.nabble.com/Remove-part-of-string-in-colname-and-calculate-mean-for-columns-groups-tp1014652p1014724.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] processing all files with certain extension in a directory
Hi all, I'm trying to process all files with a certain extension *.ext in a directory like this: R --slave --args /my/dir dir_plot.r where I then I want to do something like: myarg - commandArgs() inputdir - myarg[length(myarg)] print(inputdir) for file with extension *.ext in inputdir do data = process.data(file) outfile = paste(file,.png,sep=) png(outfile,width=3200,height=2400) do.a.plot(data) dev.off() done q() How can I do the file looping bit? Thanks in advance, Cheers, Albert. __ 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] processing all files with certain extension in a directory
Albert,
try something like this:
extfiles - list.files(pattern=.ext)
for(f in extfiles){
process.data(f)
#etc
}
greetings,
Remko
-
Remko Duursma
Post-Doctoral Fellow
Centre for Plants and the Environment
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753
Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia
Mobile: +61 (0)422 096908
www.remkoduursma.com
On Fri, Jan 15, 2010 at 10:43 PM, Albert Vilella avile...@gmail.com wrote:
Hi all,
I'm trying to process all files with a certain extension *.ext in a
directory like this:
R --slave --args /my/dir dir_plot.r
where I then I want to do something like:
myarg - commandArgs()
inputdir - myarg[length(myarg)]
print(inputdir)
for file with extension *.ext in inputdir
do
data = process.data(file)
outfile = paste(file,.png,sep=)
png(outfile,width=3200,height=2400)
do.a.plot(data)
dev.off()
done
q()
How can I do the file looping bit?
Thanks in advance,
Cheers,
Albert.
__
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and provide commented, minimal, self-contained, reproducible code.
__
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Re: [R] processing all files with certain extension in a directory
theFiles - list.files(inputdir, full=T, pattern=\\.[eE][xX][tT]$)
for (file in theFiles){
...
}
On Fri, Jan 15, 2010 at 11:43 AM, Albert Vilella avile...@gmail.com wrote:
Hi all,
I'm trying to process all files with a certain extension *.ext in a
directory like this:
R --slave --args /my/dir dir_plot.r
where I then I want to do something like:
myarg - commandArgs()
inputdir - myarg[length(myarg)]
print(inputdir)
for file with extension *.ext in inputdir
do
data = process.data(file)
outfile = paste(file,.png,sep=)
png(outfile,width=3200,height=2400)
do.a.plot(data)
dev.off()
done
q()
How can I do the file looping bit?
Thanks in advance,
Cheers,
Albert.
__
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] How to delete matrix rows based on NA frequency?
Hi all, I would like to remove rows from a matrix, based on the frequency of missing values. If there are more than 10 % missing values, the row should be deleted. I use the following to calculate the frequencies, thereby getting a new matrix with the frequencies: freqNA=rowMeans(is.na(exprdata)) But is there a shorter way to remove the rows based on (1-freqNA)0.1 than looping through the whole matrix using a for loop? All the best, Joel _ Hitta kärleken i vinter! http://dejting.se.msn.com/channel/index.aspx?trackingid=1002952 [[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] How to delete matrix rows based on NA frequency?
Joel, try this: # sample matrix m - matrix(sample(c(1:10, NA),150,replace=T),byrow=T,ncol=15) # nr of missing values per row nacounts - apply(m, 1, function(x)length(x[is.na(x)])) # new matrix newm - m[nacounts/ncol(m) 0.1,] greetings, Remko - Remko Duursma Post-Doctoral Fellow Centre for Plants and the Environment University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 www.remkoduursma.com 2010/1/15 Joel Fürstenberg-Hägg joel_furstenberg_h...@hotmail.com: Hi all, I would like to remove rows from a matrix, based on the frequency of missing values. If there are more than 10 % missing values, the row should be deleted. I use the following to calculate the frequencies, thereby getting a new matrix with the frequencies: freqNA=rowMeans(is.na(exprdata)) But is there a shorter way to remove the rows based on (1-freqNA)0.1 than looping through the whole matrix using a for loop? All the best, Joel _ Hitta kärleken i vinter! http://dejting.se.msn.com/channel/index.aspx?trackingid=1002952 [[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] How to delete matrix rows based on NA frequency?
Try this: m[prop.table(rowSums(is.na(m))) 0.1,] 2010/1/15 Joel Fürstenberg-Hägg joel_furstenberg_h...@hotmail.com: Hi all, I would like to remove rows from a matrix, based on the frequency of missing values. If there are more than 10 % missing values, the row should be deleted. I use the following to calculate the frequencies, thereby getting a new matrix with the frequencies: freqNA=rowMeans(is.na(exprdata)) But is there a shorter way to remove the rows based on (1-freqNA)0.1 than looping through the whole matrix using a for loop? All the best, Joel _ Hitta kärleken i vinter! http://dejting.se.msn.com/channel/index.aspx?trackingid=1002952 [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] advice/opinion on - vs = in teaching R
Barry Rowlingson wrote:
On Fri, Jan 15, 2010 at 6:57 AM, Ted Harding
ted.hard...@manchester.ac.ukwrote:
There is at least one context where the distinction must be
preserved. Example:
pnorm(1.5)
# [1] 0.9331928
pnorm(x=1.5)
# Error in pnorm(x = 1.5) : unused argument(s) (x = 1.5)
pnorm(x-1.5)
# [1] 0.9331928
x
# [1] 1.5
Ted.
I would regard modifying a variable within the parameters of a function
call as pretty tasteless. What does:
foo(x-2,x)
or
foo(x,x-3)
do that couldn't be done clearer with two lines of code?
The most common use I see that I like is within a conditional test like
if ( !is.null(x - get(x, somehow)) length(x) == 1) { dosomething }
The x variable is only used for the test, but since it is used twice
there, the assignment saves getting it twice. You could expand it to
two lines
x - get(x, somehow)
if ( !is.null(x) length(x) == 1) { dosomething }
but I find that a tiny bit harder to read.
On the other hand, I would never use the examples you gave, because I'd
have no idea what the value of x would be, since it depends on the order
of evaluation of the arguments. In R, I don't even know for sure if the
assignment would be evaluated at all, let alone before the x argument.
Duncan Murdoch
Remember: 'eschew obfuscation'.
Barry
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Re: [R] Best method
Dear Vladimir,
You can use a logistic regression. First define Y0 as 30 - Y. Then Y is
the number of days with headache and Y0 the number of days without.
Then the model looks like: glm(cbind(Y, Y0) ~ X1 + X2 + X3, family =
binomial)
HTH,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
Namens Vladimir Pekar
Verzonden: vrijdag 15 januari 2010 11:26
Aan: r-help@r-project.org
Onderwerp: [R] Best method
Hi,
I would like to ask for advice about best statistics method for my
problem.
I was done questionnaire about headache.
My data are:
Y - frequency of symptoms occur - times per month in range 0..30
(where 30 is daily and zero for never) and independent variables:
X1 - sex - category {M,F}
X2 - age - linear value
X3 - type of work {administrative, manual, ...} ...
Which model is the best for my problem: to describe weight of factors
in equation chance_to_present_symptom ~ variables:
Y~X1+X2+X3
Y is not linear value with normal distribution.
Y describe something like chance of to have symptom.
I can't use linear regression, but something like logistic regression.
Logistic is only for two (or more) Y value which is categorised not
linear.
Thank for any advice.
-vladimir-
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[R] transposing a list of vectors
I have a list of vectors, all forced to be the same length: testlist - list( shape=c(0, 0, 2), cell.fill=c(red,blue,green), back.fill=rep(white,3), scale.max=rep(100,3) ) str(testlist) List of 4 $ shape: num [1:3] 0 0 2 $ cell.fill: chr [1:3] red blue green $ back.fill: chr [1:3] white white white $ scale.max: num [1:3] 100 100 100 I need to 'transpose' them into a list of lists with named values like so: wanted - list( list(shape=0, cell.fill=red, back.fill=white, scale.max=100), list(shape=0, cell.fill=blue, back.fill=white, scale.max=100), list(shape=2, cell.fill=green, back.fill=white, scale.max=100) ) str(wanted) List of 3 $ :List of 4 ..$ shape: num 0 ..$ cell.fill: chr red ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape: num 0 ..$ cell.fill: chr blue ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape: num 2 ..$ cell.fill: chr green ..$ back.fill: chr white ..$ scale.max: num 3 How can I do this in general? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ 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] Replacing NAs with 0 for variables with the same ending
Jim Lemon schrieb: On 01/15/2010 07:10 PM, Uli Kleinwechter wrote: Dear all, I'm looking for a way to replace NA's with 0 for a number of variables which share the same ending and which constitute a subset of a data frame. Say, for example, there is data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) , ay=c(5,NA,2,NA,0) , by=c(4,2,NA,2,1)) data ax bx ay by 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 I wish to apply something like // // / data[is.na(data)]- 0/ // but not to the entire data frame, rather only to the variables ending with x. Hi Uli, How about: data[,grep(x,names(data))][is.na(data[,grep(x,names(data))])]-0 Jim Hi Jim, thanks a lot. I'm just afraid that grep matches any occurence of x in the variable name. So variables which would contain x at any position, not necessarily only at the last one would be selected, as well. To refine my example (sorry for having been so imprecise before...): data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) ,ay=c(5,NA,2,NA,0) , xy=c(4,2,NA,2,1)) data ax bx ay xy 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 The task, again, would be to replace NA's with 0 in ax and bx, but not in ay and xy Best, Uli __ 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] transposing a list of vectors
Does this do it:
testlist - list(
+ shape=c(0, 0, 2),
+ cell.fill=c(red,blue,green),
+ back.fill=rep(white,3),
+ scale.max=rep(100,3)
+ )
wanted - lapply(seq(length(testlist[[1]])), function(x){
+ # iterate for each element of the list
+ result - lapply(names(testlist), function(.name){
+ list(testlist[[.name]][x])
+ })
+ names(result) - names(testlist)
+ result
+ })
dput(wanted)
list(structure(list(shape = list(0), cell.fill = list(red),
back.fill = list(white), scale.max = list(100)), .Names = c(shape,
cell.fill, back.fill, scale.max)), structure(list(shape = list(
0), cell.fill = list(blue), back.fill = list(white),
scale.max = list(100)), .Names = c(shape, cell.fill,
back.fill, scale.max)), structure(list(shape = list(2), cell.fill =
list(
green), back.fill = list(white), scale.max = list(100)), .Names =
c(shape,
cell.fill, back.fill, scale.max)))
On Fri, Jan 15, 2010 at 8:09 AM, Michael Friendly frien...@yorku.ca wrote:
I have a list of vectors, all forced to be the same length:
testlist - list(
shape=c(0, 0, 2),
cell.fill=c(red,blue,green),
back.fill=rep(white,3),
scale.max=rep(100,3)
)
str(testlist)
List of 4
$ shape: num [1:3] 0 0 2
$ cell.fill: chr [1:3] red blue green
$ back.fill: chr [1:3] white white white
$ scale.max: num [1:3] 100 100 100
I need to 'transpose' them into a list of lists with named values like so:
wanted - list(
list(shape=0, cell.fill=red, back.fill=white, scale.max=100),
list(shape=0, cell.fill=blue, back.fill=white, scale.max=100),
list(shape=2, cell.fill=green, back.fill=white, scale.max=100)
)
str(wanted)
List of 3
$ :List of 4
..$ shape: num 0
..$ cell.fill: chr red
..$ back.fill: chr white
..$ scale.max: num 3
$ :List of 4
..$ shape: num 0
..$ cell.fill: chr blue
..$ back.fill: chr white
..$ scale.max: num 3
$ :List of 4
..$ shape: num 2
..$ cell.fill: chr green
..$ back.fill: chr white
..$ scale.max: num 3
How can I do this in general?
--
Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology
Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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http://www.R-project.org/posting-guide.htmlhttp://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?
[[alternative HTML version deleted]]
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[R] call R with un expression (String)?
Hello all, I want to call R from java. And I have a expression in Java as a String, example : (variable 1 + variable 2)* variable 3 and i want R calculate this expression. How can I do? ex: Java -int x1,x2; -float x3; -String s=( x1.toString()+x2.toString() ) * x3.toString(); R: calculate expression s and return in to Java? Thanks Jin -- View this message in context: http://n4.nabble.com/call-R-with-un-expression-String-tp1014832p1014832.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] Can I save R graphs as a R objects
On 1/15/10, vikrant vikrant.shi...@tcs.com wrote: can I edit my chart as in Excel. Sort of, using playwith. You can always try to place the the plot call inside playwith(). For example, require(playwith) playwith(plot(1:10)) Liviu __ 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] transposing a list of vectors
fingers too fast; didn't need the enclosing 'list':
testlist - list(
+ shape=c(0, 0, 2),
+ cell.fill=c(red,blue,green),
+ back.fill=rep(white,3),
+ scale.max=rep(100,3)
+ )
wanted - lapply(seq(length(testlist[[1]])), function(x){
+ # iterate for each element of the list
+ result - lapply(names(testlist), function(.name){
+ testlist[[.name]][x]
+ })
+ names(result) - names(testlist)
+ result
+ })
dput(wanted)
list(structure(list(shape = 0, cell.fill = red, back.fill = white,
scale.max = 100), .Names = c(shape, cell.fill, back.fill,
scale.max)), structure(list(shape = 0, cell.fill = blue,
back.fill = white, scale.max = 100), .Names = c(shape,
cell.fill, back.fill, scale.max)), structure(list(shape = 2,
cell.fill = green, back.fill = white, scale.max = 100), .Names =
c(shape,
cell.fill, back.fill, scale.max)))
On Fri, Jan 15, 2010 at 8:09 AM, Michael Friendly frien...@yorku.ca wrote:
I have a list of vectors, all forced to be the same length:
testlist - list(
shape=c(0, 0, 2),
cell.fill=c(red,blue,green),
back.fill=rep(white,3),
scale.max=rep(100,3)
)
str(testlist)
List of 4
$ shape: num [1:3] 0 0 2
$ cell.fill: chr [1:3] red blue green
$ back.fill: chr [1:3] white white white
$ scale.max: num [1:3] 100 100 100
I need to 'transpose' them into a list of lists with named values like so:
wanted - list(
list(shape=0, cell.fill=red, back.fill=white, scale.max=100),
list(shape=0, cell.fill=blue, back.fill=white, scale.max=100),
list(shape=2, cell.fill=green, back.fill=white, scale.max=100)
)
str(wanted)
List of 3
$ :List of 4
..$ shape: num 0
..$ cell.fill: chr red
..$ back.fill: chr white
..$ scale.max: num 3
$ :List of 4
..$ shape: num 0
..$ cell.fill: chr blue
..$ back.fill: chr white
..$ scale.max: num 3
$ :List of 4
..$ shape: num 2
..$ cell.fill: chr green
..$ back.fill: chr white
..$ scale.max: num 3
How can I do this in general?
--
Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology
Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
__
R-help@r-project.org mailing list
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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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] transposing a list of vectors
Try this: #'1) But apply converts all to 'character' apply(as.data.frame(testlist), 1, as.list) #2) lapply(split(x - as.data.frame(testlist), 1:nrow(x)), as.list) On Fri, Jan 15, 2010 at 11:09 AM, Michael Friendly frien...@yorku.ca wrote: I have a list of vectors, all forced to be the same length: testlist - list( shape=c(0, 0, 2), cell.fill=c(red,blue,green), back.fill=rep(white,3), scale.max=rep(100,3) ) str(testlist) List of 4 $ shape : num [1:3] 0 0 2 $ cell.fill: chr [1:3] red blue green $ back.fill: chr [1:3] white white white $ scale.max: num [1:3] 100 100 100 I need to 'transpose' them into a list of lists with named values like so: wanted - list( list(shape=0, cell.fill=red, back.fill=white, scale.max=100), list(shape=0, cell.fill=blue, back.fill=white, scale.max=100), list(shape=2, cell.fill=green, back.fill=white, scale.max=100) ) str(wanted) List of 3 $ :List of 4 ..$ shape : num 0 ..$ cell.fill: chr red ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape : num 0 ..$ cell.fill: chr blue ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape : num 2 ..$ cell.fill: chr green ..$ back.fill: chr white ..$ scale.max: num 3 How can I do this in general? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Replacing NAs with 0 for variables with the same ending
In grep use: grep(x$, names(data)). '$' matchs 'x' in the end of string On Fri, Jan 15, 2010 at 11:14 AM, Uli Kleinwechter u.kleinwech...@uni-hohenheim.de wrote: Jim Lemon schrieb: On 01/15/2010 07:10 PM, Uli Kleinwechter wrote: Dear all, I'm looking for a way to replace NA's with 0 for a number of variables which share the same ending and which constitute a subset of a data frame. Say, for example, there is data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) , ay=c(5,NA,2,NA,0) , by=c(4,2,NA,2,1)) data ax bx ay by 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 I wish to apply something like // // / data[is.na(data)]- 0/ // but not to the entire data frame, rather only to the variables ending with x. Hi Uli, How about: data[,grep(x,names(data))][is.na(data[,grep(x,names(data))])]-0 Jim Hi Jim, thanks a lot. I'm just afraid that grep matches any occurence of x in the variable name. So variables which would contain x at any position, not necessarily only at the last one would be selected, as well. To refine my example (sorry for having been so imprecise before...): data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) ,ay=c(5,NA,2,NA,0) , xy=c(4,2,NA,2,1)) data ax bx ay xy 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 The task, again, would be to replace NA's with 0 in ax and bx, but not in ay and xy Best, Uli __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] transposing a list of vectors
This gives the result you asked for: DF - as.data.frame(testlist) lapply(split(DF, 1:nrow(DF)), unclass) although it might be good enough to just do this depending on what you need: DF - as.data.frame(testlist) split(DF, 1:nrow(DF) On Fri, Jan 15, 2010 at 8:09 AM, Michael Friendly frien...@yorku.ca wrote: I have a list of vectors, all forced to be the same length: testlist - list( shape=c(0, 0, 2), cell.fill=c(red,blue,green), back.fill=rep(white,3), scale.max=rep(100,3) ) str(testlist) List of 4 $ shape : num [1:3] 0 0 2 $ cell.fill: chr [1:3] red blue green $ back.fill: chr [1:3] white white white $ scale.max: num [1:3] 100 100 100 I need to 'transpose' them into a list of lists with named values like so: wanted - list( list(shape=0, cell.fill=red, back.fill=white, scale.max=100), list(shape=0, cell.fill=blue, back.fill=white, scale.max=100), list(shape=2, cell.fill=green, back.fill=white, scale.max=100) ) str(wanted) List of 3 $ :List of 4 ..$ shape : num 0 ..$ cell.fill: chr red ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape : num 0 ..$ cell.fill: chr blue ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape : num 2 ..$ cell.fill: chr green ..$ back.fill: chr white ..$ scale.max: num 3 How can I do this in general? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ 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] Replacing NAs with 0 for variables with the same ending
Uli Kleinwechter a écrit : data[,grep(x,names(data))][is.na(data[,grep(x,names(data))])]-0 thanks a lot. I'm just afraid that grep matches any occurence of x in the variable name. So variables which would contain x at any position, not necessarily only at the last one would be selected, as well. To refine my example (sorry for having been so imprecise before...): Replacing x with x$ in grep calls should do the job... Olivier. __ 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] Replacing NAs with 0 for variables with the same ending
That's it, thanks a lot to all of you! Uli Henrique Dallazuanna schrieb: In grep use: grep(x$, names(data)). '$' matchs 'x' in the end of string On Fri, Jan 15, 2010 at 11:14 AM, Uli Kleinwechter u.kleinwech...@uni-hohenheim.de wrote: Jim Lemon schrieb: On 01/15/2010 07:10 PM, Uli Kleinwechter wrote: Dear all, I'm looking for a way to replace NA's with 0 for a number of variables which share the same ending and which constitute a subset of a data frame. Say, for example, there is data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) , ay=c(5,NA,2,NA,0) , by=c(4,2,NA,2,1)) data ax bx ay by 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 I wish to apply something like // // / data[is.na(data)]- 0/ // but not to the entire data frame, rather only to the variables ending with x. Hi Uli, How about: data[,grep(x,names(data))][is.na(data[,grep(x,names(data))])]-0 Jim Hi Jim, thanks a lot. I'm just afraid that grep matches any occurence of x in the variable name. So variables which would contain x at any position, not necessarily only at the last one would be selected, as well. To refine my example (sorry for having been so imprecise before...): data- data.frame(ax=c(1,2,3,NA,0) , bx=c(3,5,NA,5,1) ,ay=c(5,NA,2,NA,0) , xy=c(4,2,NA,2,1)) data ax bx ay xy 1 1 3 5 4 2 2 5 NA 2 3 3 NA 2 NA 4 NA 5 NA 2 5 0 1 0 1 The task, again, would be to replace NA's with 0 in ax and bx, but not in ay and xy Best, Uli __ 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] FW: Problems connecting with MySQL using odbcDriverConnect (RODBC package) on Linux
Ok.
Caveman
On Thu, Jan 14, 2010 at 5:19 PM, Marcus, Jeffrey
jeffrey.mar...@nuance.com wrote:
Orvalho:
Thanks for pointing our RMySQL. The reason is that we have similar data
stored in both SQL server and MySQL databases and I want to reuse code as
much as possible.
Jeff
-Original Message-
From: Orvalho Augusto [mailto:orvaq...@gmail.com]
Sent: Wednesday, January 13, 2010 10:57 PM
To: Marcus, Jeffrey
Cc: r-help@r-project.org
Subject: Re: [R] FW: Problems connecting with MySQL using odbcDriverConnect
(RODBC package) on Linux
Thanks you solved and share with us.
But, why don't you use the RMySQL, which connects to MySQL without the
need of ODBC?
Caveman
On Wed, Jan 13, 2010 at 1:48 AM, Marcus, Jeffrey
jeffrey.mar...@nuance.com wrote:
I think I figured this out. I should not have put the Driver name in
braces. Changing it from {MySQL} to MySQL seems to work.
-Original Message-
From: Marcus, Jeffrey
Sent: Tuesday, January 12, 2010 6:09 PM
To: 'r-help@r-project.org'
Subject: Problems connecting with MySQL using odbcDriverConnect (RODBC
package) on Linux
I am sure I'm doing something wrong here but not sure what.
Our system administrator recently installed UnixODBC and the MyODBC
driver on a Linux box running Linux version 2.6 x86_64.
I have an .odbc.ini file in my home directory with following lines:
[mydb]
Description = MySQL server on my-server
Driver=/usr/lib64/libmyodbc3.so
SERVER=my-server
I can successfully do the following:
library(RODBC)
channel - odbcConnect(mydb)
sqlQuery(channel, show databases)
And in general, I have no problems using odbcConnect to connect to the
mydb DSN.
However, for various reasons I want to make a DSN-less connection
using odbcDriverConnect. However, everything I've tried generated a
data source not found message (see below for details)
After reading through various documents, I tried doing following.
(1) Put an odbcinst.ini file in my home directory with following lines
[MySQL]
Description = ODBC for MySQL
Driver=/usr/lib64/libmyodbc3.so
Setup = /usr/lib/libodbcmyS.so
FileUsage = 1
(2) Install it with odbcinst -i -f. This seems to work as when I type
odbcinst -j I get
DRIVERS: /home/jmarcus/odbcinst.ini
SYSTEM DATA SOURCES: /home/jmarcus/odbc.ini
USER DATA SOURCES..: /home/jmarcus/.odbc.ini
(2) Set the environment variable to point to this file:
bash-3.2$ ODBCSYSINI=/home/jmarcus
bash-3.2$ export ODBCSYSINI
(3) Start R
Note that R has inherited environment variable
Sys.getenv(ODBCSYSINI)
ODBCSYSINI
/home/jmarcus
(4) Try to connect to the MySQL server
conn -
odbcDriverConnect(connection=Driver={MySQL};Server=my-server;Database=m
y_database;Uid=my_username;Pwd=my_password)
This generates following:
Warning messages:
1: In odbcDriverConnect(connection =
Driver={MySQL};Server=my-server;Database=my_database;Uid=my_username;Pw
d=my_password) :
[RODBC] ERROR: state IM002, code 0, message [unixODBC][Driver
Manager]Data source name not found, and no default driver specified
2: In odbcDriverConnect(connection =
Driver={MySQL};Server=my-server;Database=my_database;Uid=my_username;Pw
d=my_password) :
ODBC connection failed
Can anyone see what I'm doing wrong? Thanks.
Jeff
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OpenSource Software Consultant
CENFOSS (www.cenfoss.co.mz)
SP Tech (www.sptech.co.mz)
email: orvaq...@cenfoss.co.mz
cell: +258828810980
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CENFOSS (www.cenfoss.co.mz)
SP Tech (www.sptech.co.mz)
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cell: +258828810980
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] the sample() function
You can access the sources yourself. How to find the right file is described in Ligges, U. (2006): R Help Desk: Accessing the Sources. R News 6 (4), 43-45. http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf Best wishes, Uwe Ligges On 15.01.2010 10:54, Federico Bonofiglio wrote: hello R-Wizards! again i'm invoking your presence!! since all the fuss about the paradoxes on a computer algorithm generating caos or un-determinancy, i recently grew quite curious about the mechanism underlying the procedure of NUMBER RADOMIZATION. could anyone of you, masters, attach me the algorithm (or source code? is it right?) behind the *sample()* function, so i can inspect in detail the mechanism of this so gossiped radomization? thank you, sincerely federico bonofiglio, student of statistics at milano bicocca university, italia [[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] How to color a splom?
On 14.01.2010 11:11, Marius Hofert wrote: Dear R-Users, I would like to color the data in a splom according to their position in the matrix, i.e. I would like to have all data shown in the upper left corner to be blue, all entries below that to be black, and the data to the right to be all red. I tried to color the splom with the following call... splom(~iris[1:3],col=c(black,blue,red)) ...however, the colors are mixed. I also constructed a matrix containing the required colors, but that also did not work. How do I color the splom according to the location in the matrix as mentioned above? Do you mean color by the levels of Species? splom( ~ iris[1:3], col = c(black,blue,red)[iris[,4]]) Best wishes, Uwe Cheers, Marius __ 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] transposing a list of vectors
Thanks, Henrique I *do* need to preserve the type of each list element (num or chr). Thus, a first step might be as.data.frame(testlist, stringsAsFactors=FALSE) shape cell.fill back.fill scale.max 1 0 red white 100 2 0 blue white 100 3 2 green white 100 str(as.data.frame(testlist, stringsAsFactors=FALSE)) 'data.frame': 3 obs. of 4 variables: $ shape: num 0 0 2 $ cell.fill: chr red blue green $ back.fill: chr white white white $ scale.max: num 100 100 100 I think, with this mod, your #2 gives me what I want: wanted.henrique - lapply(split(x - as.data.frame(testlist, stringsAsFactors=FALSE), 1:nrow(x)), as.list) str(wanted.henrique) List of 3 $ 1:List of 4 ..$ shape: num 0 ..$ cell.fill: chr red ..$ back.fill: chr white ..$ scale.max: num 100 $ 2:List of 4 ..$ shape: num 0 ..$ cell.fill: chr blue ..$ back.fill: chr white ..$ scale.max: num 100 $ 3:List of 4 ..$ shape: num 2 ..$ cell.fill: chr green ..$ back.fill: chr white ..$ scale.max: num 100 Henrique Dallazuanna wrote: Try this: #'1) But apply converts all to 'character' apply(as.data.frame(testlist), 1, as.list) #2) lapply(split(x - as.data.frame(testlist), 1:nrow(x)), as.list) On Fri, Jan 15, 2010 at 11:09 AM, Michael Friendly frien...@yorku.ca wrote: I have a list of vectors, all forced to be the same length: testlist - list( shape=c(0, 0, 2), cell.fill=c(red,blue,green), back.fill=rep(white,3), scale.max=rep(100,3) ) str(testlist) List of 4 $ shape: num [1:3] 0 0 2 $ cell.fill: chr [1:3] red blue green $ back.fill: chr [1:3] white white white $ scale.max: num [1:3] 100 100 100 I need to 'transpose' them into a list of lists with named values like so: wanted - list( list(shape=0, cell.fill=red, back.fill=white, scale.max=100), list(shape=0, cell.fill=blue, back.fill=white, scale.max=100), list(shape=2, cell.fill=green, back.fill=white, scale.max=100) ) str(wanted) List of 3 $ :List of 4 ..$ shape: num 0 ..$ cell.fill: chr red ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape: num 0 ..$ cell.fill: chr blue ..$ back.fill: chr white ..$ scale.max: num 3 $ :List of 4 ..$ shape: num 2 ..$ cell.fill: chr green ..$ back.fill: chr white ..$ scale.max: num 3 How can I do this in general? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ 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. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ 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] How to calculate the row wise means for grouped columns in matrix?
Hi all, I want to calculate the row wise mean of groups of columns in a matrix M. All columns belonging to the same group have the same column name. My idea is to create a new vector V containing these column names, but after first removing the duplicates. Then I would calculate the means using for instance rowMean() and by comparing the column names of M with the vector V, getting the indices of the columns to use. What do you think, is it a good idea or not? If yes, any suggestions how to do it? If no, is there any alternative solution that might work better? All the best, Joel _ Lagra alla dina foton på Skydrive. Det är enkelt och säkert! http://www.skydrive.live.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.
Re: [R] estimating rho of Poisson distributed data
On Jan 15, 2010, at 5:59 AM, Titus von der Malsburg wrote: Mean and variance of Poisson distributed data are specified by \rho. How can I estimate \rho for a set of measurements in R? rho - mean(x) 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] estimating rho of Poisson distributed data
On Fri, Jan 15, 2010 at 09:19:23AM -0500, David Winsemius wrote: On Jan 15, 2010, at 5:59 AM, Titus von der Malsburg wrote: Mean and variance of Poisson distributed data are specified by \rho. How can I estimate \rho for a set of measurements in R? rho - mean(x) Yeah, thanks :-) I was looking for a general way to fit a distribution. Should've made that clear. I'm surprised that nobody is complaining because I called lambda rho! __ 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] advice/opinion on - vs = in teaching R
I've only been using R for about 2.5 years but and I'm not all that good but I vote for - . I think the deciding factor is in RSiteSearch() and the various manuals. Almost everything I see uses - . Why introduce = when it is not used normally? It will just confuse the students who are trying to use any of the documentation. Not to mention they might slammed for bad syntax on the R-help mailing list. :) --- On Thu, 1/14/10, Erin Hodgess erinm.hodg...@gmail.com wrote: From: Erin Hodgess erinm.hodg...@gmail.com Subject: [R] advice/opinion on - vs = in teaching R To: R help r-h...@stat.math.ethz.ch Received: Thursday, January 14, 2010, 10:45 PM Hi R People: I'm teaching a statistical computing class using R starting next week (yay!) and I have an opinion type question, please. I'm old school and use - in an assignment. However, I'm starting to see the = in the literature. Which should I use or does it matter, please? Thanks for your input! Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.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. __ The new Internet Explorer® 8 - Faster, safer, easier. Optimized for Yahoo! Get it Now for Free! at http://downloads.yahoo.com/ca/internetexplorer/ __ 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] optimization problem
Dear R-experts, this is not a direct R-problem but I hope you can help me anyway. I would like to minimize || PG-I || over P, where P is a p x p permutation matrix (obtained by permuting the rows and/or columns of the identity matrix), G is a given p x p matrix with full rank and I the identity matrix. ||.|| is the frobenius norm. Does anyone know an algorithm to solve such a problem? And if yes, is it implemented in R? Currently I minimize it by going through all possible permutations - but this is not feasible for higher dimensional problems as I would like to consider too. Any help is appreciated! Thanks in advance, Klaus -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3.5 - sicherer, schneller und einfacher! http://portal.gmx.net/de/go/chbrowser __ 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] What is the newline escape sequence when using the Hershey fontfamily?
Hello! The question is simple: What is the escape sequence for a new line when using Hershey fonts? I obviously tried '\n' but it didn't work (see the sample below). I looked at 'demo(Hershey)' but all it only shows escape sequences for printable characters. The sample I've been using to try to find the escape sequence is below. You can comment or un-comment the fontfamily line to turn Hershey on or off. xx - c(1:10) yy - c(11:20) xyplot(yy~xx, main=list(This title should\nhave two lines #, fontfamily=HersheySans ) ) Thanks, Douglas __ 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] Advantages of using SQLite for data import in comparison to csv files
Thanks for your answer. I've thought of the possibility of an index when using a SQLite database, but as you mentioned, I don't really benefit from it in regard of rather small data sets. What I am considering as a problem when using csv files is the occurrence of data redundancy: When I wan't to print a table in a document, it is often not necessary to insert all columns of a table. You might choose to leave out certain parameters that are aren't of interest for the reader. I feared that the generation of a second table with less information would be unavoidable in this case before including it in LaTeX with Sweave. However, after having tried to get started with sqldf, this powerful addition to R's data analysis and manipulation abilities is probably sufficient for my purposes. Best regards, Juliet RSQLite is actually much more than a driver for data import. It basically allows any manipulation of SQLite databases, including reading, writing, or updating and munging data within the database. Regarding the original question of data import: I use csv and sqlite files interchangeably to store my data, and converting between one and the other is generally trivial (read one format into a data.frame and then write it into the other). For me, the key determinant is whether a given data set is so big that reading it into a data.frame with read.csv() every time I need it is a pain. I usually keep all my original data in csv files and write routines to write the contents of huge files into sqlite databases. sqldf is a great package as well, but it definitely does not obviate the need to actually be able to manipulate data base files. For one thing, you cannot index a csv file or a data.frame. If you have to repeatedly select subsets of your large data set, creating an index on the relevant column in the sqlite table is an absolute life saver. (However, with a 1000x20 data set, you will probably not have to worry about the speed of selecting from the table. Unless you need to use bigger data sets, the simplest way is probably to just use csv files, read the contents into a data.frame with read.csv, and then use sqldf on the data.frame if you need to do complicated subsetting) Best, Magnus __ 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] gWidgets: loading problem
Dear list, i try to set up a GUI with gWidgets. For this project, RGtk2 is required. By loading the package, i encounter the following error prompt: ---C Symbolname S_gtk_icon_factory_new not in DLL for package RGtk2--- Any suggestions how to fix this? And: is there a good resource for gWidgets templates on the web? Best regards Alex __ 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] Lattice: How to color the data points in splom() according to the panel they are plotted?
Dear ExpeRts,
I have the scatter plot matrix as given below. I would like the different
sub-plots in the scatter plot matrix to be colored differently. How do I get
all points shown in the upper-left plot (on position (1,1) in the scatter plot
matrix) to be plotted in blue, and the points shown in the plot to the right
(on position (1,2) in the scatter plot matrix) to be plotted in red? More
generally, how can I provide a matrix of colors to be used by splom() such that
all data points in the corresponding sub-plot of the scatter plot matrix are
shown in the specified color?
Cheers,
Marius
Here is the code:
library(lattice)
entrymat=matrix(0,nrow=3,ncol=3)
entrymat[1,2]=black
entrymat[1,3]=blue
entrymat[2,3]=red
entrymat=t(entrymat)
splom(~iris[,1:3],superpanel=function(z,...){
mymat.df=data.frame(rows=as.vector(row(entrymat)),cols=as.vector(col(entrymat)),entries=as.vector(entrymat))
mymat.df=subset(mymat.df,colsrows)
with(mymat.df,{
panel.text(x=rows,y=cols,labels=entries)
})
panel.pairs(z,upper.panel=panel.splom,lower.panel=function(...){},...)
},varnames=c(1,2,3)
)
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Re: [R] To add text in a matrix
One way to add the text is to use a list with named elements for the row and column names: (M - matrix(1:9, ncol=3, byrow=TRUE, + dimnames=list( =LETTERS[1:3], + THIS IS AN EXAMPLE\nOF a 3x3 MATRIX=LETTERS[1:3])) ) THIS IS AN EXAMPLE OF a 3x3 MATRIX A B C A 1 2 3 B 4 5 6 C 7 8 9 Larry Hotchkiss - Original Post - Message: 7 Date: Thu, 14 Jan 2010 11:04:27 +0100 From: carfer...@alum.us.es To: r-help@r-project.org Subject: [R] To add text in a matrix Message-ID: f61eaf1f1d8d7.4b4ef...@us.es Content-Type: text/plain; charset=us-ascii Dear colleagues, I would need to add text (some rows of information) in a matrix. For example, given this matrix 1 2 3 4 5 6 7 8 9 I would need to add this info: THIS IS AN EXAMPLE OF a 3x3 MATRIX 1 2 3 4 5 6 7 8 9 I have been looking for a function that works similar to fopen in matlab, but unfortunately I have not found It in R. Thank you in advance for your help! Carlos Fernandez __ 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] How to calculate the row wise means for grouped columns in matrix?
adapted from the help files of rowsum x - matrix(runif(100), ncol=5) group - sample(1:8, 20, TRUE) xsum - rowsum(x, group) sweep(xsum, 1, table(group), /) or aggregate(x, list(group), mean)[-1] b 2010/1/15 Joel Fürstenberg-Hägg joel_furstenberg_h...@hotmail.com: Hi all, I want to calculate the row wise mean of groups of columns in a matrix M. All columns belonging to the same group have the same column name. My idea is to create a new vector V containing these column names, but after first removing the duplicates. Then I would calculate the means using for instance rowMean() and by comparing the column names of M with the vector V, getting the indices of the columns to use. What do you think, is it a good idea or not? If yes, any suggestions how to do it? If no, is there any alternative solution that might work better? All the best, Joel _ Lagra alla dina foton på Skydrive. Det är enkelt och säkert! http://www.skydrive.live.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] estimating rho of Poisson distributed data
Titus von der Malsburg wrote: On Fri, Jan 15, 2010 at 09:19:23AM -0500, David Winsemius wrote: On Jan 15, 2010, at 5:59 AM, Titus von der Malsburg wrote: Mean and variance of Poisson distributed data are specified by \rho. How can I estimate \rho for a set of measurements in R? rho - mean(x) Yeah, thanks :-) I was looking for a general way to fit a distribution. Should've made that clear. I'm surprised that nobody is complaining because I called lambda rho! Why would anyone complain? You're free to call it 'applesauce' if that suits you. What do you mean by 'general way to fit a distribution'? Maximum likelihood might be one way. -Peter Ehlers __ 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 403.202.3921 __ 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] Comparing percentages
Hi all, This question is more stats related than R related, but as I will be doing these analyses in R, there may be some programming questions to follow. I figured it best to start here. To keep things relatively simple, assume that I recently fielded a survey over three weeks. I have three dichotomous variables that indicate what week a respondent responded in. I would like test to see if the percent responding in each week is significantly different. (For example, 24% responded in week 1 and 28% in week 2. Were there significantly more respondents in week 2?) Here is the data layout: ID Week1 Week2 Week3 1 10 0 2 01 0 3 10 0 4 01 0 5 01 0 6 00 1 7 00 1 It seems like this could be done as difference of percentages test, but I am not sure how to account for the third option. Any help is appreciated. Bryan [[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] estimating rho of Poisson distributed data
On Fri, Jan 15, 2010 at 08:33:52AM -0700, Peter Ehlers wrote: Why would anyone complain? You're free to call it 'applesauce' if that suits you. Good idea, I will do this from now on! ;-) What do you mean by 'general way to fit a distribution'? Maximum likelihood might be one way. Somebody else pointed me to fitdistr from MASS which does the job. Thanks for the reply! Titus __ 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] estimating rho of Poisson distributed data
On Jan 15, 2010, at 9:46 AM, Titus von der Malsburg wrote: On Fri, Jan 15, 2010 at 09:19:23AM -0500, David Winsemius wrote: On Jan 15, 2010, at 5:59 AM, Titus von der Malsburg wrote: Mean and variance of Poisson distributed data are specified by \rho. How can I estimate \rho for a set of measurements in R? rho - mean(x) Yeah, thanks :-) Hey, ask a simple question, get a simple answer. I was looking for a general way to fit a distribution. Should've made that clear. I'm surprised that nobody is complaining because I called lambda rho! There is a fitdistr function in MASS which would be extreme overkill for the problem posed and: http://cran.r-project.org/doc/contrib/Ricci-distributions-en.pdf What other trivial searching can I do for you? -- 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] advice/opinion on quot; lt; -quot; vs quot; =quot; in teaching R
John Kane jrkrideau at yahoo.ca writes: I've only been using R for about 2.5 years but and I'm not all that good but I vote for - . I think the deciding factor is in RSiteSearch() and the various manuals. Almost everything I see uses - . Why introduce = when it is not used normally? It will just confuse the students who are trying to use any of the documentation. Not to mention they might slammed for bad syntax on the R-help mailing list. :) Those are all good reasons. I have said something similar before (see http://www.mail-archive.com/r-help@r-project.org/msg16904.html), but I tend to use = because it seems to be more intuitive for students, despite being logically confused at a deeper level, and I want to spare them any additional cognitive load when they are first getting introduced to R. I'm not particularly convinced by the - is more general and there are some contexts where = doesn't work, because I'm not trying to be absolutely rigorous, nor teach all the possible ins and outs of R syntax. I would be very surprised if any of the examples given actually came up in the course of a first-semester statistics/modeling R course. I just want to do what works best for the students -- the problem is deciding on the balance between short term benefit (- is one more odd thing to get used to) and long term benefit (they will see - in other contexts, so they might as well get used to it eventually). Ben Bolker __ 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] advice/opinion on - vs = in teaching R
On Fri, 15 Jan 2010, Barry Rowlingson wrote: On Fri, Jan 15, 2010 at 6:57 AM, Ted Harding ted.hard...@manchester.ac.ukwrote: There is at least one context where the distinction must be preserved. Example: pnorm(1.5) # [1] 0.9331928 pnorm(x=1.5) # Error in pnorm(x = 1.5) : unused argument(s) (x = 1.5) pnorm(x-1.5) # [1] 0.9331928 x # [1] 1.5 Ted. I would regard modifying a variable within the parameters of a function call as pretty tasteless. What does: foo(x-2,x) or foo(x,x-3) do that couldn't be done clearer with two lines of code? It allows the lazy evaluation mechanism to determine whether the assignment happens. That would be very hard to do in two lines of code. -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] advice/opinion on - vs = in teaching R
On Thu, 14 Jan 2010, Erin Hodgess wrote: Hi R People: I'm teaching a statistical computing class using R starting next week (yay!) and I have an opinion type question, please. I'm old school and use - in an assignment. However, I'm starting to see the = in the literature. Which should I use or does it matter, please? I would say to use = if you are teaching people familiar with C or Java, and to use - otherwise. -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] estimating rho of Poisson distributed data
If you use
fit1-glm(y~x,offset=offset,family=poisson(link=log))
you will get values for the Null deviance and residual deviance along with
degrees of freedom for these parameters. One of these deviances divided by its
degrees of freedom might be what you are looking for. but I am not sure.
Perhaps other list members will either confirm my suspicion, or correct my
misconception.
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) Peter
Ehlers ehl...@ucalgary.ca 1/15/2010 10:33 AM
Titus von der Malsburg wrote:
On Fri, Jan 15, 2010 at 09:19:23AM -0500, David Winsemius wrote:
On Jan 15, 2010, at 5:59 AM, Titus von der Malsburg wrote:
Mean and variance of Poisson distributed data are specified by \rho.
How can I estimate \rho for a set of measurements in R?
rho - mean(x)
Yeah, thanks :-) I was looking for a general way to fit a
distribution. Should've made that clear. I'm surprised that nobody
is complaining because I called lambda rho!
Why would anyone complain? You're free to call it 'applesauce'
if that suits you.
What do you mean by 'general way to fit a distribution'?
Maximum likelihood might be one way.
-Peter Ehlers
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--
Peter Ehlers
University of Calgary
403.202.3921
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] gWidgets: loading problem
Walther, Alexander awalthermail at googlemail.com writes: Dear list, i try to set up a GUI with gWidgets. For this project, RGtk2 is required. By loading the package, i encounter the following error prompt: ---C Symbolname S_gtk_icon_factory_new not in DLL for package RGtk2- -- This sounds like an RGtk2 issue and for that it depends on your system. Can you load RGtk2 by itself and issue some command, say gtkWindow()? If not, that is where to look. Any suggestions how to fix this? And: is there a good resource for gWidgets templates on the web? There is a vignette with the package, and some examples at www.math.csi.cuny.edu/pmg/gWidgets/Examples. As well, there are some examples at www.math.csi.cuny.edu/gWidgetsWWW that should work here as well. Those might get you started. --John Best regards Alex __ 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] Sampling from a Postgres database
On 01/15/2010 01:49 AM, Bart Joosen wrote: One way could be to first select only the unique ID's, sample this and then select only the relevant records: strQuery = SELECT ID from tblFoo; IDs - sqlQuery(channel, strQuery) sample.IDs - sample(IDs,10) strQuery = paste(SELECT ID from tblFoo WHRE ID IN(, sample.IDs, );) IDs - sqlQuery(channel, strQuery) Better is to use the built-in random() function in Postgres: #select count(*) from visits; count - 4846604 (1 row) # select count(*) from visits where random() 0.005; count --- 24391 (1 row) HTH, Joe signature.asc Description: OpenPGP digital signature __ 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] panel.bpplot
Hi everybody, I am a newbie in R. I would like to use the panel.bpplot function on my data set but I have some problems. Can this function work on matrix? My data set have some NaN and when I run panel.bpplot function it returns error due to the presence of NaN. How Can I solve this? Thank you so much for your help netrunner -- View this message in context: http://n4.nabble.com/panel-bpplot-tp1015050p1015050.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] optimization problem
klausch at gmx.de writes:
Dear R-experts,
this is not a direct R-problem but I hope you can help me anyway.
I would like to minimize || PG-I || over P, where P is a p x p permutation
matrix (obtained by permuting the rows
and/or columns of the identity matrix), G is a given p x p matrix with full
rank and I the identity matrix.
||.|| is the frobenius norm.
Does anyone know an algorithm to solve such a problem? And if yes, is it
implemented in R?
Currently I minimize it by going through all possible permutations - but this
is not feasible for higher
dimensional problems as I would like to consider too.
Any help is appreciated!
Thanks in advance,
Klaus
This could be modeled as a MIQP problem:
min sum((i,j),sqr(V(i,j)))
v(i,j) = sum(k, P(i,k)*G(k,j)) - Id(i,j);
sum(i, P(i,j)) = 1
sum(j, P(i,j)) = 1
P(i,j) in {0,1}
If you have access to Cplex then http://cran.r-
project.org/web/packages/Rcplex/Rcplex.pdf can help.
If you can use a different norm it may be possible to use linear MIP technology
allowing a wider range of solvers.
This is combinatorial, so for p 20 say it may become slow (this also depends
on the data).
Erwin
Erwin Kalvelagen
Amsterdam Optimization Modeling Group
er...@amsterdamoptimization.com
http://amsterdamoptimization.com
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[R] Can an object reference itself?
Dear List,
I am not really familiar with any other language than R, but Ive heard that
in other languages there is something called self referencing.
Heres what Im trying to get an answer for:
Suppose there is a function that takes as its input a value of a slot of an
S4 object. The function itself is stored in another slot of the SAME S4
object. Is it then possible to have the function automatically recognize
the name of the object in which slot it is placed via some sort of self
referencing of the S4 object (to avoid having to explicitly state the
required function argument for different S4 object instances with different
names)?
I hope the following code snippets will give you an idea what Im trying to
do:
obj.for.slot - data.frame(a=1); obj.for.slot - data.frame(a=100)
save(obj.for.slot, file=C:/obj.1.for.slot.Rdata); save(obj.for.slot,
file=C:/obj.2.for.slot.Rdata)
slotfun - function(obj.name)
{
file.fqn.char - paste(file.fqn - , obj.name, @file.fqn,
sep=)
eval(parse(text=file.fqn.char))
load(file=file.fqn)
return(obj.for.slot)
}
setClass(
Class=Testclass,
representation=representation(
file.fqn=character,
data=function
),
prototype=prototype(
file.fqn=blabla,
data=slotfun
)
)
test- new(Testclass)
test.mod- new(Testclass)
t...@file.fqn - C:/obj.1.for.slot.Rdata
test@file.fqn - C:/obj.2.for.slot.Rdata
t...@data(obj.name=test)
test@data(obj.name=test.mod)
I'm trying to have slotfun() be stated in a way that does not require an
explicit stating of argument obj.name):
t...@data()
test@data()
Any hints in the right directions greatly appreciated!
Regards,
Janko Thyson
janko.thy...@kuei.de
Catholic University of Eichstätt-Ingolstadt
Ingolstadt School of Management
Statistics and Quantitative Methods
Auf der Schanz 49
D-85049 Ingolstadt
www.wfi.edu/lsqm
Fon: +49 841 937-1923
Fax: +49 841 937-1965
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Re: [R] panel.bpplot
netrunner wrote: Hi everybody, I am a newbie in R. I would like to use the panel.bpplot function on my data set but I have some problems. Can this function work on matrix? My data set have some NaN and when I run panel.bpplot function it returns error due to the presence of NaN. How Can I solve this? Thank you so much for your help netrunner Read documentation for lattice graphics. Get your problem solved with bwplot() without panel=panel.bpplot then add the panel=. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ 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] panel.bpplot
netrunner wrote: I am a newbie in R. I would like to use the panel.bpplot function on my data set but I have some problems. Can this function work on matrix? My data set have some NaN and when I run panel.bpplot function it returns error due to the presence of NaN. How Can I solve this? You should never use panel.bpplot directly, but rather in a bwplot() function. See the examples coming with the documentation in package Hmisc. Used correctly, it has no problem with NA. In general, one would use it with a data.frame, because grouping is often a factor. If this does not solve your problem, please repost with a modification of the sample below that shows the problem. Dieter library(Hmisc) set.seed(13) data = data.frame(x =rnorm(1000), g - sample(1:6, 1000, replace=TRUE)) bwplot(g ~ x, panel=panel.bpplot, data=data) # Add NA data$x[1:3] = NA data$x[data$g==6] = NA bwplot(g ~ x, panel=panel.bpplot, data=data) -- View this message in context: http://n4.nabble.com/panel-bpplot-tp1015050p1015105.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] Can an object reference itself?
On Fri, Jan 15, 2010 at 5:30 PM, Janko Thyson
janko.thy...@ku-eichstaett.de wrote:
Dear List,
I am not really familiar with any other language than R, but I’ve heard that
in other languages there is something called “self referencing”.
Here’s what I’m trying to get an answer for:
Suppose there is a function that takes as its input a value of a slot of an
S4 object. The function itself is stored in another slot of the SAME S4
object. Is it then possible to have the function automatically “recognize”
the name of the object in which slot it is placed via some sort of “self
referencing” of the S4 object (to avoid having to explicitly state the
required function argument for different S4 object instances with different
names)?
I hope the following code snippets will give you an idea what I’m trying to
do:
obj.for.slot - data.frame(a=1); obj.for.slot - data.frame(a=100)
save(obj.for.slot, file=C:/obj.1.for.slot.Rdata); save(obj.for.slot,
file=C:/obj.2.for.slot.Rdata)
slotfun - function(obj.name)
{
file.fqn.char - paste(file.fqn - , obj.name, @file.fqn,
sep=)
eval(parse(text=file.fqn.char))
load(file=file.fqn)
return(obj.for.slot)
}
setClass(
Class=Testclass,
representation=representation(
file.fqn=character,
data=function
),
prototype=prototype(
file.fqn=blabla,
data=slotfun
)
)
test - new(Testclass)
test.mod - new(Testclass)
t...@file.fqn - C:/obj.1.for.slot.Rdata
test@file.fqn - C:/obj.2.for.slot.Rdata
t...@data(obj.name=test)
test@data(obj.name=test.mod)
An object does not have a unique name. What would happen in the
following situations?
t3 - test.mod
tests - list(
test,
test.mod
)
Hadley
--
http://had.co.nz/
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Advantages of using SQLite for data import in comparison to csv files
Just to comment on this bit : For one thing, you cannot index a csv file or a data.frame. If you have to repeatedly select subsets of your large data set, creating an index on the relevant column in the sqlite table is an absolute life saver. This is one reason the data.table package was created. It is very similar to a data.frame, with the addition of things like keys. If you consider an index in sqlite a life saver then data.table might be up your street. Its really simple to do this in R. For example, lets say you have a 10,000,000 row table of 2 columns : id(integer), v(double). So this is a tiny example at just 115MB i.e. (4+8)*1e7/1024^2. This is many times smaller than most desktop users have RAM available to R on their 32bit machines, so you can run this example yourself. W'll start off with data.frame and then show how data.table compares. n=1e7 DF = data.frame(id=sample(LETTERS,n,replace=TRUE),v=rnorm(n)) head(DF) id v 1 P -0.57695495 2 A -0.33388390 3 P 0.05277701 4 K 0.49610573 5 F 0.31031501 6 C 1.26861215 dim(DF) [1] 10002 system.time(DF[DF$id==G,]) # table scan i.e. the == in R tests all 10m items, there is no index used as you said user system elapsed 1.230.171.41 system.time(DF[DF$id==G,]) # good idea to repeat all timings in case the first one was slow due to a garbage collect user system elapsed 1.360.171.53 DT = data.table(DF)# convert the data.frame to a data.table object.size(DF) 120001608 bytes object.size(DT) 120001640 bytes# so a DT is the same structure as a data.frame taking the same space. data.frame is efficiently stored. Can't get lower than the 115MB calculation for this dataset. data.table doesn't do any magic with regard to storage # Now comes the fun : setkey(DT,id)# sort the data.table by id and marks it as sorted by id. The key is now id. This is analogous to building the index that you do in sqllite. You don't have to assign the result of setkey() anywhere, unlike most R functions. Its a special function which operates on DT and changes it directly. tables()# view all our tables in memory, theres just one in this example. It assumes you view the result in a font such as courier. NAME NROW MB COLS KEY [1,] DT 10,000,000 115 id,v id Total: 115MB # R is looking a bit like a database now. Usually you have lots of tables returned by tables(), just like you would with sqlTables() in RODBC. Its not difficult to use the key, its very like using rownames : system.time(DT[G,mult=all]) user system elapsed 0.090.000.09 system.time(DT[G,mult=all]) # repeat the timing test. confirmed that 1.5s reduces to 0.1s user system elapsed 0.1 0.0 0.1 identical( DF[DF$id==G,]$v, DT[G,mult=all]$v ) [1] TRUE The mult=all is needed because otherwise you'd just get the first row of the G group (the default for mult is first when multiple rows match the key value) Its very important to realise that in a data.table query you have the option to do table scans too e.g. : system.time(DT[id==G]) # its the == operator that results in a table scan, its not the class of the table per se user system elapsed 1.390.121.52 So its up to the user of data.table. The user has the option to use data.table badly (by not using the key), just like you can use SQL badly (by not using an index) Ok, who cares. 1 second saved. Why all the effort ? Two reasons. Firstly, try doubling the rows in DF and the time doubles to 3 seconds, double the rows in the DT though and that time stays constant at 0.1 seconds. Keep on doubling and the savings get bigger and bigger. Secondly, if you're repeating that 'query' inside a loop then the time saving adds up. There are other advantages of data.table but it seemed appropriate just to mention the keys this time. HTH Magnus Torfason zulutime@gmail.com wrote in message news:4b4f9c70.2050...@gmail.com... RSQLite is actually much more than a driver for data import. It basically allows any manipulation of SQLite databases, including reading, writing, or updating and munging data within the database. Regarding the original question of data import: I use csv and sqlite files interchangeably to store my data, and converting between one and the other is generally trivial (read one format into a data.frame and then write it into the other). For me, the key determinant is whether a given data set is so big that reading it into a data.frame with read.csv() every time I need it is a pain. I usually keep all my original data in csv files and write routines to write the contents of huge files into sqlite databases. sqldf is a great package as well, but it definitely does not obviate the need to actually be able to manipulate data base files. For one thing, you
[R] cbind or ?
Hey Guys, It sure seems I get stuck on things that should be easy. Heres my question: PARCELS-by(ResImp[ , ACCOUNTNO], ResImp[Property], length) PARCELS Property: UNSOLD [1] 9053 --- Property: SOLD [1] 578 --- Property: SubSale [1] 52 QuanImpUnsold-with(ResImp, by(Appraisal, Property, FUN=function(x)quantile(x, probs = c(1,25,50,75,90)/100))) QuanImpUnsold Property: UNSOLD 1% 25% 50% 75% 90% 18106.4 92817.0 131794.0 185742.0 262365.0 --- Property: SOLD 1% 25% 50% 75% 90% 35335.65 105034.25 138967.00 181971.25 254946.00 --- Property: SubSale 1% 25% 50% 75% 90% 37255.72 117055.50 149314.00 196207.00 259288.60 tb-cbind(PARCELS, QuanImpUnsold) tb PARCELS QuanImpUnsold UNSOLD 9053Numeric,5 SOLD578 Numeric,5 SubSale 52 Numeric,5 This is what I want tb Property: UNSOLD Parcels 1% 25% 50% 75% 90% 905318106.4 92817.0 131794.0 185742.0 262365.0 --- Property: SOLD Parcels 1% 25% 50% 75% 90% 57835335.65 105034.25 138967.00 181971.25 254946.00 --- Property: SubSale Parcels 1% 25% 50% 75% 90% 52 37255.72 117055.50 149314.00 196207.00 259288.60 Any suggestions? Thanks, L.A. Don't know if this helps: str(PARCELS) 'by' int [1:3(1d)] 9053 578 52 - attr(*, dimnames)=List of 1 ..$ Property: chr [1:3] UNSOLD SOLD SubSale - attr(*, call)= language by.default(data = ResImp[, ACCOUNTNO], INDICES = ResImp[Property], FUN = length) str(QuanImpUnsold) List of 3 $ UNSOLD : Named num [1:5] 18106 92817 131794 185742 262365 ..- attr(*, names)= chr [1:5] 1% 25% 50% 75% ... $ SOLD : Named num [1:5] 35336 105034 138967 181971 254946 ..- attr(*, names)= chr [1:5] 1% 25% 50% 75% ... $ SubSale: Named num [1:5] 37256 117056 149314 196207 259289 ..- attr(*, names)= chr [1:5] 1% 25% 50% 75% ... - attr(*, dim)= int 3 - attr(*, dimnames)=List of 1 ..$ Property: chr [1:3] UNSOLD SOLD SubSale - attr(*, call)= language by.default(data = Appraisal, INDICES = Property, FUN = function(x) quantile(x, probs = c(1, 25, 50, 75, 90)/100)) - attr(*, class)= chr by -- View this message in context: http://n4.nabble.com/cbind-or-tp1015187p1015187.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] cbind or ?
Try this: `class-`(lapply(1:length(QuanImpUnsold), function(idx)c(QuanImpUnsold[[idx]], PARCELS[[idx]])), by) On Fri, Jan 15, 2010 at 5:06 PM, L.A. ro...@millect.com wrote: Hey Guys, It sure seems I get stuck on things that should be easy. Heres my question: PARCELS-by(ResImp[ , ACCOUNTNO], ResImp[Property], length) PARCELS Property: UNSOLD [1] 9053 --- Property: SOLD [1] 578 --- Property: SubSale [1] 52 QuanImpUnsold-with(ResImp, by(Appraisal, Property, FUN=function(x)quantile(x, probs = c(1,25,50,75,90)/100))) QuanImpUnsold Property: UNSOLD 1% 25% 50% 75% 90% 18106.4 92817.0 131794.0 185742.0 262365.0 --- Property: SOLD 1% 25% 50% 75% 90% 35335.65 105034.25 138967.00 181971.25 254946.00 --- Property: SubSale 1% 25% 50% 75% 90% 37255.72 117055.50 149314.00 196207.00 259288.60 tb-cbind(PARCELS, QuanImpUnsold) tb PARCELS QuanImpUnsold UNSOLD 9053 Numeric,5 SOLD 578 Numeric,5 SubSale 52 Numeric,5 This is what I want tb Property: UNSOLD Parcels 1% 25% 50% 75% 90% 9053 18106.4 92817.0 131794.0 185742.0 262365.0 --- Property: SOLD Parcels 1% 25% 50% 75% 90% 578 35335.65 105034.25 138967.00 181971.25 254946.00 --- Property: SubSale Parcels 1% 25% 50% 75% 90% 52 37255.72 117055.50 149314.00 196207.00 259288.60 Any suggestions? Thanks, L.A. Don't know if this helps: str(PARCELS) 'by' int [1:3(1d)] 9053 578 52 - attr(*, dimnames)=List of 1 ..$ Property: chr [1:3] UNSOLD SOLD SubSale - attr(*, call)= language by.default(data = ResImp[, ACCOUNTNO], INDICES = ResImp[Property], FUN = length) str(QuanImpUnsold) List of 3 $ UNSOLD : Named num [1:5] 18106 92817 131794 185742 262365 ..- attr(*, names)= chr [1:5] 1% 25% 50% 75% ... $ SOLD : Named num [1:5] 35336 105034 138967 181971 254946 ..- attr(*, names)= chr [1:5] 1% 25% 50% 75% ... $ SubSale: Named num [1:5] 37256 117056 149314 196207 259289 ..- attr(*, names)= chr [1:5] 1% 25% 50% 75% ... - attr(*, dim)= int 3 - attr(*, dimnames)=List of 1 ..$ Property: chr [1:3] UNSOLD SOLD SubSale - attr(*, call)= language by.default(data = Appraisal, INDICES = Property, FUN = function(x) quantile(x, probs = c(1, 25, 50, 75, 90)/100)) - attr(*, class)= chr by -- View this message in context: http://n4.nabble.com/cbind-or-tp1015187p1015187.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] bootstrapping
Hi All, I'm new to R so please bear with me. I have a dataset with 337 turn angles ranging from -180 to 180 degrees. I need to bootstrap (sample with replacement) 1,000 times to create expected average turn angle with 95% CIs. The code is pretty straightforward (-boot(data =, statistic = ,R =)) but I am unsure how to input my observed mean (6 degrees) and standard deviation (66 degrees) into the statistic component. I realize there is a 'function' code but I can't seem to carry the results over to the 'boot' code. Thanks, Aaron M. Foley PhD Candidate Caesar Kleberg Wildlife Research Institute Texas AM University - Kingsville Cousins Hall, Room 201 Kingsville, TX 78363 [[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] 'nlme' library - lme function results
Dear R-helpers I am running a simple mixed effects model using lme(). The call looks like this: fit - lme(Analyte~Sample, data=Data, random=~1 | Run) I am particularly interested in the estimated random effects. When I print the 'fit' object, it looks something like example below: (...) Random effects: Formula: ~1 | Run (Intercept) Residual StdDev:3.483794 3.637523 (...) While I have no problem obtaining the 'Residual' value by calling fit$sigma, I have no idea how to obtain the '(Intercept)' value from the 'fit' object. Anyone can help with that? Best regards, -- Michal J. Figurski, PhD HUP, Pathology Laboratory Medicine Biomarker Research Laboratory 3400 Spruce St. 7 Maloney Philadelphia, PA 19104 tel. (215) 662-3413 __ 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] Possible to write text inside a bar of a barplot?
How can I write text inside a bar of a barplot? I tried using text(), but I am only able to specify the numeric y-coordinate. The different columns of my barplot correspond to factors and not numbers, so I don't know how to access the horizontal positions of the bars. I tried fiddling with different values of the adj argument, but this appears unreliable. Background: I have created a barplot visualization where the bars represent the size of different items (e.g. US state populations), and the sub-bars represent the size of the different sub-components of each item (e.g. counties). Picture: http://drop.io/hjcodjj/asset/capture-png I would like to put in a label inside each sub-bar (e.g. indicating the name of the county represented by that sub-bar). Rex p.s.: In case anyone finds this visualization useful I'll share my code afterward, but just need to get the labeling working properly first. [[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 package dependencies
On 1/13/10 11:21 AM, James W. MacDonald wrote: Hi Colin, The pkgDepTools package from Bioconductor will help with question #1: http://bioconductor.org/packages/2.5/bioc/html/pkgDepTools.html I am not positive on this, but I believe this package is also used to determine the reverse dependencies that would be listed on that page if there were any for this package. An example with reverse dependencies is e.g., the IRanges package: http://bioconductor.org/packages/2.5/bioc/html/IRanges.html The maintainer (Seth Falcon) would know for sure if the package will do reverse dependencies as well. There is an example in the vignette for pkgDepTools that shows how to get reverse dependencies: The edge directions of the dependency graph can be reversed and the resulting graph used to determine the set of packages that make use of (even indirectly) a given package. For example, one might like to know which packages make use of the methods package. Here is one way to do that: example follows in the vignette + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user __ 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] (no subject)
Hello, I am running R on cygwin for windows. File R1234 contains data - read.table(data) q() On the command line I type R --no-save -q R_PROFILE=R1234 returns Error: could not find function read.table 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.
Re: [R] advice/opinion on quot; lt; -quot; vs quot; =quot; in teaching R
On Fri, Jan 15, 2010 at 10:00 AM, Ben Bolker bol...@ufl.edu wrote: John Kane jrkrideau at yahoo.ca writes: I've only been using R for about 2.5 years but and I'm not all that good but I vote for - . I think the deciding factor is in RSiteSearch() and the various manuals. Almost everything I see uses - . Why introduce = when it is not used normally? It will just confuse the students who are trying to use any of the documentation. Not to mention they might slammed for bad syntax on the R-help mailing list. :) Those are all good reasons. I have said something similar before (see http://www.mail-archive.com/r-help@r-project.org/msg16904.html), but I tend to use = because it seems to be more intuitive for students, despite being logically confused at a deeper level, and I want to spare them any additional cognitive load when they are first getting introduced to R. I'm not particularly convinced by the - is more general and there are some contexts where = doesn't work, because I'm not trying to be absolutely rigorous, nor teach all the possible ins and outs of R syntax. I would be very surprised if any of the examples given actually came up in the course of a first-semester statistics/modeling R course. I teach the idiom summary(fm1 - lm(y ~ x, mydata)) in my introductory courses. I just want to do what works best for the students -- the problem is deciding on the balance between short term benefit (- is one more odd thing to get used to) and long term benefit (they will see - in other contexts, so they might as well get used to it eventually). Ben Bolker __ 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] Possible to write text inside a bar of a barplot?
Thanks for the replies! The answer is that barplot() returns the x coordinates of the bars. On Fri, Jan 15, 2010 at 12:01 PM, Rex C. Eastbourne rex.eastbou...@gmail.com wrote: How can I write text inside a bar of a barplot? I tried using text(), but I am only able to specify the numeric y-coordinate. The different columns of my barplot correspond to factors and not numbers, so I don't know how to access the horizontal positions of the bars. I tried fiddling with different values of the adj argument, but this appears unreliable. Background: I have created a barplot visualization where the bars represent the size of different items (e.g. US state populations), and the sub-bars represent the size of the different sub-components of each item (e.g. counties). Picture: http://drop.io/hjcodjj/asset/capture-png I would like to put in a label inside each sub-bar (e.g. indicating the name of the county represented by that sub-bar). Rex p.s.: In case anyone finds this visualization useful I'll share my code afterward, but just need to get the labeling working properly first. [[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] Eigenvectors and values in R and SAS
Here is an example that may be helpful.
A - matrix(c(-3,5,4,-2),nrow=2,byrow=TRUE)
eigs - eigen(A)
eigs
$values
[1] -7 2
$vectors
[,1] [,2]
[1,] -0.7808688 -0.7071068
[2,] 0.6246950 -0.7071068
The eigenvectors may be scaled differently because they are not unique
(or have a different sign), but Ax = lambda x, for an eigenvalue
lambda.
#Ax
A %*% eigs$vectors[,1]
[,1]
[1,] 5.466082
[2,] -4.372865
# λx
-7 * eigs$vectors[,1,drop=FALSE]
[,1]
[1,] 5.466082
[2,] -4.372865
The eigenvectors for proc iml are scaled similarly, but have different signs.
proc iml;
A = {-3 5, 4 -2};
print A;
eigval = eigval(A);
evec = eigvec(A);
print eigval;
print evec;
A_x = A*evec[,1];
lambda_x = eigval[1,1]*evec[,1];
print A_x;
print lambda_x;
quit;
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Re: [R] Can I save R graphs as a R objects
As a general rule, you really do not want to edit graphs by pointing/clicking/dragging. It may seem an easy way to make some modifications, but in the long run it will become more of a headache than a help. Better to create a script with the commands to create the plot, then if there is some change you want made, find the correct change or addition to the script and rerun the script. That way when later on you have a similar project and want to create the same or similar graph, you can just run the script again with the new data, making any minor changes that you need. On the other hand if you create the basic plot then edit it using point/click/drag style tools, then a couple months later when you find that there was a typo in the data and you need to recreate the graph (not as rare an event as we would like), you will first need to remember how you created the graph, then you will need to remember all the point/click/drag steps that you took (and redo them). It is just simpler to use the script. Having said that, if you still feel the need to modify a plot using a mouse (don't complain when you have to redo all the steps to redo the graph) then some options include: Save the graph as an svg file (Cairo device, or other package) then use inkscape or other program to edit it. Save the graph as a fig file and use xfig/winfig/jfig to edit it. Save/copy the graph as a windows meta file and use Excel/Word to edit it. But the R paradigm is really to use a script to create the correct graph in the first place rather than give an incorrect graph and expect the user to use non-reproducible post-hoc modifications. 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 vikrant Sent: Friday, January 15, 2010 2:27 AM To: r-help@r-project.org Subject: [R] Can I save R graphs as a R objects Can I save R graphs as a R objects ? IF yes then if I click this R object can I edit my chart as in Excel. Please suggest your views -- View this message in context: http://n4.nabble.com/Can-I-save-R-graphs- as-a-R-objects-tp1014621p1014621.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.
[R] randomForest maxnodes
Has anyone sucessfully used the maxnodes feature in randomForest? I tried setting it, but when it is non-NULL I always get back a forest in which all trees have size 1. I am using a continuous response (regression). Any help would be appreciated. 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.
Re: [R] (no subject)
Saleem, I have no idea about this, but may be you can use other data.frame name instead of data because data is a name of a function (see ?data). good luck milton On Fri, Jan 15, 2010 at 3:33 PM, saleem mukhtar saleem...@yahoo.com wrote: Hello, I am running R on cygwin for windows. File R1234 contains data - read.table(data) q() On the command line I type R --no-save -q R_PROFILE=R1234 returns Error: could not find function read.table 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.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.
[R] weighting (survey) data
Hi, is there a function in R equivalent to the weight by-command in SPSS? I'm working with survey datasets and the data need to be weighted by a survey/ probability/ design weight (to compensate for different probabilities to be included in the sample in each country). The weight variables are included in the datasets. I did find functions in the Hmisc and survey packages that might fit some of my needs but I need to do a bunch of procedures for all of which the data must be weighted, as far as I can see. (I'm quite new to R and the prospect of having to write my own functions for all of them is really scaring me ;)) Thanks, Vera __ 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] weighting (survey) data
On Jan 15, 2010, at 5:13 PM, vivi ane wrote: Hi, is there a function in R equivalent to the weight by-command in SPSS? I'm working with survey datasets and the data need to be weighted by a survey/ probability/ design weight (to compensate for different probabilities to be included in the sample in each country). The weight variables are included in the datasets. I did find functions in the Hmisc and survey packages that might fit some of my needs but I need to do a bunch of procedures for all of which the data must be weighted, as far as I can see. (I'm quite new to R and the prospect of having to write my own functions for all of them is really scaring me ;)) RSiteSearch(survey) -- 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] (no subject)
?Startup Read this help page **carefully**. It tells you what happens when R starts up. The profile file is executed with **only the base package loaded**, and read.table is not in the base package. If you replace your read statement with data - utils::read.table(data) it would work (if there is a data file in the working directory. Otherwise it will fail because it can't find data). (The use of the name data for an R object is bad form, as Milton mentioned. But it is not the cause of your problem). Query to core team: As this seems to have come up several times recently, should this be in the FAQ in a question like: Why can't R find the function called in my Profile file when R starts up? (I'd be happy to write a first draft if so). Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of milton ruser Sent: Friday, January 15, 2010 2:07 PM To: saleem mukhtar Cc: r-help@r-project.org Subject: Re: [R] (no subject) Saleem, I have no idea about this, but may be you can use other data.frame name instead of data because data is a name of a function (see ?data). good luck milton On Fri, Jan 15, 2010 at 3:33 PM, saleem mukhtar saleem...@yahoo.com wrote: Hello, I am running R on cygwin for windows. File R1234 contains data - read.table(data) q() On the command line I type R --no-save -q R_PROFILE=R1234 returns Error: could not find function read.table 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.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. __ 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] randomForest maxnodes
Please try to follow the posting guide and give a reproducible example,
as below:
R library(randomForest)
randomForest 4.5-34
Type rfNews() to see new features/changes/bug fixes.
R iris2 = iris[-5]
R iris.rf = randomForest(Petal.Width~., iris2, maxnodes=4, ntree=50)
R nodesize(iris.rf)
Error: could not find function nodesize
R treesize(iris.rf)
[1] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
4 4 4 4
[39] 4 4 4 4 4 4 4 4 4 4 4 4
Andy
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Epic John
Sent: Friday, January 15, 2010 4:50 PM
To: r-help@r-project.org
Subject: [R] randomForest maxnodes
Has anyone sucessfully used the maxnodes feature in
randomForest? I tried
setting it, but when it is non-NULL I always get back a
forest in which all
trees have size 1. I am using a continuous response
(regression). Any help
would be appreciated.
Thanks.
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
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Re: [R] bootstrapping
Hi Aaron, try the argument statistic=mean. Then boot() will give you the mean turn angle in your actual data (which appears to be 6 degrees, judging from what you write), as well as the means of the bootstrapped data. Then you can get (nonparametric) bootstrap CIs by quantile(boot$t,probs=c(.025,.975)). As far as I can see, there is really no need to look at sd(). A more interesting question would be how to deal with the fact that -180=+180, there may be something to think about here... HTH, Stephan aaron.fo...@students.tamuk.edu schrieb: Hi All, I'm new to R so please bear with me. I have a dataset with 337 turn angles ranging from -180 to 180 degrees. I need to bootstrap (sample with replacement) 1,000 times to create expected average turn angle with 95% CIs. The code is pretty straightforward (-boot(data =, statistic = ,R =)) but I am unsure how to input my observed mean (6 degrees) and standard deviation (66 degrees) into the statistic component. I realize there is a 'function' code but I can't seem to carry the results over to the 'boot' code. Thanks, Aaron M. Foley PhD Candidate Caesar Kleberg Wildlife Research Institute Texas AM University - Kingsville Cousins Hall, Room 201 Kingsville, TX 78363 [[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.
