[R] Creating a directory for my data
Hi everyone,
I am currently working with a very large data set. It is data collected a
few times a day, so there are repeated titles in the data set. I want to
assign an id number to each different title and enter this information in a
directory that I can access whenever I am working with the data.
An example of a data I am workin with follows:
1 title A
2 title C
3 title B
1 title A
2 title B
3 title C
1 title D
2 title A
3 title C
1 title B
2 title A
3 title C
What I have tried thus far is for loops.
r-matrix(x[,1])
t-matrix(x[,2])
for(i in 1:length(t)) {
for(k in 1:length(r)) {
z = matrix(c(i,t))
A = Article A
for(j in 1:length(z)){
if(B==Article A)
else{enter article in z}
}
}
This is of course giving me a lot of errors. I just have no idea where to go
with this. Does anyone have any ideas on where I can go from here to create
my directory?
I appreciate all your help.
Thank you in advance.
--
View this message in context:
http://www.nabble.com/Creating-a-directory-for-my-data-tp22448335p22448335.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] Converting a dataframe to a matrix
If I have a dataframe which is organized like this: name color likes? 1 sally red0 2 sally blue1 3 sally green1 4 jake red0 5 jake blue1 6 jake green1 7 tom red1 8 tom blue0 9 tom green0 And I want to create a matrix in the form: red blue green sally 01 1 jake01 1 tom 10 0 Are there any built-in commands that might help me do this? Also, I can't assume that there is an observation for every person-color. In other words, in the original dataset, there might be some colors for which sally offered no opinion. In some cases, this may be represented by NA, in others, it may mean that no row exists for sally for that color. Thank you! __ 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] North Arrow (.png file) on a Map
Is this arrow satisfactory for you?
north.arrow = function(x, y, h) {
polygon(c(x, x, x + h/2), c(y - h, y, y - (1 + sqrt(3)/2) * h),
col = black, border = NA)
polygon(c(x, x + h/2, x, x - h/2), c(y - h, y - (1 + sqrt(3)/2) *
h, y, y - (1 + sqrt(3)/2) * h))
text(x, y, N, adj = c(0.5, 0), cex = 4)
}
plot(1, type = n, ylim = c(0, 1))
north.arrow(1, 0.8, 0.3)
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
On Tue, Mar 10, 2009 at 7:21 PM, Rodrigo Aluizio r.alui...@gmail.com wrote:
Hi list.
I would like to know how do I insert a North arrow, stored as a png file in
my computer, in a map? I found lots of post asking similar things, one of
them mentioned the pixmap package. The map was done using map() and
shapefiles (the code is below). I’m using the pixmap () and addlogo()
functions. Well I can import the png with pixmap() function (I guess, once
there’s no error message), but I can’t put It on the map, I got an error
message telling me that:
“Error at t(x...@index[nrow(x...@index):1, , drop = FALSE]) :
index out of limits”
Well I tried changing coordinates but I always got the same result. How do I
do this correctly? Is there a better way?
Thanks for the help and attention.
Here is the complete map script:
library(RODBC)
library(maps)
library(mapdata)
library(maptools)
library(pixmap)
#Carregar Coordenadas e dados dos Pontos Amostrais
Dados-odbcConnectExcel('Campos.xls',readOnly=T)
Coord-sqlFetch(Dados,'CoordMed',colnames=F,rownames='Ponto')
odbcClose(Dados)
N-pixmap('Norte.png',nrow=166,ncol=113)
# Carregar pontos e shapes
Batimetria-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontol
ogia/Campos/ShapeFiles/Batimetria_BC.shp')
Estados-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontologi
a/Campos/ShapeFiles/Estados_Sudeste.shp')
Faciologia-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontol
ogia/Campos/ShapeFiles/Faciologia_BC.shp')
# Mapa com os Pontos da Bacia
postscript('MapaCampos.eps',paper='special',onefile=F,horizontal=F,width=3.5
,height=4.5,bg='white',pointsize=3)
par(mar=c(3,2,2,0))
map('worldHires','brazil',ylim=c(23.9,20.3),xlim=c(42.1,39.2),type='n')
plot(Faciologia,ylab='',xlab='',col=c('lightgreen','lightgreen','lightgreen'
,'lightgreen','lightgreen','lightgray','lightgray','lightgray','lightgray','
lightgray','lightgray','lightgray','lightgray','lightgray','lightgray','ligh
tgray','lightgray','lightgray','lightgray','lightgray','lightgray','lightyel
low','lightyellow','lightyellow'),add=T,lwd=0.5,border=0)
plot(Batimetria,ylab='',xlab='',col='darkgray',lty='solid',lwd=0.2,add=T)
plot(Estados,ylab='',xlab='',lty='solid',add=T,lwd=0.8)
text(Coord$Longitude[Coord$Réplicas=='1'],Coord$Latitude[Coord$Réplicas=='1'
],rownames(Coord)[Coord$Réplicas=='1'],col='red',cex=0.5,font=2)
text(Coord$Longitude[Coord$Réplicas=='2'],Coord$Latitude[Coord$Réplicas=='2'
],rownames(Coord)[Coord$Réplicas=='2'],col='yellow',cex=0.5,font=2)
text(Coord$Longitude[Coord$Réplicas=='3'],Coord$Latitude[Coord$Réplicas=='3'
],rownames(Coord)[Coord$Réplicas=='3'],col='blue',cex=0.5,font=2)
points(Coord$Longitude,Coord$Latitude-0.045,pch=20,cex=0.7)
text(c(41.5,41.3),c(21.7,20.6),c('RJ','ES'))
axis(1,xaxp=c(42.1,39.2,2),cex.axis=1)
axis(2,yaxp=c(23.9,20.3,4),cex.axis=1)
title(main='Bacia')
legend(40.2,23.5,c('Uma','Duas','Três'),pch=21,cex=1,pt.bg=c('red','yellow',
'blue'),bty='n',pt.cex=2,pt.lwd=0.6,title='Réplicas')
legend(39.8,23.5,c('Areia','Calcário','Lama'),pch=21,cex=1,pt.bg=c('lightyel
low','lightgray','lightgreen'),bty='n',pt.cex=2,pt.lwd=0.6,title='Faciologia
')
addlogo(N,px=c(40,39.8),py=c(21,20.8))
dev.off()
q('no')
-
MSc. Rodrigo Aluizio mailto:r.alui...@gmail.com
Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
[[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] perform subgroup meta-analysis and create forest plot displaying subgroups
Steven Lubitz schrieb: Hello, I'm using the rmeta package to perform a meta analysis using summary statistics rather than raw data, and would like to analyze the effects in three different subgroups of my data. Furthermore, I'd like to plot this on one forest plot, with corresponding summary weighted averages of the effects displayed beneath each subgroup. I am able to generate the subgroup analyses by simply performing 3 separate meta-analyses with the desired subset of data. However, I can't manage to plot everything on the same forest plot. Maybe I'm wrong but the 'forest'-function (package 'meta', http://cran.at.r-project.org/web/packages/meta/meta.pdf) should be able to do what you want. I guess you could be interested in the 'byvar' argument. Bernd __ 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] example of panel data in R
.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color:
#66; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
I'm studing about the panel data. Can i find a example of panel data in R? also
what kind of data file structure in reading this panel data? help me ^^
À̸§ : Á¤½ÂȯE-mail : jung6...@hanmail.netºÎ¼ : ¿¬¼¼´ëÇб³ »ó°æ´ëÇÐȸ»çÀüÈ :
Æѽº : À̵¿Åë½Å : 010-2301-0824ȨÆäÀÌÁö :
[[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] Changing factor to numeric
Dear Users, I have a variable in my dataset which is of type factor. But it actually contains numeric entries which like 5.735 4.759 . This is because the data was read from a CSV file into R and this variable contained other charaters which were not numeric. I have now dropped the records with the characters which are not numeric for this variable and want to change it to numeric srotage type. I have tried using as.numeric() function but it changes the values in the variable to what I think are the ranks of the individual values of the varible in the dataset. For example if 5.735 is the current content in the field, then the new object created by as.numeric will contain a value like 680 if the 5.735 was the highest value for the varible and the dataset had 680 records. How can I change the storage type without changing the contents of this variable in this case? Thanks for your consideration. -- Ojal John Owino P.O Box 230-80108 Kilifi, Kenya. Mobile:+254 728 095 710 [[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] foreign package install on Solaris 10 + R-2.7.1
Hello, I've been having trouble installing package spdep for R-2.7.1 on our Solaris 10 (sparc) server. Namely the two dependencies for this package do not install properly: foreign and maptools I understand that Solaris 10 may not be an officially supported platform but any help/feedback you can offer would be most appreciated. I've updated all packages currently installed on this version of R but the install of package foreign complains about an invalid priority field in the DESCRIPTION file. I've not had any issues with the other packages. I'm including our systemInfo() output here: == R version 2.7.1 (2008-06-23) sparc-sun-solaris2.10 locale: /en_CA.ISO8859-1/C/C/en_CA.ISO8859-1/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base And, I'm including the transcript from the package install attempt: == 1 /home/sjamal R R version 2.7.1 (2008-06-23) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. install.packages(foreign) Warning in install.packages(foreign) : argument 'lib' is missing: using '/home/sjamal/R/sparc-sun-solaris2.10-library /2.7' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://probability.ca/cran/src/contrib/foreign_0.8-33.tar.gz' Content type 'application/x-gzip' length 315463 bytes (308 Kb) opened URL == downloaded 308 Kb * Installing *source* package 'foreign' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ANSI C... none needed checking whether gcc -std=gnu99 accepts -Wno-long-long... yes checking how to run the C preprocessor... gcc -std=gnu99 -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking byteswap.h usability... no checking byteswap.h presence... no checking for byteswap.h... no checking for double... yes checking size of double... 8 checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 4 configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/swap_bytes.h config.status: creating src/var.h Error: Invalid DESCRIPTION file Invalid Priority field. Packages with priorities 'base' or 'recommended' or 'defunct-base' must already be known to R. See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted ERROR: installing package DESCRIPTION failed ** Removing '/home/sjamal/R/sparc-sun-solaris2.10-library/2.7/foreign' ** Restoring previous '/home/sjamal/R/sparc-sun-solaris2.10-library/2.7/foreign' The downloaded packages are in /tmp/RtmpkcXy1L/downloaded_packages Warning message: In install.packages(foreign) : installation of package 'foreign' had non-zero exit status I look forward to your insights. Thank you, Sarosh --- Sarosh Jamal Geographic Computing Specialist Department of Geography http://geog.utm.utoronto.ca Staff co-Chair, United Way Campaign http://www.utm.utoronto.ca/unitedway University of Toronto Mississauga sarosh.ja...@utoronto.ca 905.569.4497 __ 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: Customizing point-sizes with groups
Hello, I am creating a scatter-plot in lattice, and I would like to customize the size of each point so that some points are larger and others smaller. Here's a toy example: library(lattice); temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, cex = temp$cex, pch = 19); This works just fine if I create a straight xy-plot, without groups. However when I introduce groupings the cex argument specifies the point-size for the entire group. For example: xyplot(y ~ x, temp, cex = temp$cex, pch = 19, group = groups); Is it possible to combine per-spot sizing with groups in some way? One work-around is to manually specify all graphical parameters, but I thought there might be a better way than this: temp$col - rep(blue, 10); temp$col[temp$groups == B] - red; xyplot(y ~ x, temp, cex = temp$cex, pch = 19, col = temp$col); Any suggestions/advice is much appreciated! 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] Problem with capabilities() in R2-8.1
capabilities(iconv) does work in R 2.8.1 on Window (for me and many,
many otherss, as well as on the machine that ran 'make check'), so you
have done something to your installation. Most likely you have
somehow mixed it up with a much earliier version of R for which the
error message would have been true. so if you have any uch version
installed, please remove it. Then try starting R with --vanulla,
since you may hav ebeen picking up libraries containing packages from
earlier versions.
On Mon, 9 Mar 2009, Marcus, Jeffrey wrote:
I just installed R 2.8.1 on Windows XP. When I ran the source command,
I got the error:
Error in capabilities(iconv) :
1 argument passed to .Internal(capabilities) which requires 0
I looked at the code for source and it indeed has a call to
capabilities(iconv)
if (capabilities(iconv)) {
if (identical(encoding, unknown)) {
enc - utils::localeToCharset()
encoding - enc[length(enc)]
}
So then I ran capabilities itself:
capabilities(iconv)
Error in capabilities(iconv) :
1 argument passed to .Internal(capabilities) which requires 0
I made sure that I hadn't by accident aliased either source or
capabilities by doing
find(source)
find (capabilites)
and both came back with package::base.
Any help would be appreciated. Thanks.
That's only a partial test. searchpaths() will show where you loaded
capabiliites() from.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with capabilities() in R2-8.1
On Tue, 2009-03-10 at 06:50 +, Prof Brian Ripley wrote:
capabilities(iconv) does work in R 2.8.1 on Window (for me and many,
many otherss, as well as on the machine that ran 'make check'), so you
have done something to your installation. Most likely you have
somehow mixed it up with a much earliier version of R for which the
error message would have been true. so if you have any uch version
installed, please remove it. Then try starting R with --vanulla,
since you may hav ebeen picking up libraries containing packages from
earlier versions.
M. Vanulla. Arg
S.
On Mon, 9 Mar 2009, Marcus, Jeffrey wrote:
I just installed R 2.8.1 on Windows XP. When I ran the source command,
I got the error:
Error in capabilities(iconv) :
1 argument passed to .Internal(capabilities) which requires 0
I looked at the code for source and it indeed has a call to
capabilities(iconv)
if (capabilities(iconv)) {
if (identical(encoding, unknown)) {
enc - utils::localeToCharset()
encoding - enc[length(enc)]
}
So then I ran capabilities itself:
capabilities(iconv)
Error in capabilities(iconv) :
1 argument passed to .Internal(capabilities) which requires 0
I made sure that I hadn't by accident aliased either source or
capabilities by doing
find(source)
find (capabilites)
and both came back with package::base.
Any help would be appreciated. Thanks.
That's only a partial test. searchpaths() will show where you loaded
capabiliites() from.
--
Simon Blomberg, BSc (Hons), PhD, MAppStat.
Lecturer and Consultant Statistician
School of Biological Sciences
The University of Queensland
St. Lucia Queensland 4072
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
http://www.uq.edu.au/~uqsblomb
email: S.Blomberg1_at_uq.edu.au
Policies:
1. I will NOT analyse your data for you.
2. Your deadline is your problem.
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.
__
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] foreign package install on Solaris 10 + R-2.7.1
On Mon, 9 Mar 2009, Sarosh Jamal wrote: Hello, I've been having trouble installing package spdep for R-2.7.1 on our Solaris 10 (sparc) server. Namely the two dependencies for this package do not install properly: foreign and maptools I understand that Solaris 10 may not be an officially supported platform but any help/feedback you can offer would be most appreciated. It is a platform we test on. WHat is not supported is 2.7.1, so please update to at least 2.8.1 (as requested in the posting guide). Something is wrong with your R installation: 'foreign' should be known to R 2.7.1, *and* installed as part of the basic installation. So re-installing seems the best option, especially as an update is in order. I've updated all packages currently installed on this version of R but the install of package foreign complains about an invalid priority field in the DESCRIPTION file. I've not had any issues with the other packages. I'm including our systemInfo() output here: == R version 2.7.1 (2008-06-23) sparc-sun-solaris2.10 locale: /en_CA.ISO8859-1/C/C/en_CA.ISO8859-1/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base And, I'm including the transcript from the package install attempt: == 1 /home/sjamal R R version 2.7.1 (2008-06-23) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. install.packages(foreign) Warning in install.packages(foreign) : argument 'lib' is missing: using '/home/sjamal/R/sparc-sun-solaris2.10-library /2.7' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://probability.ca/cran/src/contrib/foreign_0.8-33.tar.gz' Content type 'application/x-gzip' length 315463 bytes (308 Kb) opened URL == downloaded 308 Kb * Installing *source* package 'foreign' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ANSI C... none needed checking whether gcc -std=gnu99 accepts -Wno-long-long... yes checking how to run the C preprocessor... gcc -std=gnu99 -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking byteswap.h usability... no checking byteswap.h presence... no checking for byteswap.h... no checking for double... yes checking size of double... 8 checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 4 configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/swap_bytes.h config.status: creating src/var.h Error: Invalid DESCRIPTION file Invalid Priority field. Packages with priorities 'base' or 'recommended' or 'defunct-base' must already be known to R. See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted ERROR: installing package DESCRIPTION failed ** Removing '/home/sjamal/R/sparc-sun-solaris2.10-library/2.7/foreign' ** Restoring previous '/home/sjamal/R/sparc-sun-solaris2.10-library/2.7/foreign' The downloaded packages are in /tmp/RtmpkcXy1L/downloaded_packages Warning message: In install.packages(foreign) : installation of package 'foreign' had non-zero exit status I look forward to your insights. Thank you, Sarosh --- Sarosh Jamal Geographic Computing Specialist Department of Geography http://geog.utm.utoronto.ca Staff co-Chair, United Way Campaign http://www.utm.utoronto.ca/unitedway University of Toronto Mississauga sarosh.ja...@utoronto.ca 905.569.4497 __ 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,
Re: [R] Changing factor to numeric
From ?factor: The interpretation of a factor depends on both the codes and the levels attribute. Be careful only to compare factors with the same set of levels (in the same order). In particular, as.numeric applied to a factor is meaningless, and may happen by implicit coercion. To transform a factor f to its original numeric values, as.numeric(levels(f))[f] is recommended and slightly more efficient than as.numeric(as.character(f)). Uwe Ligges ojal john owino wrote: Dear Users, I have a variable in my dataset which is of type factor. But it actually contains numeric entries which like 5.735 4.759 . This is because the data was read from a CSV file into R and this variable contained other charaters which were not numeric. I have now dropped the records with the characters which are not numeric for this variable and want to change it to numeric srotage type. I have tried using as.numeric() function but it changes the values in the variable to what I think are the ranks of the individual values of the varible in the dataset. For example if 5.735 is the current content in the field, then the new object created by as.numeric will contain a value like 680 if the 5.735 was the highest value for the varible and the dataset had 680 records. How can I change the storage type without changing the contents of this variable in this case? Thanks for your consideration. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with concatinating string while taking as a path of a file
See ?file.path Uwe Ligges Simon Blomberg wrote: Does this do what you want? paste(FPATH, Fname, sep=\\) Simon. On Tue, 2009-03-10 at 10:48 +0530, venkata kirankumar wrote: Hi all, I have a problem with concatinating strings while taking as a path here the problem is i have to take path as FPATH-D:\\Kiran and file name as Fname-FINDINGS.CSV and while I am reading this table I have to take path with using these two strings because in FPATH there is many files like findings.csv, and path will be D:\\Kiran\\FINDINGS.CSV here i tried with FPATH+\\+Fname, FPATH~\\~Fname , FPATH\\Fname and FPATH::\\::Fname but I am not able to get path like D:\\Kiran\\FINDINGS.CSV. can any one help me out of this problem. thanks in advance. [[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] nlme: problem with fitting logistic function
Douglas Bates bates at stat.wisc.edu writes: 3) Use lmer in lme4. Your mileage may vary, I could not find a speedup for my problems, but larger problem might give one. Did you mean nlmer in the lme4 package? If so, it may be worthwhile trying the development branch but that is not something for the faint-hearted. Thanks, Doug, for you comments. To be fair, I wrote these unordered thoughts to get you out of the snowhole :-) 4) Use C for the core function. This is very effective, and there is at least on example coming with nlme (was it SSlogist?). Do you think that evaluation of the model function takes a substantial portion of the computing time? I am asking for my interest, not because I think I know the answer. So, for example, have you profiled difficult nlme fits and found that the model function evaluation was expensive? No, I did not profile that function, but 8 years ago tried it once because at that time I thought it would help. Nowadays, I am more inclined to think that failure of nlme with a more complex model is a failure of the model, not of nlme; I don't have speed problems with my data. However, I remember that in a similar case with ode/lsoda, using c function made a factor of 20++, so I would have a look into it again if speed was a concern for me. Dieter __ 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] nlme: problem with fitting logistic function
Douglas Bates bates at stat.wisc.edu writes: 3) Use lmer in lme4. Your mileage may vary, I could not find a speedup for my problems, but larger problem might give one. Did you mean nlmer in the lme4 package? If so, it may be worthwhile trying the development branch but that is not something for the faint-hearted. Thanks, Doug, for you comments. To be fair, I wrote these unordered thoughts to get you out of the snowhole :-) 4) Use C for the core function. This is very effective, and there is at least on example coming with nlme (was it SSlogist?). Do you think that evaluation of the model function takes a substantial portion of the computing time? I am asking for my interest, not because I think I know the answer. So, for example, have you profiled difficult nlme fits and found that the model function evaluation was expensive? No, I did not profile that function, but 8 years ago tried it once because at that time I thought it would help. Nowadays, I am more inclined to think that failure of nlme with a more complex model is a failure of the model, not of nlme; I don't have speed problems with my data. However, I remember that in a similar case with ode/lsoda, using c function made a factor of 20++, so I would have a look into it again if speed was a concern for me. Dieter __ 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] Adding text to both grid and base graphs
Dear Dieter, The perfect solution; works a charm! Thanks! Rik -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dieter Menne Sent: 09 March 2009 18:06 To: r-h...@stat.math.ethz.ch Subject: Re: [R] Adding text to both grid and base graphs Rik Schoemaker RikSchoemaker at zonnet.nl writes: Unfortunately that doesn't help because it requires you to know beforehand what sort of graph you're generating. I want to be able to generate a graph (irrespective of the type) and then use a common process to label them so I don't have to think about which way I generated the graph to start with... Set a hook. http://finzi.psych.upenn.edu/R/Rhelp08/2009-February/188168.html Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R on netbooks et al?
Hi, For what it's worth, it's a trivial operation to replace the on-board 1Gb with a 2Gb module, which doesn't cost too much. Okay, being a bit demanding I also replaced the hard-disk with a 320 Gb one to harbour a dual boot ubuntu-eee / windows XP. But that does give a machine which is a worthy replacement of the once state-of-the art Acer Travelmate 800 I used to have. I happily run R and even virtual machines using VMWare. Truth be told, it being a netbook, you may want to rely on and connect to external computational resources for the real heavy stuff. Cheers, Tsjerk On Sun, Mar 8, 2009 at 7:20 PM, Ted Harding ted.hard...@manchester.ac.uk wrote: On 08-Mar-09 17:44:18, Douglas Bates wrote: On Sun, Mar 8, 2009 at 7:08 AM, Michael Dewey i...@aghmed.fsnet.co.uk wrote: At 08:47 05/03/2009, herrdittm...@yahoo.co.uk wrote: Dear useRs, With the rise of netbooks and 'lifestyle laptops I am tempted to get one of these to mainly run R on it. Processor power and hard disk space seem to be ok. What I wonder is the handling and feel with respect to R. Has anyone here installed or is running R on one of these, and if so, what is your experience? Would it be more of a nice looking gadget than a feasable platform to do some stats on? One issue is whether you wish to use Linux or Windows. If you do use Linux I would advise picking a netbook with one of the standard distributions. The early EEE PC had Xandros and dire warnings about using the Debian repositiories. In fact I had no problem despite a total lack of experience although I am not sure what will happy with the recent move to lenny. Because I have used Debian Linux and Debian-based distributions like Ubuntu for many years, I installed a eee-specific version of Ubuntu within a day or two of getting an ASUS eee pc1000. There are currently at least two versions of Ubuntu, easy peasy and eeebuntu, that are specific to the eee pc models. I started with easy peasy at the time it was called something else (Ubuntu eee?) and later switched to eeebuntu. In both cases packages for the latest versions of R from the Ubuntu package repository on CRAN worked flawlessly. I find the netbook to be very convenient. Having a 5 hour battery life and a weight of less than 3 pounds is wonderful. I teach all of my classes with it and even use it at home (attached to a monitor, USB keyboard and mouse and an external hard drive) in lieu of a desktop computer. (I have been eyeing the eee box covetously but have not yet convinced myself that I really need yet another computer). I develop R packages on it and don't really notice that it is under-powered by today's standards. Of course, when I started computing and even when I started working with the S language the memory capacity of computers was measured in kilobytes so the thought of only 1Gb of memory doesn't cause me to shriek in horror. Thanks for sharing your experiences, Doug. Given that devices like the EeePC are marketed in terms of less demanding users, it's good to know what it is like for a hard user. Further related comments would be welcome! I have to agree about the RAM issue too. My once-trusty old Sharp MZ-80B CP/M machine (early 1980s), with its 64KB and occupying a good 0.25 m^3 of physical space, would have to be replicated 2^14 = 16384 times over to give the same RAM (and occupy some 400 m^3 of space, say 7.4m x 7.4m x 7.4m, or about the size of my house). Now I have things on my desk, about the size of my thumb, with 8MB in each. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 08-Mar-09 Time: 18:20:45 -- 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. -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 __ 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] example of panel data in R
google: the plm package
-
cuncta stricte discussurus
-
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im
Auftrag von ???
Gesendet: Tuesday, March 10, 2009 1:32 AM
An: r-help@r-project.org
Betreff: [R] example of panel data in R
.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border:
#8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #66;
font-family: 'Courier New' , Monospace;background-color: #ff9933; } I'm studing
about the panel data. Can i find a example of panel data in R? also what kind
of data file structure in reading this panel data? help me ^^
@L8' : A$=BH/E-mail : jung6...@hanmail.net:N- : ?,4kGP13 ;s0f4kGPH8;g@|H- :
FQ=: : @L5?Ek=E : 010-2301-0824H(f...@lav :
[[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] mean reverting model: THANKS !
dear useRs (especially andrew and gabor), you have helped me a lot, the ar(1)/ornstein-uhlenbeck type is exactly it (0a1 is necessary). thank you, josuah __ 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] FW: Adding text to both grid and base graphs
Dear Dieter, The perfect solution; works a charm! Thanks! Rik -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dieter Menne Sent: 09 March 2009 18:06 To: r-h...@stat.math.ethz.ch Subject: Re: [R] Adding text to both grid and base graphs Rik Schoemaker RikSchoemaker at zonnet.nl writes: Unfortunately that doesn't help because it requires you to know beforehand what sort of graph you're generating. I want to be able to generate a graph (irrespective of the type) and then use a common process to label them so I don't have to think about which way I generated the graph to start with... Set a hook. http://finzi.psych.upenn.edu/R/Rhelp08/2009-February/188168.html Dieter __ 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] HAC corrected standard errors
Hi, I have a simple linear regression for which I want to obtain HAC corrected standard errors, since I have significant serial/auto correlation in my residuals, and also potential heteroskedasticity. Would anyone be able to direct me to the function that implements this in R? It's a basic question and I'm sure I'm missing something obvious here. I looked up this post: http://www.nabble.com/Re%3A-Moving-Window-regressions-with-corrections-for-Heteroscedasticity-and-Autocorrelations(HAC)-td6075371.html#a6075371 which recommended that I use the coeftest() function in package lmtest, but when I tried to assign an object: result - coeftest(regre, NeweyWest), where regre is an object of class lm, this returned an error. I'd be grateful for any advice, since I'm sure I'm making one of those simple bloopers. Thanks! Shruthi -- View this message in context: http://www.nabble.com/HAC-corrected-standard-errors-tp22430163p22430163.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] Changing factor to numeric
If the real problem is that R reads your data file and converts everything it can into factors try including stringsAsFactors=FALSE in your read.table (or similar) statement. I run into this often enough that I set it as an option (I think it's: options(stringsAsFactors=FALSE). Then you can do the conversion as needed. Using as.numeric(as.character(f)) often changes values (due to the whole factor/levels business). ... I also seem to remember read.table will let you pre-specify the data type of each column. Krzysztof Uwe Ligges wrote: From ?factor: The interpretation of a factor depends on both the codes and the levels attribute. Be careful only to compare factors with the same set of levels (in the same order). In particular, as.numeric applied to a factor is meaningless, and may happen by implicit coercion. To transform a factor f to its original numeric values, as.numeric(levels(f))[f] is recommended and slightly more efficient than as.numeric(as.character(f)). Uwe Ligges ojal john owino wrote: Dear Users, I have a variable in my dataset which is of type factor. But it actually contains numeric entries which like 5.735 4.759 . This is because the data was read from a CSV file into R and this variable contained other charaters which were not numeric. I have now dropped the records with the characters which are not numeric for this variable and want to change it to numeric srotage type. I have tried using as.numeric() function but it changes the values in the variable to what I think are the ranks of the individual values of the varible in the dataset. For example if 5.735 is the current content in the field, then the new object created by as.numeric will contain a value like 680 if the 5.735 was the highest value for the varible and the dataset had 680 records. How can I change the storage type without changing the contents of this variable in this case? Thanks for your consideration. __ 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. -- --- Krzysztof Sakrejda-Leavitt Organismic and Evolutionary Biology University of Massachusetts, Amherst 319 Morrill Science Center South 611 N. Pleasant Street Amherst, MA 01003 work #: 413-325-6555 email: sakre...@nsm.umass.edu __ 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] Lattice: Customizing point-sizes with groups
Try this: xyplot(y ~ x, temp, groups = groups, par.settings = list( superpose.symbol = list( cex = c(1, 3), pch = 19, col = c(blue, red See: str(trellis.par.get()) for other settings you might want to change. Also, you should drop the ; from all your scripts. HTH, --sundar On Mon, Mar 9, 2009 at 6:49 PM, Paul Boutros paul.bout...@utoronto.ca wrote: Hello, I am creating a scatter-plot in lattice, and I would like to customize the size of each point so that some points are larger and others smaller. Here's a toy example: library(lattice); temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, cex = temp$cex, pch = 19); This works just fine if I create a straight xy-plot, without groups. However when I introduce groupings the cex argument specifies the point-size for the entire group. For example: xyplot(y ~ x, temp, cex = temp$cex, pch = 19, group = groups); Is it possible to combine per-spot sizing with groups in some way? One work-around is to manually specify all graphical parameters, but I thought there might be a better way than this: temp$col - rep(blue, 10); temp$col[temp$groups == B] - red; xyplot(y ~ x, temp, cex = temp$cex, pch = 19, col = temp$col); Any suggestions/advice is much appreciated! 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. __ 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] popular R packages
Gabor Grothendieck wrote: R-Forge already has this but I don't think its used much. R-Forge does allow authors to opt out which seems sensible lest it deter potential authors from submitting packages. I think objective quality metrics are better than ratings, e.g. does package have a vignette, has package had a release within the last year, does package have free software license, etc. That would have the advantage that authors might react to increase their package's quality assessment resulting in an overall improvement in quality on CRAN that would result in more of a pro-active cycle whereas ratings are reactive and don't really encourage improvement. I beg to offer an alternative assessment of quality. Do users download the package and find it useful? If so, they are likely to download it again when it is updated. Much as I appreciate the convenience of vignettes, regular updates and the absolute latest GPL license, a perfectly dud package can have all of these things. If a package is downloaded upon first release and not much thereafter, the maintainer might be motivated to attend to its shortcomings of utility rather than incrementing the version number every month or so. Downloads, as many have pointed out, are not a direct assessment of quality, but if I saw a package that just kept getting downloaded, version after version, I would be much more likely to check it out myself and perhaps even write a review for Hadley's neat site. Which I will try to do tonight. 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] rcorr.cens Goodman-Kruskal gamma
Thanks to David and Frank for the suggestions. With a 2-dimensional input
rcorr.cens and John Baron's implementation works good. But I am not able to
calculate gamma for a multivariate matrix
example: columns=species; rows=releves; the numbers are BB-values (ordinal
scale; 13 but 3-1 is not necessarily 2)
K. ceratoides S. caucasica A. tibeticum
A13 11
A20 32
A31 10
A42 20
A50 32
B11 11
B24 31
I want to calculate a distance matrix with scale unit Goodman-Kruskals gamma
(instead of classical euclidean, bray curtis, manhattan etc.) which I can use
for hierachical cluster analysis (e.g. amap, vegan, cluster) in order to
compare the different releves.
Further suggestions would be greatly appreciated,
Thank you very much,
Kim
Original-Nachricht
Datum: Mon, 09 Mar 2009 13:27:29 -0500
Von: Frank E Harrell Jr f.harr...@vanderbilt.edu
An: David Winsemius dwinsem...@comcast.net
CC: Kim Vanselow vanse...@gmx.de, r-help@r-project.org
Betreff: Re: [R] rcorr.cens Goodman-Kruskal gamma
David Winsemius wrote:
I looked at the help page for rcorr.cens and was surprised that
function, designed for censored data and taking input as a Surv object,
was being considered for that purpose. This posting to r-help may be of
interest. John Baron offers a simple implementation that takes its input
as (x,y):
http://finzi.psych.upenn.edu/R/Rhelp02/archive/19749.html
goodman - function(x,y){
Rx - outer(x,x,function(u,v) sign(u-v))
Ry - outer(y,y,function(u,v) sign(u-v))
S1 - Rx*Ry
return(sum(S1)/sum(abs(S1)))}
I then read Frank's response to John and it's clear that my impression
regarding potential uses of rcorr.cens was too limited. Appears that you
could supply a y vector to the S argument and get more efficient
execution.
Yes rcorr.cens was designed to handle censored data but works fine with
uncensored Y. You may need so specify Surv(Y) but first try just Y. It
would be worth testing the execution speed of the two approaches.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
Dear r-helpers!
I want to classify my vegetation data with hierachical cluster analysis.
My Dataset consist of Abundance-Values (Braun-Blanquet ordinal scale; ranked)
for each plant species and relevé.
I found a lot of r-packages dealing with cluster analysis, but none of them is
able to calculate a distance measure for ranked data.
Podani recommends the use of Goodman and Kruskals' Gamma for the distance. I
found the function rcorr.cens (outx=true) of the Hmisc package which should do
it.
What I don't understand is how to define the input vectors x, y with my
vegetation dataset. The other thing how I can use the output of rcorr.cens for
a distance measure in the cluster analysis (e.g. in vegan or amap).
Any help would be greatly appreciated,
Thank you very much,
Kim
--
Computer Bild Tarifsieger! GMX FreeDSL - Telefonanschluss + DSL
für nur 17,95 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a
__
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] HAC corrected standard errors
sandwich package is what you want. Best 2009/3/10 Shruthi Jayaram shruthi.jayaram...@gmail.com: Hi, I have a simple linear regression for which I want to obtain HAC corrected standard errors, since I have significant serial/auto correlation in my residuals, and also potential heteroskedasticity. Would anyone be able to direct me to the function that implements this in R? It's a basic question and I'm sure I'm missing something obvious here. I looked up this post: http://www.nabble.com/Re%3A-Moving-Window-regressions-with-corrections-for-Heteroscedasticity-and-Autocorrelations(HAC)-td6075371.html#a6075371 which recommended that I use the coeftest() function in package lmtest, but when I tried to assign an object: result - coeftest(regre, NeweyWest), where regre is an object of class lm, this returned an error. I'd be grateful for any advice, since I'm sure I'm making one of those simple bloopers. Thanks! Shruthi -- View this message in context: http://www.nabble.com/HAC-corrected-standard-errors-tp22430163p22430163.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. -- HUANG Ronggui, Wincent Tel: (00852) 3442 3832 PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html A sociologist is someone who, when a beautiful women enters the room and everybody look at her, looks at everybody. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating an Excel file with multiple spreadsheets
On Mon, 09-Mar-2009 at 02:34PM -0400, Jorge Ivan Velez wrote: | DeaR all, | | I'd like to know how to create an Excel file with multiple | spreadsheets from R. I searched the help files and found [1] but it | is not what I want to do. If you're happy to limit yourself to distributing your excel file to people who have excel 2007 (or have the converters for the older versions of office), or with a manual step of opening it yourself in 2007 and saving-as in an older version, I have a script that utilises the xml format that Excel now accepts. It's a bit ugly as it's got lots of stuff specific to my organisation, but if you want it can be obtained from http://bioinformatics.cancerresearchuk.org/cms/index.php?page=gpk-resources I really should contact the authors of the r/excel packages to see if any of them would want a cleaned up version of this. Regards - Gavin [[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] problem with creating webserver
Hi all, I am not able to built a webservice with using R-Project is there any package I have to import while building webservice my problem here is I installed in one server and while I am working in another server i have to pass a request to the server where r-project is installed and I have to execute the function what ever I am running in in present server for that i have to write a webservice function which calls the server having r-project can any one help me out to get solved this problem. thanks in advance [[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] Install JRI?
Hi all, Who can help me to install JRI I downloaed the file JRI_0.3-6.tar and although I read the documentation I don't know what to do now. I use Windows XP, Java 1.5.0_17 and R 2.8.1. Thanks for your response, Max -- View this message in context: http://www.nabble.com/Install-JRI--tp22430947p22430947.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] Interpreting GLM coefficients
Thank you very much! It helps a lot. You are right about the NA´s in the coefficients, the model needs some simplification. Thank you again. --- Pablo Pita Orduna Grupo de Recursos Marinos y Pesquerías. Universidade de A Coruña. Campus da Zapateira s/n. E-15071. A Coruña, Spain. Tel. +34(981) 167000 ext. 2204 Fax. +34(981) 167065. www.fismare.net/verdeprofundo www.recursosmarinos.net - Original Message - From: joris meys To: Pablo Pita Orduna Cc: r-help@r-project.org ; jfre...@udc.es ; ppitaord...@gmail.com Sent: Saturday, March 07, 2009 12:28 AM Subject: Re: [R] Interpreting GLM coefficients One thing I notice immediately is a number of NA values for your coefficients. If I were you, I would try a model with less parameters, and use the anova() function to compare models, to see if the extra terms really improve the model. e.g. fit1 - glm(Y~X1+X2+X3,...) fit2 - glm(Y~X1+X2+X3+X1:X2,...) anova(fit1, fit2, test=F) If you checked all these, understanding the interaction terms will be most easy if you normalized your numeric data before the analysis. For the interpretations, you just fill in some values to get an idea. For example : given the model : Y= a+b1*X1+b2*X2+b3*X1*X2 Say X1 and X2 are numeric : interpretation of the main term : Y increases with b2 for an increase of 1 unit in X2, given X1 is average. interpretation of the interaction term : For an X1 value of n units from the mean, X2 increases with b2+n*b3 (n is negative when value is lower than the mean). In a Y ~ X2 plot, you can make this visible by plotting 3 different functions : one for a low X1 value, one for an average X1 value and one for a high X1 value. This gives you an indication of the effect of X1 on X2. for an interaction between a categorical terms or a categorical and a numerical, you follow exact the same reasoning, but keep in mind that the reference level represents a 0, and the mentioned level represents a 1. Fill in the values in the equation, and you can understand the meaning of the terms. Then again, you can plot a seperate function Y~X1 for every level of a certain factor. This isn't a straight answer on your question, but I'm afraid there is none. I hope this helps you with building your model. Kind regards. Joris On Fri, Mar 6, 2009 at 11:04 PM, Pablo Pita Orduna pp...@udc.es wrote: Hi all, I´m fitting GLM´s and I can´t interprete the coefficients when I run a model with interaction terms. When I run the simpliest model there is no problem: Model1-glm (Fishes ~ Year + I(Year^2) + Kind.Geographic + Kind.Fishers + Zone.2 + Hours + Fishers + Month, family = poisson(log)) # Fishes, Year, Hours, and Fishers are numeric, Kind.Geographic, Kind.Fishers, Zone.2 and Month are factors with 4, 3, 5 and 12 levels respectively. Model1$coefficients (whith Helmert contrasts): (Intercept) Year IYear^2 Kind.Geographic1 Kind.Geographic2 Kind.Geographic3Kind.Fishers1Kind.Fishers2 Zone.21 Zone.22 Zone.23 Zone.24 -4.416915e+02 4.758455e-01-1.270986e-04-5.436199e-01 -1.068809e-01-1.498580e-01 2.958462e-01 1.316589e-01 -1.328204e-01-1.605802e-01 5.281869e-03 7.422885e-02 Hours Fishers Month1 Month2 Month3 Month4 Month5 Month6 Month7 Month8 Month9 Month10 9.772076e-02-2.709955e-03-1.586887e-01-1.887837e-02 -5.183241e-03 5.870942e-02 7.075386e-02 2.061223e-02 7.372268e-03-1.204835e-02-5.047994e-03 2.441498e-02 Month11 -5.665261e-03 So I can write, for example: y = -4.416915e+02 + -1.270986e-04*x^2 + 4.758455e-01*x # And add this function to a plot(Year,Fishes). My problem is to understand the coefficients for the model with interaction: Model2-glm(Fishes ~ Year + I(Year^2) + Kind.Geographic + Kind.Fishers + Zone.2 + Hours + Fishers + Month + Year:Kind.Geographic + Year:Kind.Fishers + Year:Zone.2 + Year:Hours + Year:Fishers + Year:Month + Kind.Geographic:Hours + Kind.Fishers:Hours + Zone.2:Hours + Hours:Fishers + Hours:Month +Kind.Geographic:Fishers + Zone.2:Fishers + Fishers:Month , poisson (log)) Model2$coefficients (with Helmert contrast): (Intercept) YearI(Year^2) Kind.Geographic1 Kind.Geographic2 Kind.Geographic3 Kind.Fishers1Kind.Fishers2 1.641473e+03-1.748703e+00 4.664752e-04 -6.721427e+00 1.856033e+01 -3.762727e-02 2.903564e+01 9.022858e+01 Zone.21
[R] North Arrow (.png file) on a Map
Hi list.
I would like to know how do I insert a North arrow, stored as a png file in
my computer, in a map? I found lots of post asking similar things, one of
them mentioned the pixmap package. The map was done using map() and
shapefiles (the code is below). Im using the pixmap () and addlogo()
functions. Well I can import the png with pixmap() function (I guess, once
theres no error message), but I cant put It on the map, I got an error
message telling me that:
Error at t(x...@index[nrow(x...@index):1, , drop = FALSE]) :
index out of limits
Well I tried changing coordinates but I always got the same result. How do I
do this correctly? Is there a better way?
Thanks for the help and attention.
Here is the complete map script:
library(RODBC)
library(maps)
library(mapdata)
library(maptools)
library(pixmap)
#Carregar Coordenadas e dados dos Pontos Amostrais
Dados-odbcConnectExcel('Campos.xls',readOnly=T)
Coord-sqlFetch(Dados,'CoordMed',colnames=F,rownames='Ponto')
odbcClose(Dados)
N-pixmap('Norte.png',nrow=166,ncol=113)
# Carregar pontos e shapes
Batimetria-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontol
ogia/Campos/ShapeFiles/Batimetria_BC.shp')
Estados-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontologi
a/Campos/ShapeFiles/Estados_Sudeste.shp')
Faciologia-readShapeSpatial('C:/Users/Rodrigo/Documents/UFPR/Micropaleontol
ogia/Campos/ShapeFiles/Faciologia_BC.shp')
# Mapa com os Pontos da Bacia
postscript('MapaCampos.eps',paper='special',onefile=F,horizontal=F,width=3.5
,height=4.5,bg='white',pointsize=3)
par(mar=c(3,2,2,0))
map('worldHires','brazil',ylim=c(23.9,20.3),xlim=c(42.1,39.2),type='n')
plot(Faciologia,ylab='',xlab='',col=c('lightgreen','lightgreen','lightgreen'
,'lightgreen','lightgreen','lightgray','lightgray','lightgray','lightgray','
lightgray','lightgray','lightgray','lightgray','lightgray','lightgray','ligh
tgray','lightgray','lightgray','lightgray','lightgray','lightgray','lightyel
low','lightyellow','lightyellow'),add=T,lwd=0.5,border=0)
plot(Batimetria,ylab='',xlab='',col='darkgray',lty='solid',lwd=0.2,add=T)
plot(Estados,ylab='',xlab='',lty='solid',add=T,lwd=0.8)
text(Coord$Longitude[Coord$Réplicas=='1'],Coord$Latitude[Coord$Réplicas=='1'
],rownames(Coord)[Coord$Réplicas=='1'],col='red',cex=0.5,font=2)
text(Coord$Longitude[Coord$Réplicas=='2'],Coord$Latitude[Coord$Réplicas=='2'
],rownames(Coord)[Coord$Réplicas=='2'],col='yellow',cex=0.5,font=2)
text(Coord$Longitude[Coord$Réplicas=='3'],Coord$Latitude[Coord$Réplicas=='3'
],rownames(Coord)[Coord$Réplicas=='3'],col='blue',cex=0.5,font=2)
points(Coord$Longitude,Coord$Latitude-0.045,pch=20,cex=0.7)
text(c(41.5,41.3),c(21.7,20.6),c('RJ','ES'))
axis(1,xaxp=c(42.1,39.2,2),cex.axis=1)
axis(2,yaxp=c(23.9,20.3,4),cex.axis=1)
title(main='Bacia')
legend(40.2,23.5,c('Uma','Duas','Três'),pch=21,cex=1,pt.bg=c('red','yellow',
'blue'),bty='n',pt.cex=2,pt.lwd=0.6,title='Réplicas')
legend(39.8,23.5,c('Areia','Calcário','Lama'),pch=21,cex=1,pt.bg=c('lightyel
low','lightgray','lightgreen'),bty='n',pt.cex=2,pt.lwd=0.6,title='Faciologia
')
addlogo(N,px=c(40,39.8),py=c(21,20.8))
dev.off()
q('no')
-
MSc. Rodrigo Aluizio mailto:r.alui...@gmail.com
Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
[[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] Is there any method to identify the distribution of a given dataset?
Thanks for everybody, I feel shame after I posting the above message because I found there is a tutorial Fitting Distributions with R on http://cran.ii.uib.no/ It's seems not everybody check the dataset's distribution. Bert Gunter wrote: Below. Brief summary is: You **need** to consult a statistician. You know far too little statistics to do statistical analysis on your own. -- Bert Bert Gunter Genentech Nonclinical Biostatistics 650-467-7374 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of GreenBrower Sent: Monday, March 09, 2009 9:12 AM To: r-help@r-project.org Subject: [R] Is there any method to identify the distribution of a given dataset? It's important to identify the distribution of a dataset before do analysis and inference. -- Not necessarily. Indeed, often not. Is there any method to identify the distribution of a given dataset? -- Yes. It's discrete. The question you mean to ask is : How do I choose a suitable model for my data? For example, I want to identify a dataset belong to normal of poisson distribution, how can I do that? -- Whew! That you even ask this question is why you need to work with someone who knows more about statistics. No insult intended. It's kind of like me asking a biologist what's the difference between a mitochondrion and a nucleus. If I know so little about cell biology that I must ask, I probably need to work with someone more knowledgeable. -- View this message in context: http://www.nabble.com/Is-there-any-method-to-identify-the-distribution-of-a- given-dataset--tp22413674p22413674.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. -- View this message in context: http://www.nabble.com/Is-there-any-method-to-identify-the-distribution-of-a-given-dataset--tp22413674p22430437.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R-question
Hello, Im a french student in Master level Statistics and Econometrics . Now Im in training for a marketing firm. I dont find the information about the capacity of R . Can you tell me how much lignes and colones can R manipulates? Can I work with a data of 2 milions lignes? When I asked M.Maechler , he advices me to ask you about this. Thank you very much. Date: Sun, 8 Mar 2009 20:03:02 +0100 Subject: Re: Hello From: mmaech...@gmail.com To: chelliguetha...@hotmail.com Dear M. Thabet Chelligue, please do ask such questions on one of the public R mailing lists; typically 'R-help' is perfect. -- http://stat.ethz.ch/mailman/listinfo/r-help On Fri, Mar 6, 2009 at 17:05, thabet chelligue chelliguetha...@hotmail.com wrote: Hello, Im a french student in Master level Statistics and Econometrics . Now Im in training for a marketing firm. I dont find the information about the capacity of R . Can you respond me how much lignes and colones can R manipulates? Can I work with a data of 2 milions lignes? Thank you . Découvrez toutes les possibilités de communication avec vos proches _ [[elided Hotmail spam]] [[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] understanding the output from survival analysis
Ullrika Sahlin ullrika.sahlin at ekol.lu.se writes: Why do I get different sign of the coefficients of covariates when I run the semi-parametric proportional hazard model (coxph) compared to the parametric proportional hazard model (survreg)? Anyone with experience in extracting information from survreg to make predictions are free to contact me. Cheers, Ullrika coxph fits a proportional hazards model. survreg fits an accelerated failure time model. These are parametrized differently. In the first, a higher linear predictor means greater hazard (i.e., shorter lifetime). In the second, a higher linear predictor means greater expected (log) lifetime. Consult an introductory survival text such as Klein and Moeschberger for more on these types of model. The Design library may help you with predictions. Chris __ 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-question
Let's assume that you are running on a system with 2GB of memory. All of R's data is held in memory and I would suggest that no single object have more that 25% of memory. That would suggest that 500MB for a single object would be a reasonable limit. If you are working with something like 2M rows of numeric data (each element takes 8 bytes), then you should be able to handle about 32 columns in the matrix without much trouble. If you have a 64-bit version of R, then the limit is how much you want to spend on memory. On Tue, Mar 10, 2009 at 7:12 AM, thabet chelligue chelliguetha...@hotmail.com wrote: Hello, I’m a french student in Master level “Statistics and Econometrics” . Now I’m in training for a marketing firm. I don’t find the information about the capacity of R . Can you tell me how much lignes and colones can R manipulates? Can I work with a data of 2 milions lignes? When I asked M.Maechler , he advices me to ask you about this. Thank you very much. Date: Sun, 8 Mar 2009 20:03:02 +0100 Subject: Re: Hello From: mmaech...@gmail.com To: chelliguetha...@hotmail.com Dear M. Thabet Chelligue, please do ask such questions on one of the public R mailing lists; typically 'R-help' is perfect. -- http://stat.ethz.ch/mailman/listinfo/r-help On Fri, Mar 6, 2009 at 17:05, thabet chelligue chelliguetha...@hotmail.com wrote: Hello, I’m a french student in Master level “Statistics and Econometrics” . Now I’m in training for a marketing firm. I don’t find the information about the capacity of R . Can you respond me how much lignes and colones can R manipulates? Can I work with a data of 2 milions lignes? Thank you . Découvrez toutes les possibilités de communication avec vos proches _ [[elided Hotmail spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] popular R packages
On Tue, Mar 10, 2009 at 6:14 AM, Jim Lemon j...@bitwrit.com.au wrote: Gabor Grothendieck wrote: R-Forge already has this but I don't think its used much. R-Forge does allow authors to opt out which seems sensible lest it deter potential authors from submitting packages. I think objective quality metrics are better than ratings, e.g. does package have a vignette, has package had a release within the last year, does package have free software license, etc. That would have the advantage that authors might react to increase their package's quality assessment resulting in an overall improvement in quality on CRAN that would result in more of a pro-active cycle whereas ratings are reactive and don't really encourage improvement. I beg to offer an alternative assessment of quality. Do users download the package and find it useful? If so, they are likely to download it again when it is updated. I was referring to motivating authors, not users, so that CRAN improves. Much as I appreciate the convenience of vignettes, regular updates and the absolute latest GPL license, a perfectly dud package can have all of these things. If a package is downloaded upon first release and These are nothing but the usual FUD against quality improvement, i.e. the quality metrics are not measuring what you want but the fact is that quality metrics can work and have had huge successes. Also I think objective measures would be more accepted by authors than ratings. No one is going to be put off that their package has no vignette when obviously it doesn't and the authors are free to add one and instantly improve their package's rating. not much thereafter, the maintainer might be motivated to attend to its shortcomings of utility rather than incrementing the version number every month or so. Downloads, as many have pointed out, are not a direct assessment of quality, but if I saw a package that just kept getting downloaded, version after version, I would be much more likely to check it out myself and perhaps even write a review for Hadley's neat site. Which I will try to do tonight. I was arguing for objective metrics rather than ratings. Downloading is not a rating but is objective although there are measurement problems as has been pointed out. Also, the worst feature is that it does not react to changes in quality very quickly making it anti-motivating. __ 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] rcorr.cens Goodman-Kruskal gamma
Kim Vanselow wrote:
Thanks to David and Frank for the suggestions. With a 2-dimensional input
rcorr.cens and John Baron's implementation works good. But I am not able to
calculate gamma for a multivariate matrix
example: columns=species; rows=releves; the numbers are BB-values (ordinal scale;
13 but 3-1 is not necessarily 2)
K. ceratoides S. caucasica A. tibeticum
A13 11
A20 32
A31 10
A42 20
A50 32
B11 11
B24 31
I want to calculate a distance matrix with scale unit Goodman-Kruskals gamma
(instead of classical euclidean, bray curtis, manhattan etc.) which I can use for
hierachical cluster analysis (e.g. amap, vegan, cluster) in order to compare the
different releves.
Further suggestions would be greatly appreciated,
Thank you very much,
Kim
Original-Nachricht
Datum: Mon, 09 Mar 2009 13:27:29 -0500
Von: Frank E Harrell Jr f.harr...@vanderbilt.edu
An: David Winsemius dwinsem...@comcast.net
CC: Kim Vanselow vanse...@gmx.de, r-help@r-project.org
Betreff: Re: [R] rcorr.cens Goodman-Kruskal gamma
David Winsemius wrote:
I looked at the help page for rcorr.cens and was surprised that
function, designed for censored data and taking input as a Surv object,
was being considered for that purpose. This posting to r-help may be of
interest. John Baron offers a simple implementation that takes its input
as (x,y):
http://finzi.psych.upenn.edu/R/Rhelp02/archive/19749.html
goodman - function(x,y){
Rx - outer(x,x,function(u,v) sign(u-v))
Ry - outer(y,y,function(u,v) sign(u-v))
S1 - Rx*Ry
return(sum(S1)/sum(abs(S1)))}
I then read Frank's response to John and it's clear that my impression
regarding potential uses of rcorr.cens was too limited. Appears that you
could supply a y vector to the S argument and get more efficient
execution.
Yes rcorr.cens was designed to handle censored data but works fine with
uncensored Y. You may need so specify Surv(Y) but first try just Y. It
would be worth testing the execution speed of the two approaches.
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
Dear r-helpers!
I want to classify my vegetation data with hierachical cluster analysis.
My Dataset consist of Abundance-Values (Braun-Blanquet ordinal scale; ranked)
for each plant species and relevé.
I found a lot of r-packages dealing with cluster analysis, but none of them is
able to calculate a distance measure for ranked data.
Podani recommends the use of Goodman and Kruskals' Gamma for the distance. I
found the function rcorr.cens (outx=true) of the Hmisc package which should do
it.
What I don't understand is how to define the input vectors x, y with my
vegetation dataset. The other thing how I can use the output of rcorr.cens for
a distance measure in the cluster analysis (e.g. in vegan or amap).
Any help would be greatly appreciated,
Thank you very much,
Kim
A function related to that is Hmisc's varclus function which will use
Spearman, Pearson, or Hoeffding indexes for similarity measures.
Frank
--
Frank E Harrell Jr Professor and Chair School 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] popular R packages
Gabor Grothendieck wrote: On Tue, Mar 10, 2009 at 6:14 AM, Jim Lemon j...@bitwrit.com.au wrote: Gabor Grothendieck wrote: R-Forge already has this but I don't think its used much. R-Forge does allow authors to opt out which seems sensible lest it deter potential authors from submitting packages. I think objective quality metrics are better than ratings, e.g. does package have a vignette, has package had a release within the last year, does package have free software license, etc. That would have the advantage that authors might react to increase their package's quality assessment resulting in an overall improvement in quality on CRAN that would result in more of a pro-active cycle whereas ratings are reactive and don't really encourage improvement. I beg to offer an alternative assessment of quality. Do users download the package and find it useful? If so, they are likely to download it again when it is updated. I was referring to motivating authors, not users, so that CRAN improves. Much as I appreciate the convenience of vignettes, regular updates and the absolute latest GPL license, a perfectly dud package can have all of these things. If a package is downloaded upon first release and These are nothing but the usual FUD against quality improvement, i.e. the quality metrics are not measuring what you want but the fact is that quality metrics can work and have had huge successes. Also I think objective measures would be more accepted by authors than ratings. No one is going to be put off that their package has no vignette when obviously it doesn't and the authors are free to add one and instantly improve their package's rating. not much thereafter, the maintainer might be motivated to attend to its shortcomings of utility rather than incrementing the version number every month or so. Downloads, as many have pointed out, are not a direct assessment of quality, but if I saw a package that just kept getting downloaded, version after version, I would be much more likely to check it out myself and perhaps even write a review for Hadley's neat site. Which I will try to do tonight. I was arguing for objective metrics rather than ratings. Downloading is not a rating but is objective although there are measurement problems as has been pointed out. Also, the worst feature is that it does not react to changes in quality very quickly making it anti-motivating. Gabor I think your approach will have more payoff in the long run. I would suggest one other metric: the number of lines of code in the 'examples' section of all the package's help files. Frank -- Frank E Harrell Jr Professor and Chair School 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.
[R] Course - March/April ** R / Splus ** course in New York City and San Francisco*** by XLSolutions Corp
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce our*** R/Splus Fundamentals and Programming Techniques and R Advanced Programming***courses at USA locations for March - April 2009. * New York City ** March 19-20, 2009 * San Francisco ** April 23-24, 2009 R/Splus Fundamentals and Programming Techniques http://www.xlsolutions-corp.com/rplus.asp Looking for R/Splus Advanced Programming ? http://www.xlsolutions-corp.com/rplus.asp * San Francisco ** April 27-28, 2009 * New York City ** April 20-21, 2009 Ask for group discount and reserve your seat Now - Earlybird Rates. Payment due after the class! Email Sue Turner: s...@xlsolutions-corp.com Phone: 206-686-1578 Please let us know if you and your colleagues are interested in this class to take advantage of group discount. Register now to secure your seat! Cheers, Elvis Miller, PhD Manager Training. XLSolutions Corporation 206 686 1578 www.xlsolutions-corp.com el...@xlsolutions-corp.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] find the important inputs to the neural network model in nnet package
Hi, I have a binary variable and many explanatory variables and I want to use the package nnet to model these data, (instead of logistic regression). I want to find the more effective variables (inputs to the network) in the neural network model. how can I do this? thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simple question beginner
Hi there, I am beginner in R and I have some basic question. Suppose I run a common procedure such as a t test or cox model like below: out-coxph( Surv(tstart,tstop, death1) ~ x1+x1:log(tstop+1) , test1,method=c(breslow)) Which yields the following result: Call: coxph(formula = Surv(tstart, tstop, death1) ~ x1 + x1:log(tstop + 1), data = test1, method = c(breslow)) coef exp(coef) se(coef) z p x1 -9.58 6.89e-05 6.83 -1.40 0.16 x1:log(tstop + 1) 6.90 9.93e+02 5.63 1.23 0.22 Likelihood ratio test=2.97 on 2 df, p=0.226 n= 120 Now I simply want to create an array (let a) with the coefficients. I.e. I want a-c(-9.58, 6.90) Generally how can take the elements I want from the output matrix above for further manipulation? Thanks in advance for any answer!! ___ ×ñçóéìïðïéåßôå Yahoo!; ÂáñåèÞêáôå ôá åíï÷ëçôéêÜ ìçíýìáôá (spam); Ôï Yahoo! Mail äéáèÝôåé ôçí êáëýôåñç äõíáôÞ ðñïóôáóßá êáôÜ ôùí åíï÷ëçôéêþí ìçíõìÜôùí http://login.yahoo.com/config/mail?.intl=gr [[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] find the important inputs to the neural network model in nnet package
One thought is to train the net and obtain a performance measure on a testing corpus. Next, for each input, run the testing corpus again, but zero all values for that input and obtain a measure of performance. Zeroing an important node will hurt performance more than zeroing an unimportant node. On Tue, Mar 10, 2009 at 9:41 AM, abbas tavassoli tavassoli...@yahoo.com wrote: Hi, I have a binary variable and many explanatory variables and I want to use the package nnet to model these data, (instead of logistic regression). I want to find the more effective variables (inputs to the network) in the neural network model. how can I do this? 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. -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University Looking to arrange a meeting? Check my public calendar: http://tinyurl.com/mikes-public-calendar ~ Certainty is folly... I think. ~ __ 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] simple question beginner
names() is a great function for finding out how to get info from objects of unknown structure, so try: names(out) 2009/3/10 Λεωνίδας Μπαντής bleonida...@yahoo.gr: Hi there, I am beginner in R and I have some basic question. Suppose I run a common procedure such as a t test or cox model like below: out-coxph( Surv(tstart,tstop, death1) ~ x1+x1:log(tstop+1) , test1,method=c(breslow)) Which yields the following result: Call: coxph(formula = Surv(tstart, tstop, death1) ~ x1 + x1:log(tstop + 1), data = test1, method = c(breslow)) coef exp(coef) se(coef) z p x1 -9.58 6.89e-05 6.83 -1.40 0.16 x1:log(tstop + 1) 6.90 9.93e+02 5.63 1.23 0.22 Likelihood ratio test=2.97 on 2 df, p=0.226 n= 120 Now I simply want to create an array (let a) with the coefficients. I.e. I want a-c(-9.58, 6.90) Generally how can take the elements I want from the output matrix above for further manipulation? Thanks in advance for any answer!! ___ ×ñçóéìïðïéåßôå Yahoo!; ÂáñåèÞêáôå ôá åíï÷ëçôéêÜ ìçíýìáôá (spam); Ôï Yahoo! Mail äéáèÝôåé ôçí êáëýôåñç äõíáôÞ ðñïóôáóßá êáôÜ ôùí åíï÷ëçôéêþí ìçíõìÜôùí http://login.yahoo.com/config/mail?.intl=gr [[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. -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University Looking to arrange a meeting? Check my public calendar: http://tinyurl.com/mikes-public-calendar ~ Certainty is folly... I think. ~ __ 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] Changing factor to numeric
Try:
as.numeric(as.character(x))
I usually define the following for this purpose:
factor.to.number=function(x){
as.numeric(as.character(x))
}
On Tue, Mar 10, 2009 at 2:25 AM, ojal john owino
ojal.johnow...@googlemail.com wrote:
Dear Users,
I have a variable in my dataset which is of type factor. But it actually
contains numeric entries which like 5.735 4.759 . This is because the
data was read from a CSV file into R and this variable contained other
charaters which were not numeric. I have now dropped the records with the
characters which are not numeric for this variable and want to change it to
numeric srotage type.
I have tried using as.numeric() function but it changes the values in the
variable to what I think are the ranks of the individual values of the
varible in the dataset. For example if 5.735 is the current content in the
field, then the new object created by as.numeric will contain a value like
680 if the 5.735 was the highest value for the varible and the dataset had
680 records.
How can I change the storage type without changing the contents of this
variable in this case?
Thanks for your consideration.
--
Ojal John Owino
P.O Box 230-80108
Kilifi, Kenya.
Mobile:+254 728 095 710
[[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.
--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
Looking to arrange a meeting? Check my public calendar:
http://tinyurl.com/mikes-public-calendar
~ Certainty is folly... I think. ~
__
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] Changing factor to numeric
Hi Ojal, I don't know why it happens, but try as.numeric(as.character(XXX)) Good luck miltinho astronauta brazil On Tue, Mar 10, 2009 at 1:25 AM, ojal john owino ojal.johnow...@googlemail.com wrote: Dear Users, I have a variable in my dataset which is of type factor. But it actually contains numeric entries which like 5.735 4.759 . This is because the data was read from a CSV file into R and this variable contained other charaters which were not numeric. I have now dropped the records with the characters which are not numeric for this variable and want to change it to numeric srotage type. I have tried using as.numeric() function but it changes the values in the variable to what I think are the ranks of the individual values of the varible in the dataset. For example if 5.735 is the current content in the field, then the new object created by as.numeric will contain a value like 680 if the 5.735 was the highest value for the varible and the dataset had 680 records. How can I change the storage type without changing the contents of this variable in this case? Thanks for your consideration. -- Ojal John Owino P.O Box 230-80108 Kilifi, Kenya. Mobile:+254 728 095 710 [[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] Changing factor to numeric
If you don't need any factors use read.csv(...whatever..., as.is = TRUE) and then as.numeric will work. On Tue, Mar 10, 2009 at 1:25 AM, ojal john owino ojal.johnow...@googlemail.com wrote: Dear Users, I have a variable in my dataset which is of type factor. But it actually contains numeric entries which like 5.735 4.759 . This is because the data was read from a CSV file into R and this variable contained other charaters which were not numeric. I have now dropped the records with the characters which are not numeric for this variable and want to change it to numeric srotage type. I have tried using as.numeric() function but it changes the values in the variable to what I think are the ranks of the individual values of the varible in the dataset. For example if 5.735 is the current content in the field, then the new object created by as.numeric will contain a value like 680 if the 5.735 was the highest value for the varible and the dataset had 680 records. How can I change the storage type without changing the contents of this variable in this case? Thanks for your consideration. -- Ojal John Owino P.O Box 230-80108 Kilifi, Kenya. Mobile:+254 728 095 710 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: simple question beginner
Hi r-help-boun...@r-project.org napsal dne 10.03.2009 12:21:38: Hi there, I am beginner in R and I have some basic question. Suppose I run a common procedure such as a t test or cox model like below: out-coxph( Surv(tstart,tstop, death1) ~ x1+x1:log(tstop+1) , test1,method=c (breslow)) Which yields the following result: Call: coxph(formula = Surv(tstart, tstop, death1) ~ x1 + x1:log(tstop + 1), data = test1, method = c(breslow)) coef exp(coef) se(coef) zp x1-9.58 6.89e-05 6.83 -1.40 0.16 x1:log(tstop + 1) 6.90 9.93e+02 5.63 1.23 0.22 Likelihood ratio test=2.97 on 2 df, p=0.226 n= 120 Now I simply want to create an array (let a) with the coefficients. I.e. I want Most probably coef will work here If you had tried help.search ??coefficients you would find several appropriate items. Besides str(object) is also a good starting point for inspection of any object. Regards Petr a-c(-9.58, 6.90) Generally how can take the elements I want from the output matrix above for further manipulation? Thanks in advance for any answer!! ___ ×ńçóéěďđďéĺßôĺ Yahoo!; ÂáńĺčŢęáôĺ ôá ĺíď÷ëçôéęÜ ěçíýěáôá (spam); Ôď Yahoo! Mail äéáčÝôĺé ôçí ęáëýôĺńç äőíáôŢ đńďóôáóßá ęáôÜ ôůí ĺíď÷ëçôéęţí ěçíőěÜôůí http://login.yahoo.com/config/mail?.intl=gr [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using chm help files under linux
Hi, Chm (compiled help) is a microsoft invention. It's the default help system under windows, but not so under linux. I found that (at times) I like better how chm help looks. Since there are chm viewers under linux, using chm help files should be possible. Has anybody tried to set R so it opens chm by default? I'm sure there's some flag or Rprofile var that could get this done. Thanks, -- -Jose -- Jose Quesada, PhD http://josequesada.name __ 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] understanding the output from survival analysis
Why do I get different sign of the coefficients of covariates when I run the semi-parametric proportional hazard model (coxph) compared to the parametric proportional hazard model (survreg)? Survreg models the time till death, a postive coefficient -- a longer time. Coxph models the death rate, a positive coefficient -- higher death rate. So in the first a positive is good, in the second it is bad. Anyone with experience in extracting information form survreg to make predictions are free to contact me. Commonly one would use predict(fit) to get predictions. There are several options. Terry Therneau __ 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] reliability, scale scores in the psych package
Dear Professor Revelle and R-helpers, This is a two-part question: the first part is general, and the second is specific to the psych package. First question: In the past I've constructed composite variables from questionnaire data by using rowMeans(), and then correlating items with the scale using cor() as an informal check for bad items. Over the weekend I decided to take a look at some of the packages in the psychometric task view, to see if there was a way to simplify this process. I looked at several packages, including psychometric, CTT, and psych. I'm interested in hearing from others who need to do this kind of thing frequently. What approach do you use? Do you use one of the packages mentioned above? Are there other packages I might want to take a look at? Second question: I spent some time with the psych package trying to figure out how to use the score.items() function, and it's become clear to me that I don't understand what it's doing. I assumed that setting a key equal to -1 would result in the item being reverse scored, but I get weird results, as shown below. When I try to reverse score (by setting a value of -1 in the key), I get scale scores that don't add up (e.g., the mean score is reported as being larger than the maximum item score). How is the score.items() function intended to be used? Do I need to reverse score items before using score.items()? Thanks, Ista ## score.items() example begins here ## library(psych) Data.score - as.data.frame(matrix(c(40,29,40,32,1,1,3,1,5,3,3,44,24,47,31,4,4,1,1,4,2,1,13,5,14,5,5,4,3,3,4,4,3,7,2,2,0,5,4,2,2,4,4,4,7,6,5,4,1,1,3,4,3,2,1,18,15,21,8,6,6,1,1,6,6,6,9,10,15,7,5,4,2,1,5,5,5,10,7,12,6,2,2,4,4,3,3,3,8,7,13,8,1,1,4,2,2,2,1,10,5,13,7,4,3,3,3,3,3,3), nrow=10, byrow=TRUE)) names(Data.score) - c(s1,s2,s3,s4,imi1,imi2,imi3,imi4,imi5,imi6,imi7) Data.score s1 s2 s3 s4 imi1 imi2 imi3 imi4 imi5 imi6 imi7 1 40 29 40 321131533 2 44 24 47 314411421 3 13 5 14 55433443 4 7 2 2 05422444 5 7 6 5 41134321 6 18 15 21 86611666 7 9 10 15 75421555 8 10 7 12 62244333 9 8 7 13 81142221 10 10 5 13 74333333 #This works fine key.list - list(silence=1:4, interest=5:11) keys - make.keys(length(names(Data.score)), key.list, item.labels=names(Data.score)) scored - score.items(keys, Data.score, missing=FALSE, totals=FALSE) scored$scores silence interest [1,] 35.25 2.428571 [2,] 36.50 2.428571 [3,]9.25 3.714286 [4,]2.75 3.571429 [5,]5.50 2.142857 [6,] 15.50 4.571429 [7,] 10.25 3.857143 [8,]8.75 3.00 [9,]9.00 1.857143 [10,]8.75 3.142857 #This does not do what I expected. Mean interest scores are higher than score of the highest item. key.list2 - list(silence=1:4, interest=c(5,6,-7,-8,9,10,11)) keys2 - make.keys(length(names(Data.score)), key.list2, item.labels=names(Data.score)) scored2 - score.items(keys2, Data.score, missing=FALSE, totals=FALSE) scored2$scores silence interest [1,] 35.25 14.71429 [2,] 36.50 15.28571 [3,]9.25 15.42857 [4,]2.75 15.85714 [5,]5.50 13.57143 [6,] 15.50 17.42857 [7,] 10.25 16.42857 [8,]8.75 14.14286 [9,]9.00 13.57143 [10,]8.75 14.85714 __ 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 console misc questions
I don't see where I can find this 'Rconsole' file on Mac. The closest I can get to is /Library/Frameworks/R.Framework/etc ... but then there is no such file. A bit more clarification would be appreciated. Oliver On Mar 8, 8:25 pm, Jun Shen jun.shen...@gmail.com wrote: Oliver, Go and find the file named 'Rconsole' under ~/etc folder, then you can change whatever you want, the font size, color etc. The settings will be your default. For your second question, you need to set it up in Rprofile.site. Refer to the Rprofile help. Jun On Sun, Mar 8, 2009 at 11:20 AM, Oliver fwa...@gmail.com wrote: hi, all I have two questions on using R console effectively (this is on Mac, not sure if it applies to win platform): First, I'd like to make the console font bigger, the default is too small for my screen. There is a Show Fonts from Format menu where you can adjust it, but it seems only for current session. Next time I start R, I have to redo everything. My question is, is there any way to save the preference? Second, Package Manager show available packages, and you can click loaded to load it. Again, it is only for current session, how can I make my selection permanent? Thanks for help. Oliver __ r-h...@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. -- Jun Shen PhD PK/PD Scientist BioPharma Services Millipore Corporation 15 Research Park Dr. St Charles, MO 63304 Direct: 636-720-1589 [[alternative HTML version deleted]] __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] reliability, scale scores in the psych package
Ista There are several functions in the MiscPsycho package that can be sued for classical item analysis. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ista Zahn Sent: Tuesday, March 10, 2009 10:28 AM To: reve...@northwestern.edu Cc: r-help@r-project.org Subject: [R] reliability, scale scores in the psych package Dear Professor Revelle and R-helpers, This is a two-part question: the first part is general, and the second is specific to the psych package. First question: In the past I've constructed composite variables from questionnaire data by using rowMeans(), and then correlating items with the scale using cor() as an informal check for bad items. Over the weekend I decided to take a look at some of the packages in the psychometric task view, to see if there was a way to simplify this process. I looked at several packages, including psychometric, CTT, and psych. I'm interested in hearing from others who need to do this kind of thing frequently. What approach do you use? Do you use one of the packages mentioned above? Are there other packages I might want to take a look at? Second question: I spent some time with the psych package trying to figure out how to use the score.items() function, and it's become clear to me that I don't understand what it's doing. I assumed that setting a key equal to -1 would result in the item being reverse scored, but I get weird results, as shown below. When I try to reverse score (by setting a value of -1 in the key), I get scale scores that don't add up (e.g., the mean score is reported as being larger than the maximum item score). How is the score.items() function intended to be used? Do I need to reverse score items before using score.items()? Thanks, Ista ## score.items() example begins here ## library(psych) Data.score - as.data.frame(matrix(c(40,29,40,32,1,1,3,1,5,3,3,44,24,47,31,4,4,1,1,4 ,2,1,13,5,14,5,5,4,3,3,4,4,3,7,2,2,0,5,4,2,2,4,4,4,7,6,5,4,1,1,3,4,3,2 ,1,18,15,21,8,6,6,1,1,6,6,6,9,10,15,7,5,4,2,1,5,5,5,10,7,12,6,2,2,4,4, 3,3,3,8,7,13,8,1,1,4,2,2,2,1,10,5,13,7,4,3,3,3,3,3,3), nrow=10, byrow=TRUE)) names(Data.score) - c(s1,s2,s3,s4,imi1,imi2,imi3,imi4,imi5,imi6,imi7 ) Data.score s1 s2 s3 s4 imi1 imi2 imi3 imi4 imi5 imi6 imi7 1 40 29 40 321131533 2 44 24 47 314411421 3 13 5 14 55433443 4 7 2 2 05422444 5 7 6 5 41134321 6 18 15 21 86611666 7 9 10 15 75421555 8 10 7 12 62244333 9 8 7 13 81142221 10 10 5 13 74333333 #This works fine key.list - list(silence=1:4, interest=5:11) keys - make.keys(length(names(Data.score)), key.list, item.labels=names(Data.score)) scored - score.items(keys, Data.score, missing=FALSE, totals=FALSE) scored$scores silence interest [1,] 35.25 2.428571 [2,] 36.50 2.428571 [3,]9.25 3.714286 [4,]2.75 3.571429 [5,]5.50 2.142857 [6,] 15.50 4.571429 [7,] 10.25 3.857143 [8,]8.75 3.00 [9,]9.00 1.857143 [10,]8.75 3.142857 #This does not do what I expected. Mean interest scores are higher than score of the highest item. key.list2 - list(silence=1:4, interest=c(5,6,-7,-8,9,10,11)) keys2 - make.keys(length(names(Data.score)), key.list2, item.labels=names(Data.score)) scored2 - score.items(keys2, Data.score, missing=FALSE, totals=FALSE) scored2$scores silence interest [1,] 35.25 14.71429 [2,] 36.50 15.28571 [3,]9.25 15.42857 [4,]2.75 15.85714 [5,]5.50 13.57143 [6,] 15.50 17.42857 [7,] 10.25 16.42857 [8,]8.75 14.14286 [9,]9.00 13.57143 [10,]8.75 14.85714 __ 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] reliability, scale scores in the psych package
snip Second question: I spent some time with the psych package trying to figure out how to use the score.items() function, and it's become clear to me that I don't understand what it's doing. I assumed that setting a key equal to -1 would result in the item being reverse scored, but I get weird results, as shown below. When I try to reverse score (by setting a value of -1 in the key), I get scale scores that don't add up (e.g., the mean score is reported as being larger than the maximum item score). How is the score.items() function intended to be used? Do I need to reverse score items before using score.items()? I did it again--it seems like I always figure out the answer just after I ask for help. The score.items() function needs to know the maximum of the scale in order to reverse score. For some reason, the maximum appears to be calculated from all the scores, not just scores that have a 1 or a -1 in the key. On a hunch I set the max argument to a vector of scale maxima, and it worked. I'm still interested in responses to question 1 though. Thanks again, Ista snip __ 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] foreign package install on Solaris 10 + R-2.7.1
Hello Prof. Ripley, I believe I downloaded R-2.7.1 from sunfreeware.com (and now going back to my notes realize that the foreign package is not included with it). They currently have R-2.7.2 available with the foreign package again not included. I'll give R-2.8.1 a try. Thank you, Sarosh --- Sarosh Jamal Geographic Computing Specialist Department of Geography http://geog.utm.utoronto.ca Staff co-Chair, United Way Campaign http://www.utm.utoronto.ca/unitedway University of Toronto Mississauga sarosh.ja...@utoronto.ca 905.569.4497 -Original Message- From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] Sent: Tuesday, March 10, 2009 3:02 AM To: Sarosh Jamal Cc: r-h...@lists.r-project.org Subject: Re: [R] foreign package install on Solaris 10 + R-2.7.1 On Mon, 9 Mar 2009, Sarosh Jamal wrote: Hello, I've been having trouble installing package spdep for R-2.7.1 on our Solaris 10 (sparc) server. Namely the two dependencies for this package do not install properly: foreign and maptools I understand that Solaris 10 may not be an officially supported platform but any help/feedback you can offer would be most appreciated. It is a platform we test on. WHat is not supported is 2.7.1, so please update to at least 2.8.1 (as requested in the posting guide). Something is wrong with your R installation: 'foreign' should be known to R 2.7.1, *and* installed as part of the basic installation. So re-installing seems the best option, especially as an update is in order. I've updated all packages currently installed on this version of R but the install of package foreign complains about an invalid priority field in the DESCRIPTION file. I've not had any issues with the other packages. I'm including our systemInfo() output here: == R version 2.7.1 (2008-06-23) sparc-sun-solaris2.10 locale: /en_CA.ISO8859-1/C/C/en_CA.ISO8859-1/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base And, I'm including the transcript from the package install attempt: == 1 /home/sjamal R R version 2.7.1 (2008-06-23) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. install.packages(foreign) Warning in install.packages(foreign) : argument 'lib' is missing: using '/home/sjamal/R/sparc-sun-solaris2.10-library /2.7' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://probability.ca/cran/src/contrib/foreign_0.8-33.tar.gz' Content type 'application/x-gzip' length 315463 bytes (308 Kb) opened URL == downloaded 308 Kb * Installing *source* package 'foreign' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ANSI C... none needed checking whether gcc -std=gnu99 accepts -Wno-long-long... yes checking how to run the C preprocessor... gcc -std=gnu99 -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking byteswap.h usability... no checking byteswap.h presence... no checking for byteswap.h... no checking for double... yes checking size of double... 8 checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 4 configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/swap_bytes.h config.status: creating src/var.h Error: Invalid DESCRIPTION file Invalid Priority field. Packages with priorities 'base' or 'recommended' or 'defunct-base' must already be known to R. See the information on DESCRIPTION files in section 'Creating R packages' of the 'Writing R Extensions' manual. Execution halted ERROR: installing package DESCRIPTION failed ** Removing
Re: [R] How to write a function that accepts unlimited number of input arguments?
I might very well be wrong, but something tells me Sean really wants: sum(1:5) or (more close to the kind of unlimited number of arguments): sum(c(1,2,3,4,5,17)) But then again, I might be mistaken. Best wishes, Adrian On Monday 09 March 2009, Gabor Grothendieck wrote: Try this: sum.test - function(...) sum(c(...)) More commonly one uses the list(...) construct. On Mon, Mar 9, 2009 at 11:32 AM, Sean Zhang seane...@gmail.com wrote: Dear R-helpers: I am an R newbie and have a question related to writing functions that accept unlimited number of input arguments. (I tried to peek into functions such as paste and cbind, but failed, I cannot see their codes..) Can someone kindly show me through a summation example? Say, we have input scalar, 1 2 3 4 5 then the ideal function, say sum.test, can do (1+2+3+4+5)==sum.test(1,2,3,4,5) Also sum.test can work as the number of input scalar changes. Many thanks in advance! -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd. 050025 Bucharest sector 5 Romania Tel.:+40 21 3126618 \ +40 21 3120210 / int.101 Fax: +40 21 3158391 [[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] S4 coerce as.data.frame for lm
#Hi,
#
#For a given class test, an object of class test cannot be used as data
in the lm method although as.data.frame was implemented... where's my
mistake?
#
#Suppose i have defined a S4 class test
#S4 Class test containting a slot data
#which is of type data.frame
setClass(Class = test, representation = representation(name =
character, data = data.frame)
temp = new(test) #temp is of class test
t...@data = faithful #assign some data to it
#now define as.data.frame for class test
setMethod(as.data.frame, test, function(x, row.names = NULL,
optional = FALSE)
{
return(x...@data)
}
)
as.data.frame(temp) #works
lm(eruptions ~ waiting, data = temp) #doesn't work
#Thank you for any hints
#Thomas Roth
#from the lm help page
|#data| - an optional data frame, list or environment (or object
coercible by |as.data.frame| to a data frame) containing the variables
in the model. If not found in |data|, the variables are taken from
|environment(formula)|, typically the #environment from which |lm| is
called.
__
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 structuring mixed model using lmer()
Hi all, This is partly a statistical question as well as a question about R, but I am stumped! I have count data from various sites across years. (Not all of the sites in the study appear in all years). Each site has its own habitat score habitat that remains constant across all years. I want to know if counts declined faster on sites with high habitat scores. I can construct a model that tests for the effect of habitat as a main effect, controlling for year model1-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) model2-lmer(count~yr+(1|site), family=quasibinomial,data=m) anova(model1,model2) , but how do I test the interaction? Thanks in advance, Simon. Dr. Simon Pickett Research Ecologist Land Use Department Terrestrial Unit British Trust for Ornithology The Nunnery Thetford Norfolk IP242PU 01842750050 [[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] puzzled by math on date-time objects
Hi, I don't understand the following. When I create a small artificial set of date information in class POSIXct, I can calculate the mean and the median: a = as.POSIXct(Sys.time()) a = a + 60*0:10; a [1] 2009-03-10 11:30:16 EDT 2009-03-10 11:31:16 EDT 2009-03-10 11:32:16 EDT [4] 2009-03-10 11:33:16 EDT 2009-03-10 11:34:16 EDT 2009-03-10 11:35:16 EDT [7] 2009-03-10 11:36:16 EDT 2009-03-10 11:37:16 EDT 2009-03-10 11:38:16 EDT [10] 2009-03-10 11:39:16 EDT 2009-03-10 11:40:16 EDT median(a) [1] 2009-03-10 11:35:16 EDT mean(a) [1] 2009-03-10 11:35:16 EDT But for real data (for this post, a short subset is in object c) that I have converted into a POSIXct object, I cannot calculate the median with median(), though I do get it with summary(): c [1] 2009-02-24 14:51:18 EST 2009-02-24 14:51:19 EST 2009-02-24 14:51:19 EST [4] 2009-02-24 14:51:20 EST 2009-02-24 14:51:20 EST 2009-02-24 14:51:21 EST [7] 2009-02-24 14:51:21 EST 2009-02-24 14:51:22 EST 2009-02-24 14:51:22 EST [10] 2009-02-24 14:51:22 EST class(c) [1] POSIXt POSIXct median(c) Erreur dans Summary.POSIXct(c(1235505080.6, 1235505081.1), na.rm = FALSE) : 'sum' not defined for POSIXt objects One difference is that in my own date-time series, some events are repeated (the original data contained fractions of seconds). But then, why can I get a median through summary()? summary(c) Min. 1st Qu.Median 2009-02-24 14:51:18 EST 2009-02-24 14:51:19 EST 2009-02-24 14:51:20 EST Mean 3rd Qu. Max. 2009-02-24 14:51:20 EST 2009-02-24 14:51:21 EST 2009-02-24 14:51:22 EST Thanks in advance, Denis Chabot sessionInfo() R version 2.8.1 Patched (2009-01-19 r47650) i386-apple-darwin9.6.0 locale: fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] doBy_3.7 chron_2.3-30 loaded via a namespace (and not attached): [1] Hmisc_3.5-2 cluster_1.11.12 grid_2.8.1 lattice_0.17-20 tools_2.8.1 __ 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] perform subgroup meta-analysis and create forest plot displaying subgroups
Bernd, Thanks. I believe this will do what I need, but do you know how I can set up my meta object so that the meta is performed on each subgroup individually? I can get the overall meta of all 6 observations, or I can get a separate meta of each subgroup using the subset command, but I can't get subgroup A, subgroup B, and subgroup C all into the same object. In order to use the plot feature it appears I need a byvar, so I think I'll need them all in the same object. subgroup study beta se subgroupA site1 -0.35 0.12 subgroupA site2 -0.34 0.1 subgroupB site1 -0.28 0.06 subgroupB site2 -0.29 0.07 subgroupC site1 0.34 0.03 subgroupC site2 0.36 0.04 Generic inverse variance meta-analysismetagen(beta, se, studlab=study, sm=OR) Thanks, Steve --- On Tue, 3/10/09, Weiss, Bernd bernd.we...@uni-koeln.de wrote: From: Weiss, Bernd bernd.we...@uni-koeln.de Subject: Re: [R] perform subgroup meta-analysis and create forest plot displaying subgroups To: slubi...@yahoo.com, r-help@r-project.org Date: Tuesday, March 10, 2009, 2:31 AM Steven Lubitz schrieb: Hello, I'm using the rmeta package to perform a meta analysis using summary statistics rather than raw data, and would like to analyze the effects in three different subgroups of my data. Furthermore, I'd like to plot this on one forest plot, with corresponding summary weighted averages of the effects displayed beneath each subgroup. I am able to generate the subgroup analyses by simply performing 3 separate meta-analyses with the desired subset of data. However, I can't manage to plot everything on the same forest plot. Maybe I'm wrong but the 'forest'-function (package 'meta', http://cran.at.r-project.org/web/packages/meta/meta.pdf) should be able to do what you want. I guess you could be interested in the 'byvar' argument. Bernd [[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 console misc questions
If you are like many users of the Mac, the R GUI called R.app in your Applications Folder will be the way you start R. If that is the case for you, then you should change the console font size settings in the GUI menu with Format::Font::Bigger. As far as I can see on my Mac there is no Rconsole file (or ~/etc folder for that matter). The only such file that shows up on a search is on an old file left over from the days when I was using R on Windows. If you want packages loaded at the time of startup you will need to create an .Rprofile file. That is going to require that you get your editor to create a system file (i.e., one that starts with a period), which means in Terminal that you would need to uncheck a couple of defaults. See the R for Mac OS X FAQ which should be available within the GUI. Further questions of this sort should go to the R-SIG-Mac mailing list: r-sig-...@stat.math.ethz.ch -- David Winsemius On Mar 10, 2009, at 10:29 AM, Oliver wrote: I don't see where I can find this 'Rconsole' file on Mac. The closest I can get to is /Library/Frameworks/R.Framework/etc ... but then there is no such file. A bit more clarification would be appreciated. Oliver On Mar 8, 8:25 pm, Jun Shen jun.shen...@gmail.com wrote: Oliver, Go and find the file named 'Rconsole' under ~/etc folder, then you can change whatever you want, the font size, color etc. The settings will be your default. For your second question, you need to set it up in Rprofile.site. Refer to the Rprofile help. Jun On Sun, Mar 8, 2009 at 11:20 AM, Oliver fwa...@gmail.com wrote: hi, all I have two questions on using R console effectively (this is on Mac, not sure if it applies to win platform): First, I'd like to make the console font bigger, the default is too small for my screen. There is a Show Fonts from Format menu where you can adjust it, but it seems only for current session. Next time I start R, I have to redo everything. My question is, is there any way to save the preference? Second, Package Manager show available packages, and you can click loaded to load it. Again, it is only for current session, how can I make my selection permanent? Thanks for help. Oliver __ r-h...@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. -- Jun Shen PhD PK/PD Scientist BioPharma Services Millipore Corporation 15 Research Park Dr. St Charles, MO 63304 Direct: 636-720-1589 [[alternative HTML version deleted]] __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/ listinfo/r-help PLEASE do read the posting guidehttp://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. 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] R console misc questions
Sorry for the confusion. What I described is only for R in Windows. On Tue, Mar 10, 2009 at 10:51 AM, David Winsemius dwinsem...@comcast.netwrote: If you are like many users of the Mac, the R GUI called R.app in your Applications Folder will be the way you start R. If that is the case for you, then you should change the console font size settings in the GUI menu with Format::Font::Bigger. As far as I can see on my Mac there is no Rconsole file (or ~/etc folder for that matter). The only such file that shows up on a search is on an old file left over from the days when I was using R on Windows. If you want packages loaded at the time of startup you will need to create an .Rprofile file. That is going to require that you get your editor to create a system file (i.e., one that starts with a period), which means in Terminal that you would need to uncheck a couple of defaults. See the R for Mac OS X FAQ which should be available within the GUI. Further questions of this sort should go to the R-SIG-Mac mailing list: r-sig-...@stat.math.ethz.ch -- David Winsemius On Mar 10, 2009, at 10:29 AM, Oliver wrote: I don't see where I can find this 'Rconsole' file on Mac. The closest I can get to is /Library/Frameworks/R.Framework/etc ... but then there is no such file. A bit more clarification would be appreciated. Oliver On Mar 8, 8:25 pm, Jun Shen jun.shen...@gmail.com wrote: Oliver, Go and find the file named 'Rconsole' under ~/etc folder, then you can change whatever you want, the font size, color etc. The settings will be your default. For your second question, you need to set it up in Rprofile.site. Refer to the Rprofile help. Jun On Sun, Mar 8, 2009 at 11:20 AM, Oliver fwa...@gmail.com wrote: hi, all I have two questions on using R console effectively (this is on Mac, not sure if it applies to win platform): First, I'd like to make the console font bigger, the default is too small for my screen. There is a Show Fonts from Format menu where you can adjust it, but it seems only for current session. Next time I start R, I have to redo everything. My question is, is there any way to save the preference? Second, Package Manager show available packages, and you can click loaded to load it. Again, it is only for current session, how can I make my selection permanent? Thanks for help. Oliver __ r-h...@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. -- Jun Shen PhD PK/PD Scientist BioPharma Services Millipore Corporation 15 Research Park Dr. St Charles, MO 63304 Direct: 636-720-1589 [[alternative HTML version deleted]] __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/ listinfo/r-help PLEASE do read the posting guidehttp:// 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. David Winsemius, MD Heritage Laboratories West Hartford, CT -- Jun Shen PhD PK/PD Scientist BioPharma Services Millipore Corporation 15 Research Park Dr. St Charles, MO 63304 Direct: 636-720-1589 [[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] Lattice: Customizing point-sizes with groups
Sorry, I missed your point the first time. Why not create a group for each subset then? xyplot(y ~ x, temp, groups = interaction(cex, groups), par.settings = list( superpose.symbol = list( cex = c(1, 2, 3, 4), pch = 19, col = c(blue, red, green, purple On Tue, Mar 10, 2009 at 8:11 AM, Paul C. Boutros paul.bout...@utoronto.ca wrote: Hi Sundar, Thanks for your help! Unfortunately your code seems to give the same result. Compare this: temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), col = c( rep(blue, 5), rep(red, 5) ), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, groups = groups, par.settings = list( superpose.symbol = list( cex = c(1, 3), pch = 19, col = c(blue, red And this: xyplot(y ~ x, temp, cex = temp$cex, col = temp$col, pch = 19); Once I introduce groups, I lose the ability to customize individual data-points and seem only to be able to customize entire groups. Paul -Original Message- From: Sundar Dorai-Raj [mailto:sdorai...@gmail.com] Sent: Tuesday, March 10, 2009 5:49 AM To: paul.bout...@utoronto.ca Cc: r-help@r-project.org Subject: Re: [R] Lattice: Customizing point-sizes with groups Try this: xyplot(y ~ x, temp, groups = groups, par.settings = list( superpose.symbol = list( cex = c(1, 3), pch = 19, col = c(blue, red See: str(trellis.par.get()) for other settings you might want to change. Also, you should drop the ; from all your scripts. HTH, --sundar On Mon, Mar 9, 2009 at 6:49 PM, Paul Boutros paul.bout...@utoronto.ca wrote: Hello, I am creating a scatter-plot in lattice, and I would like to customize the size of each point so that some points are larger and others smaller. Here's a toy example: library(lattice); temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, cex = temp$cex, pch = 19); This works just fine if I create a straight xy-plot, without groups. However when I introduce groupings the cex argument specifies the point-size for the entire group. For example: xyplot(y ~ x, temp, cex = temp$cex, pch = 19, group = groups); Is it possible to combine per-spot sizing with groups in some way? One work-around is to manually specify all graphical parameters, but I thought there might be a better way than this: temp$col - rep(blue, 10); temp$col[temp$groups == B] - red; xyplot(y ~ x, temp, cex = temp$cex, pch = 19, col = temp$col); Any suggestions/advice is much appreciated! 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. __ 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] File permissions
Hello fellow R-ists, How do I change file permissions? I know that file.access can display permission information but how do I SET those permissions? Thank you Your culpritNr1 __ 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)
Dear R users, I have a table with the following form STATION X Y 1-7030 1-7030 1-7030 2-7229 2-7229 2-7229 2-7229 How want to extract unique value for those columns ... I am sure it is very simple, but I can not achieve to find the correct way ! I want to obtain something like STATIONX Y 1-7030 2-7229 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] reliability, scale scores in the psych package
Doran, Harold HDoran at air.org writes: Ista There are several functions in the MiscPsycho package that can be sued for classical item analysis. Since when is classical item analysis a crime? No wonder the USA is considered such a litigious society! Ken -- Ken Knoblauch Inserm U846 Stem-cell and Brain Research Institute Department of Integrative Neurosciences 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 http://www.sbri.fr/members/kenneth-knoblauch.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using chm help files under linux
On Tue, 10 Mar 2009, Jose Quesada wrote: Hi, Chm (compiled help) is a microsoft invention. It's the default help system under windows, but not so under linux. I found that (at times) I like better how chm help looks. Since there are chm viewers under linux, using chm help files should be possible. You don't just need a viewer, you need a help compiler. We were unable to find a complete one other than from Microsoft, and the latter seems no longer to be under development (and has a serious security alert on it). So the future of CHM help even for R under Windows is uncertain. Has anybody tried to set R so it opens chm by default? I'm sure there's some flag or Rprofile var that could get this done. There is for R for Windows, it that is what you are asking. And you can run Windows R under WINE. Personally, I like the Mac OS X compiled help system better than the Windows one, but we do not provide that even on Mac OS X. And these things *are* a matter of personal preference. Thanks, -- -Jose -- Jose Quesada, PhD http://josequesada.name -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] File permissions
On Tue, 10 Mar 2009, ig2ar-s...@yahoo.co.uk wrote: Hello fellow R-ists, How do I change file permissions? I know that file.access can display permission information but how do I SET those permissions? Well, file.info is better are displaying permission information, and Sys.chmod set them in the format used by file.info. Thank you Your culpritNr1 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] popular R packages
If is easy to get the download numbers, we should do it and deal with the interpretation issues. I'd like to know the numbers so I can understand which (of my) packages have the most usage. One other compication about # downloads: I suspect that a package being on teh depends/suggests/imports list of another package might be a big driver with respect to how many times that it was downloaded. If I remember correctly, about 5 years ago Bioconductor asked for volunteers to review packages to get detailed, specific feedback by people who use the package (and should be fairly R proficient). I think that this is pretty important and something like Crantastic is a good interface. I personally got a lot out of the comments the a JSS reviewer had for a package. -- Max __ 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)
Hi Arnaud, is very simple: unique( datos) Regards 2009/3/10 arnaud_mosn...@uqar.qc.ca Dear R users, I have a table with the following form STATION X Y 1-7030 1-7030 1-7030 2-7229 2-7229 2-7229 2-7229 How want to extract unique value for those columns ... I am sure it is very simple, but I can not achieve to find the correct way ! I want to obtain something like STATIONX Y 1-7030 2-7229 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. [[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] Re : (no subject)
see ?unique Justin BEM BP 1917 Yaoundé Tél (237) 99597295 (237) 22040246 De : arnaud_mosn...@uqar.qc.ca arnaud_mosn...@uqar.qc.ca À : r-help@r-project.org Envoyé le : Mardi, 10 Mars 2009, 17h15mn 57s Objet : [R] (no subject) Dear R users, I have a table with the following form STATION X Y 1-7030 1-7030 1-7030 2-7229 2-7229 2-7229 2-7229 How want to extract unique value for those columns ... I am sure it is very[[elided Yahoo spam]] I want to obtain something like STATIONX Y 1-7030 2-7229 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. [[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] Lattice: Customizing point-sizes with groups
Hi Sundar, Thanks for your help! Unfortunately your code seems to give the same result. Compare this: temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), col = c( rep(blue, 5), rep(red, 5) ), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, groups = groups, par.settings = list( superpose.symbol = list( cex = c(1, 3), pch = 19, col = c(blue, red And this: xyplot(y ~ x, temp, cex = temp$cex, col = temp$col, pch = 19); Once I introduce groups, I lose the ability to customize individual data-points and seem only to be able to customize entire groups. Paul -Original Message- From: Sundar Dorai-Raj [mailto:sdorai...@gmail.com] Sent: Tuesday, March 10, 2009 5:49 AM To: paul.bout...@utoronto.ca Cc: r-help@r-project.org Subject: Re: [R] Lattice: Customizing point-sizes with groups Try this: xyplot(y ~ x, temp, groups = groups, par.settings = list( superpose.symbol = list( cex = c(1, 3), pch = 19, col = c(blue, red See: str(trellis.par.get()) for other settings you might want to change. Also, you should drop the ; from all your scripts. HTH, --sundar On Mon, Mar 9, 2009 at 6:49 PM, Paul Boutros paul.bout...@utoronto.ca wrote: Hello, I am creating a scatter-plot in lattice, and I would like to customize the size of each point so that some points are larger and others smaller. Here's a toy example: library(lattice); temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, cex = temp$cex, pch = 19); This works just fine if I create a straight xy-plot, without groups. However when I introduce groupings the cex argument specifies the point-size for the entire group. For example: xyplot(y ~ x, temp, cex = temp$cex, pch = 19, group = groups); Is it possible to combine per-spot sizing with groups in some way? One work-around is to manually specify all graphical parameters, but I thought there might be a better way than this: temp$col - rep(blue, 10); temp$col[temp$groups == B] - red; xyplot(y ~ x, temp, cex = temp$cex, pch = 19, col = temp$col); Any suggestions/advice is much appreciated! 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. __ 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] nonmetric clustering
Hi all, does anybody know where it is possible to find the Riffle package? Thank you R [[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 installing Kernlab: cannot find -lgfortran
I am trying to install a package kernlab on Linux machine. After downloading and unpacking, installation goes through a number of C code compiles which ends with code linking, where error is generated as follows: g++ -shared -Bdirect,--hash-stype=both,-Wl,-O1 -o kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -L/usr/lib64/R/lib -lRblas -lgfortran -lm -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lR /usr/bin/ld: cannot find -lgfortran collect2: ld returned 1 exit status I suppose compiler cannot find libgfortran, which is in /usr/lib64/ in my case. Does anyone know where I specify or how I pass this info to R. I suppose there must be some UNIX environment variable or argument to install.packages Thanks, Andre __ 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] reliability, scale scores in the psych package
Ista, As you figured out, psych reverses items by subtracting from the maximimum + minimum possible for each item. (i.e., for items going from 1 to 4, it reverses items by subtracting from 5). If all of the items have the same potential range then you can just let it figure out the range by itself. If they differ in their ranges (some items are 0 - 1 items, some are 1-9 items, etc., then you need to give it the maximum and minimum vectors to use. The min and max are figured out from all the items used in an inventory, rather than just the items used in a particular scale. This makes particular sense when you are scoring multiple scales from the same inventory. In answer to your first question (what packages do I tend to use for scale construction?), the answer is that I tend to use the psych package for basic analysis, and then the sem package for structural equation analysis. Bill At 10:45 AM -0400 3/10/09, Ista Zahn wrote: snip Second question: I spent some time with the psych package trying to figure out how to use the score.items() function, and it's become clear to me that I don't understand what it's doing. I assumed that setting a key equal to -1 would result in the item being reverse scored, but I get weird results, as shown below. When I try to reverse score (by setting a value of -1 in the key), I get scale scores that don't add up (e.g., the mean score is reported as being larger than the maximum item score). How is the score.items() function intended to be used? Do I need to reverse score items before using score.items()? I did it again--it seems like I always figure out the answer just after I ask for help. The score.items() function needs to know the maximum of the scale in order to reverse score. For some reason, the maximum appears to be calculated from all the scores, not just scores that have a 1 or a -1 in the key. On a hunch I set the max argument to a vector of scale maxima, and it worked. I'm still interested in responses to question 1 though. Thanks again, Ista snip -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r __ 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] Lattice: Customizing point-sizes with groups
Yup, that would be my work-around. I was hoping for a cleaner way of doing this, though, because I am calculating cex based on other properties of the data-points, so that it becomes a continuous variable. -Original Message- From: Sundar Dorai-Raj [mailto:sdorai...@gmail.com] Sent: Tuesday, March 10, 2009 12:01 PM To: Paul C. Boutros Cc: r-help@r-project.org Subject: Re: [R] Lattice: Customizing point-sizes with groups Sorry, I missed your point the first time. Why not create a group for each subset then? xyplot(y ~ x, temp, groups = interaction(cex, groups), par.settings = list( superpose.symbol = list( cex = c(1, 2, 3, 4), pch = 19, col = c(blue, red, green, purple On Tue, Mar 10, 2009 at 8:11 AM, Paul C. Boutros paul.bout...@utoronto.ca wrote: Hi Sundar, Thanks for your help! Unfortunately your code seems to give the same result. Compare this: temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), col = c( rep(blue, 5), rep(red, 5) ), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, groups = groups, par.settings = list( superpose.symbol = list( cex = c(1, 3), pch = 19, col = c(blue, red And this: xyplot(y ~ x, temp, cex = temp$cex, col = temp$col, pch = 19); Once I introduce groups, I lose the ability to customize individual data-points and seem only to be able to customize entire groups. Paul -Original Message- From: Sundar Dorai-Raj [mailto:sdorai...@gmail.com] Sent: Tuesday, March 10, 2009 5:49 AM To: paul.bout...@utoronto.ca Cc: r-help@r-project.org Subject: Re: [R] Lattice: Customizing point-sizes with groups Try this: xyplot(y ~ x, temp, groups = groups, par.settings = list( superpose.symbol = list( cex = c(1, 3), pch = 19, col = c(blue, red See: str(trellis.par.get()) for other settings you might want to change. Also, you should drop the ; from all your scripts. HTH, --sundar On Mon, Mar 9, 2009 at 6:49 PM, Paul Boutros paul.bout...@utoronto.ca wrote: Hello, I am creating a scatter-plot in lattice, and I would like to customize the size of each point so that some points are larger and others smaller. Here's a toy example: library(lattice); temp - data.frame( x = 1:10, y = 1:10, cex = rep( c(1,3), 5), groups = c( rep(A, 5), rep(B, 5) ) ); xyplot(y ~ x, temp, cex = temp$cex, pch = 19); This works just fine if I create a straight xy-plot, without groups. However when I introduce groupings the cex argument specifies the point-size for the entire group. For example: xyplot(y ~ x, temp, cex = temp$cex, pch = 19, group = groups); Is it possible to combine per-spot sizing with groups in some way? One work-around is to manually specify all graphical parameters, but I thought there might be a better way than this: temp$col - rep(blue, 10); temp$col[temp$groups == B] - red; xyplot(y ~ x, temp, cex = temp$cex, pch = 19, col = temp$col); Any suggestions/advice is much appreciated! 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. __ 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 stop loop inside status ? ( haplo.stats package )
How to stop loop inside status ? require(haplo.stats) ## normal status y=rep(c(0,1),each=50) geno=as.data.frame(matrix(sample(c(A,G,T,C),600,replace=T),100,6)) hs- haplo.score(y, geno, trait.type=binomial, offset = NA, x.adj = NA, min.count=5, locus.label=NA, miss.val=c(0,NA), haplo.effect=additive, eps.svd=1e-5, simulate=TRUE, sim.control=score.sim.control(min.sim=200,max.sim=500)) hs$score.global.p.sim ## find loop inside ,and I can't stop it! geno=as.data.frame(matrix(G,100,6)) hs- haplo.score(y, geno, trait.type=binomial, offset = NA, x.adj = NA, min.count=5, locus.label=NA, miss.val=c(0,NA), haplo.effect=additive, eps.svd=1e-5, simulate=TRUE, sim.control=score.sim.control(min.sim=200,max.sim=500)) hs$score.global.p.sim How to stop loop inside status ? -- Nash - morri...@ibms.sinica.edu.tw __ 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] File permissions
Great. I tried chmod (which does not exist) but I didn't know that there was sys.chmod. Thank you. Prof Brian Ripley wrote: On Tue, 10 Mar 2009, ig2ar-s...@yahoo.co.uk wrote: Hello fellow R-ists, How do I change file permissions? I know that file.access can display permission information but how do I SET those permissions? Well, file.info is better are displaying permission information, and Sys.chmod set them in the format used by file.info. Thank you Your culpritNr1 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/File-permissions-tp22437684p22439004.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] Plots of different aspect ratios on one page, base aligned(trellis.print)
Hello, I have an example of a 2 paneled plot, with two different aspect ratios displayed on one page. An example would help n=20 x1 - cumsum(runif(n)) x2 - cumsum(runif(n)) d - data.frame(val=c(x1,x2),id=c(1:n,1:n), nt=c(rep(A,n),rep(B,n))) u1 - xyplot(val~id | nt, data=d,aspect=1,layout=c(1,2)) u2 - xyplot(val~id|nt, data=d,aspect=0.5,layout=c(1,2)) postscript(~/k.ps,colormodel=rgb,paper=letter,horiz=T) print(u1,position=c(0,0,1/3,1),more=T,newpage=T) print(u2,position=c(1/3,0,1,1),more=F,newpage=F) dev.off() The two figures are not base aligned. I would like them share the same the baseline and same height, if necessary the paper width and height can be adjusted ( i tried setting the paper width and height to no avail). Is the way to base align the two figures? Do I have to get down the grid level? Regards Saptarshi Guha __ 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] popular R packages
On Tuesday 10 March 2009, Frank E Harrell Jr wrote: Gabor Grothendieck wrote: On Tue, Mar 10, 2009 at 6:14 AM, Jim Lemon j...@bitwrit.com.au wrote: Gabor Grothendieck wrote: R-Forge already has this but I don't think its used much. R-Forge does allow authors to opt out which seems sensible lest it deter potential authors from submitting packages. I think objective quality metrics are better than ratings, e.g. does package have a vignette, has package had a release within the last year, does package have free software license, etc. That would have the advantage that authors might react to increase their package's quality assessment resulting in an overall improvement in quality on CRAN that would result in more of a pro-active cycle whereas ratings are reactive and don't really encourage improvement. I beg to offer an alternative assessment of quality. Do users download the package and find it useful? If so, they are likely to download it again when it is updated. I was referring to motivating authors, not users, so that CRAN improves. Much as I appreciate the convenience of vignettes, regular updates and the absolute latest GPL license, a perfectly dud package can have all of these things. If a package is downloaded upon first release and These are nothing but the usual FUD against quality improvement, i.e. the quality metrics are not measuring what you want but the fact is that quality metrics can work and have had huge successes. Also I think objective measures would be more accepted by authors than ratings. No one is going to be put off that their package has no vignette when obviously it doesn't and the authors are free to add one and instantly improve their package's rating. not much thereafter, the maintainer might be motivated to attend to its shortcomings of utility rather than incrementing the version number every month or so. Downloads, as many have pointed out, are not a direct assessment of quality, but if I saw a package that just kept getting downloaded, version after version, I would be much more likely to check it out myself and perhaps even write a review for Hadley's neat site. Which I will try to do tonight. I was arguing for objective metrics rather than ratings. Downloading is not a rating but is objective although there are measurement problems as has been pointed out. Also, the worst feature is that it does not react to changes in quality very quickly making it anti-motivating. Gabor I think your approach will have more payoff in the long run. I would suggest one other metric: the number of lines of code in the 'examples' section of all the package's help files. Frank Absolutely. From the perspective of a user, not an expert, packages with a good vignette and lots of examples are by far my favorite and most used. Dylan -- Dylan Beaudette Soil Resource Laboratory http://casoilresource.lawr.ucdavis.edu/ University of California at Davis 530.754.7341 __ 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] popular R packages
Pricing each download at 99 cents ( the same as a song from I Tunes) can measure users more accurately. Thats my 2 cents anyways. On Tue, Mar 10, 2009 at 9:54 PM, Max Kuhn mxk...@gmail.com wrote: If is easy to get the download numbers, we should do it and deal with the interpretation issues. I'd like to know the numbers so I can understand which (of my) packages have the most usage. One other compication about # downloads: I suspect that a package being on teh depends/suggests/imports list of another package might be a big driver with respect to how many times that it was downloaded. If I remember correctly, about 5 years ago Bioconductor asked for volunteers to review packages to get detailed, specific feedback by people who use the package (and should be fairly R proficient). I think that this is pretty important and something like Crantastic is a good interface. I personally got a lot out of the comments the a JSS reviewer had for a package. -- Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to color certain area under curve
For a given random variable rv, for instance, rv = rnorm(1000), I plot its density curve and calculate some quantiles: plot(density(rv)) P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) I would like to color the area between P10 and P90 and under the curve and mark the P50 on the curve. rv = rnorm(1000) plot(density(rv)) P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) Could you please teach me how to do these using R? Thanks, -james __ 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] help structuring mixed model using lmer()
On Tue, Mar 10, 2009 at 10:15 AM, Simon Pickett simon.pick...@bto.org wrote: This is partly a statistical question as well as a question about R, but I am stumped! I have count data from various sites across years. (Not all of the sites in the study appear in all years). Each site has its own habitat score habitat that remains constant across all years. I want to know if counts declined faster on sites with high habitat scores. I can construct a model that tests for the effect of habitat as a main effect, controlling for year model1-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) model2-lmer(count~yr+(1|site), family=quasibinomial,data=m) anova(model1,model2) I'm curious as to why you use the quasibinomial family for count data. When you say count data do you mean just presence/absence or an actual count of the number present? Generally the binomial and quasibinomial families are used when you have a binary response, and the poisson or quasipoisson family are used for responses that are counts. __ 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)
Dear Members, I have a question about using R2WinBUGS to obtain the WinBUGS results. By default, when R2WinBUGS returns summary stats, I got mean, sd, 2.5%, 25%, median, 75% and 97.5%. Could anyone tell me how to modify the code to obtain 5% and 95% summary results? Many thanks Alice _ [[elided Hotmail spam]] [[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] Alternative to interp.surface() offered
I wanted a simple function for bilinear interpolation on a 2-D grid, and
interp.surface() in the fields package didn't quite suit my needs. In
particular, it requires uniform spacing between grid points. It also
didn't have the visual reference frame I was looking for. Here is an
alternative function, followed by an example.
# A function for bilinear interpolation on a 2-d grid, based on the
# interp.surface() from the fields package and code by Steve Koehler.
# The points of the grid do not have to be uniformly spaced. Looking at
the 2-d
# grid in plan view, the origin is at upper left, so y (row) index
increases
# downward. findInterval() is used to locate the new coordinates on the
grid.
#
# Scott Waichler, scott.waich...@pnl.gov, 03/10/09.
my.interp.surface - function (obj, loc) {
# obj is a surface object like the list for contour or image.
# loc is a matrix of (x, y) locations
x - obj$x
y - obj$y
x.new - loc[,1]
y.new - loc[,2]
z - obj$z
ind.x - findInterval(x.new, x, all.inside=T)
ind.y - findInterval(y.new, y, all.inside=T)
ex - (x.new - x[ind.x]) / (x[ind.x + 1] - x[ind.x])
ey - (y.new - y[ind.y]) / (y[ind.y + 1] - y[ind.y])
# set weights for out-of-bounds locations to NA
ex[ex 0 | ex 1] - NA
ey[ey 0 | ey 1] - NA
return(
z[cbind(ind.y, ind.x)] * (1 - ex) * (1 - ey) + # upper
left
z[cbind(ind.y + 1, ind.x)] * (1 - ex) * ey + # lower
left
z[cbind(ind.y + 1, ind.x + 1)] * ex * ey + # lower
right
z[cbind(ind.y, ind.x + 1)] * ex * (1 - ey)# upper
right
)
}
## # An example.
## # z matrix, y index increasing downwards
## # 4 5 6 7 8
## # 3 4 5 6 7
## # 2 3 4 5 6
## # 1 2 3 4 5
## z.vec - c(4,5,6,7,8,3,4,5,6,7,2,3,4,5,6,1,2,3,4,5) # read in the
data for the matrix
## x.mat - 1:5# x coordinates of the z values
## y.mat - seq(100, 400, by=100) # y coordinates of the z values
## obj - list(x = x.mat, y = y.mat, z = matrix(z.vec, ncol=5, byrow=T))
# grid you want to interpolate on
## x.out - round(runif(6, min = min(x.mat), max = max(x.mat)), 2) # x
for points you want interpolate to
## y.out - round(runif(6, min = min(y.mat), max = max(y.mat)), 2) # y
for points you want interpolate to
## loc - cbind(x.out, y.out)
## z.out - my.interp.surface(obj, loc)
## cat(file=, x.out = , loc[,1], \n, y.out = , loc[,2], \n,
z.out = , round(z.out, 2), \n)
Regards,
Scott Waichler
Pacific Northwest National Laboratory
Richland, WA 99352USA
scott.waich...@pnl.gov
__
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] Changing factor to numeric
By the way, it could be that one of your numbers has space in them. in which case, R tends to turn the entire vector into a factor. try opening the file in a spreadsheet like excel, and do search replace on with . and see how many it catches. Tal On Tue, Mar 10, 2009 at 7:25 AM, ojal john owino ojal.johnow...@googlemail.com wrote: Dear Users, I have a variable in my dataset which is of type factor. But it actually contains numeric entries which like 5.735 4.759 . This is because the data was read from a CSV file into R and this variable contained other charaters which were not numeric. I have now dropped the records with the characters which are not numeric for this variable and want to change it to numeric srotage type. I have tried using as.numeric() function but it changes the values in the variable to what I think are the ranks of the individual values of the varible in the dataset. For example if 5.735 is the current content in the field, then the new object created by as.numeric will contain a value like 680 if the 5.735 was the highest value for the varible and the dataset had 680 records. How can I change the storage type without changing the contents of this variable in this case? Thanks for your consideration. -- Ojal John Owino P.O Box 230-80108 Kilifi, Kenya. Mobile:+254 728 095 710 [[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. -- -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: www.talgalili.com www.biostatistics.co.il [[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] a general question
Hello Bogdan, Put in those terms, option b looks more defensible. It sounds like a test of two proportions, sometimes called z-test. The problem is that, for that test to be used, you must be sampling from large population. You know that under regular ChIP-seq sequencing we are lucky if we get 10 reads in a particuar region of interest. So, we get a population and that population itself is small. So, z-test does not look applicable. Google for z-test and you'll see the conditions. What to do then? Well, forget comparing signal to backgroung and, instead, compare directly number of reads in the experiment versus number of reads in the control. Actually, you simplify your algorithm by not having to define (and defend) an arbitrary area to call background. An example? Sure! Check out PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls, Joel Rozowsky1, Ghia Euskirchen2, Raymond K Auerbach3, Zhengdong D Zhang1, Theodore Gibson1, Robert Bjornson4, Nicholas Carriero4, Michael Snyder1,2 Mark B Gerstein1,3,4. Nature Biotechnology, 2009. Take a look at it and let us know what you think. Your culpritNr1 PS: next time, please go for a more descriptive subject such as ChIP-seq. That would help in the future when we need to over old messages. Don't you think? Bogdan Tanasa wrote: Hi everyone, Although this question is more related to ChIP and ChIP-seq, it could be probably anchored in a more general statistical context. The question is : what method is better to assess the significance of the change in a signal (the signal can be DNA binding, for instance) given the background and 2 conditions. . condition1 (eg no treatment) : background = 1; signal = 5; . condition2 (eg hormonal treatment) : background = 3; signal = 6. The methods can be : a. substract the background : i.e. (signal_treatment - background_treatment) / (signal_no_treatment - background_no_treatment) b. calculate the fold change: i.e. (signal_treatment / background_treatment) / (signal_no_treatment / background_no_treatment) c. any other method ? i.e. (signal_treatment - signal_no_treatment) / ( background_treatment - background_no_treatment) Thank you very much. Bogdan [[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://www.nabble.com/a-general-question-tp22382289p22440722.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] puzzled by math on date-time objects
Your problem arises in R 2.8.1 (and 2.9.0-devel, but not 2.7.0) when
length(POSIXct object) is even, because median(POSIXct object)
passes a POSIXct object to median.default, which calls
sum() in the even length case.
median( as.POSIXct(Sys.time()))
[1] 2009-03-10 10:28:46 PDT
median( as.POSIXct(rep(Sys.time(),2)))
Error in Summary.POSIXct(c(1236706132.54740, 1236706132.54740), na.rm =
FALSE) :
'sum' not defined for POSIXt objects
traceback()
4: stop(gettextf('%s' not defined for \POSIXt\ objects, .Generic),
domain = NA)
3: Summary.POSIXct(c(1236706132.54740, 1236706132.54740), na.rm = FALSE)
2: median.default(as.POSIXct(rep(Sys.time(), 2)))
1: median(as.POSIXct(rep(Sys.time(), 2)))
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 8.1
year 2008
month 12
day22
svn rev47281
language R
version.string R version 2.8.1 (2008-12-22)
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
[R] puzzled by math on date-time objects
Denis Chabot chabotd at globetrotter.net
Tue Mar 10 16:44:07 CET 2009
Previous message: [R] nonmetric clustering
Next message: [R] perform subgroup meta-analysis and create forest plot
displaying subgroups
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Hi,
I don't understand the following. When I create a small artificial set
of date information in class POSIXct, I can calculate the mean and the
median:
a = as.POSIXct(Sys.time())
a = a + 60*0:10; a
[1] 2009-03-10 11:30:16 EDT 2009-03-10 11:31:16 EDT 2009-03-10
11:32:16 EDT
[4] 2009-03-10 11:33:16 EDT 2009-03-10 11:34:16 EDT 2009-03-10
11:35:16 EDT
[7] 2009-03-10 11:36:16 EDT 2009-03-10 11:37:16 EDT 2009-03-10
11:38:16 EDT
[10] 2009-03-10 11:39:16 EDT 2009-03-10 11:40:16 EDT
median(a)
[1] 2009-03-10 11:35:16 EDT
mean(a)
[1] 2009-03-10 11:35:16 EDT
But for real data (for this post, a short subset is in object c) that
I have converted into a POSIXct object, I cannot calculate the median
with median(), though I do get it with summary():
c
[1] 2009-02-24 14:51:18 EST 2009-02-24 14:51:19 EST 2009-02-24
14:51:19 EST
[4] 2009-02-24 14:51:20 EST 2009-02-24 14:51:20 EST 2009-02-24
14:51:21 EST
[7] 2009-02-24 14:51:21 EST 2009-02-24 14:51:22 EST 2009-02-24
14:51:22 EST
[10] 2009-02-24 14:51:22 EST
class(c)
[1] POSIXt POSIXct
median(c)
Erreur dans Summary.POSIXct(c(1235505080.6, 1235505081.1), na.rm =
FALSE) :
'sum' not defined for POSIXt objects
One difference is that in my own date-time series, some events are
repeated (the original data contained fractions of seconds). But then,
why can I get a median through summary()?
summary(c)
Min. 1st
Qu.Median
2009-02-24 14:51:18 EST 2009-02-24 14:51:19 EST 2009-02-24
14:51:20 EST
Mean 3rd
Qu. Max.
2009-02-24 14:51:20 EST 2009-02-24 14:51:21 EST 2009-02-24
14:51:22 EST
Thanks in advance,
Denis Chabot
sessionInfo()
R version 2.8.1 Patched (2009-01-19 r47650)
i386-apple-darwin9.6.0
locale:
fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] doBy_3.7 chron_2.3-30
loaded via a namespace (and not attached):
[1] Hmisc_3.5-2 cluster_1.11.12 grid_2.8.1 lattice_0.17-20
tools_2.8.1
__
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] puzzled by math on date-time objects
median.default was changed between 2.7.1 and 2.8.1 to
call sum(...)/2 instead of mean(...) and that causes
the problem for POSIXct objects (sum fails but mean
works for them).
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: William Dunlap
Sent: Tuesday, March 10, 2009 11:37 AM
To: 'r-help@r-project.org'
Subject: Re: [R] puzzled by math on date-time objects
Your problem arises in R 2.8.1 (and 2.9.0-devel, but not 2.7.0) when
length(POSIXct object) is even, because median(POSIXct object)
passes a POSIXct object to median.default, which calls
sum() in the even length case.
median( as.POSIXct(Sys.time()))
[1] 2009-03-10 10:28:46 PDT
median( as.POSIXct(rep(Sys.time(),2)))
Error in Summary.POSIXct(c(1236706132.54740,
1236706132.54740), na.rm = FALSE) :
'sum' not defined for POSIXt objects
traceback()
4: stop(gettextf('%s' not defined for \POSIXt\ objects, .Generic),
domain = NA)
3: Summary.POSIXct(c(1236706132.54740, 1236706132.54740),
na.rm = FALSE)
2: median.default(as.POSIXct(rep(Sys.time(), 2)))
1: median(as.POSIXct(rep(Sys.time(), 2)))
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 8.1
year 2008
month 12
day22
svn rev47281
language R
version.string R version 2.8.1 (2008-12-22)
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
[R] puzzled by math on date-time objects
Denis Chabot chabotd at globetrotter.net
Tue Mar 10 16:44:07 CET 2009
Previous message: [R] nonmetric clustering
Next message: [R] perform subgroup meta-analysis and create
forest plot displaying subgroups
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Hi,
I don't understand the following. When I create a small
artificial set
of date information in class POSIXct, I can calculate the
mean and the
median:
a = as.POSIXct(Sys.time())
a = a + 60*0:10; a
[1] 2009-03-10 11:30:16 EDT 2009-03-10 11:31:16 EDT
2009-03-10
11:32:16 EDT
[4] 2009-03-10 11:33:16 EDT 2009-03-10 11:34:16 EDT
2009-03-10
11:35:16 EDT
[7] 2009-03-10 11:36:16 EDT 2009-03-10 11:37:16 EDT
2009-03-10
11:38:16 EDT
[10] 2009-03-10 11:39:16 EDT 2009-03-10 11:40:16 EDT
median(a)
[1] 2009-03-10 11:35:16 EDT
mean(a)
[1] 2009-03-10 11:35:16 EDT
But for real data (for this post, a short subset is in object
c) that
I have converted into a POSIXct object, I cannot calculate
the median
with median(), though I do get it with summary():
c
[1] 2009-02-24 14:51:18 EST 2009-02-24 14:51:19 EST
2009-02-24
14:51:19 EST
[4] 2009-02-24 14:51:20 EST 2009-02-24 14:51:20 EST
2009-02-24
14:51:21 EST
[7] 2009-02-24 14:51:21 EST 2009-02-24 14:51:22 EST
2009-02-24
14:51:22 EST
[10] 2009-02-24 14:51:22 EST
class(c)
[1] POSIXt POSIXct
median(c)
Erreur dans Summary.POSIXct(c(1235505080.6, 1235505081.1), na.rm =
FALSE) :
'sum' not defined for POSIXt objects
One difference is that in my own date-time series, some events are
repeated (the original data contained fractions of seconds).
But then,
why can I get a median through summary()?
summary(c)
Min. 1st
Qu.Median
2009-02-24 14:51:18 EST 2009-02-24 14:51:19 EST 2009-02-24
14:51:20 EST
Mean 3rd
Qu. Max.
2009-02-24 14:51:20 EST 2009-02-24 14:51:21 EST 2009-02-24
14:51:22 EST
Thanks in advance,
Denis Chabot
sessionInfo()
R version 2.8.1 Patched (2009-01-19 r47650)
i386-apple-darwin9.6.0
locale:
fr_CA.UTF-8/fr_CA.UTF-8/C/C/fr_CA.UTF-8/fr_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] doBy_3.7 chron_2.3-30
loaded via a namespace (and not attached):
[1] Hmisc_3.5-2 cluster_1.11.12 grid_2.8.1 lattice_0.17-20
tools_2.8.1
__
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] help structuring mixed model using lmer()
Cheers, Actually I was using quasipoisson for my models, but for the puposes of my example, it doesnt really matter. I am trying to work out a way of quantifying whether the slopes (for years) are covary with habitat scores. The more I think about it, the more I am convinced that it isnt possible do to that using a glm approach. I think I have to run separate models for each site, calculate the gradient, then do a lm with gradient explained by habitat score Thanks, Simon. On Tue, Mar 10, 2009 at 10:15 AM, Simon Pickett simon.pick...@bto.org wrote: This is partly a statistical question as well as a question about R, but I am stumped! I have count data from various sites across years. (Not all of the sites in the study appear in all years). Each site has its own habitat score habitat that remains constant across all years. I want to know if counts declined faster on sites with high habitat scores. I can construct a model that tests for the effect of habitat as a main effect, controlling for year model1-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) model2-lmer(count~yr+(1|site), family=quasibinomial,data=m) anova(model1,model2) I'm curious as to why you use the quasibinomial family for count data. When you say count data do you mean just presence/absence or an actual count of the number present? Generally the binomial and quasibinomial families are used when you have a binary response, and the poisson or quasipoisson family are used for responses that are counts. __ 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] ordering
Hello, I would like to order a matrix by a specific column. For instance: test [,1] [,2] [,3] [1,]1 100 21 [2,]23 22 [3,]3 100 23 [4,]4 60 24 [5,]5 55 25 [6,]6 45 26 [7,]7 75 27 [8,]8 12 28 [9,]9 10 29 [10,] 10 22 30 test[order(test[,2]),] [,1] [,2] [,3] [1,]23 22 [2,]9 10 29 [3,]8 12 28 [4,] 10 22 30 [5,]6 45 26 [6,]5 55 25 [7,]4 60 24 [8,]7 75 27 [9,]1 100 21 [10,]3 100 23 This works well and good in the above example matrix. However in the matrix that I actually want to sort (derived from a function that I wrote) I get something like this: test[order(as.numeric(test[,2])),] ### First column is row.names f con f.1 cov f.2 minimum f.3 maximum f.4 cl asahi* 100 * 1 * 0.1 * 2 * test castet * 100 * 2 * 0.1 * 5 * test clado* 100 * 1 * 0.7 * 2 * test aulac* 33 * 0 * 0.1 * 0.1 * test buell* 33 * 0 * 0.1 * 0.1 * test camlas * 33 * 0 * 0.1 * 0.1 * test carbig * 33 * 1 * 1 * 1 * test poaarc * 67 * 0 * 0.1 * 0.1 * test polviv * 67 * 0 * 0.1 * 0.1 * test where R interprets 100 to be the lowest value and orders increasing from there. is.numeric(test[,2]) [1] FALSE is.double(test[,2]) [1] FALSE is.integer(test[,2]) [1] FALSE is.real(test[,2]) [1] FALSE My questions are: Why is this happening? and How do I fix it? Thanks in advance! Aaron Wells _ cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 [[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] ordering
Kia ora Aaron As you have identified, test[,2] is not numeric - it is probably factor. Your function must have made the conversion, so you may want to modify that. Alternative, try: test[order(as.numeric(as.character(test[,2]))),] BTW, str(test) is a good way to find out more about the structure of your object. HTH Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of aaron wells Sent: Wednesday, 11 March 2009 8:30 a.m. To: r-help@r-project.org Subject: [R] ordering Hello, I would like to order a matrix by a specific column. For instance: test [,1] [,2] [,3] [1,]1 100 21 [2,]23 22 [3,]3 100 23 [4,]4 60 24 [5,]5 55 25 [6,]6 45 26 [7,]7 75 27 [8,]8 12 28 [9,]9 10 29 [10,] 10 22 30 test[order(test[,2]),] [,1] [,2] [,3] [1,]23 22 [2,]9 10 29 [3,]8 12 28 [4,] 10 22 30 [5,]6 45 26 [6,]5 55 25 [7,]4 60 24 [8,]7 75 27 [9,]1 100 21 [10,]3 100 23 This works well and good in the above example matrix. However in the matrix that I actually want to sort (derived from a function that I wrote) I get something like this: test[order(as.numeric(test[,2])),] ### First column is row.names f con f.1 cov f.2 minimum f.3 maximum f.4 cl asahi* 100 * 1 * 0.1 * 2 * test castet * 100 * 2 * 0.1 * 5 * test clado* 100 * 1 * 0.7 * 2 * test aulac* 33 * 0 * 0.1 * 0.1 * test buell* 33 * 0 * 0.1 * 0.1 * test camlas * 33 * 0 * 0.1 * 0.1 * test carbig * 33 * 1 * 1 * 1 * test poaarc * 67 * 0 * 0.1 * 0.1 * test polviv * 67 * 0 * 0.1 * 0.1 * test where R interprets 100 to be the lowest value and orders increasing from there. is.numeric(test[,2]) [1] FALSE is.double(test[,2]) [1] FALSE is.integer(test[,2]) [1] FALSE is.real(test[,2]) [1] FALSE My questions are: Why is this happening? and How do I fix it? Thanks in advance! Aaron Wells _ cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 [[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. The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited. __ 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] Sparse PCA in R
Dear all, I would like to perform a sparse PCA, but I didn't find any library offering me this in R. Is there one available, or do I have to write the functions myself? Kind regards Joris Meys [[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 color certain area under curve
guox at ucalgary.ca writes: For a given random variable rv, for instance, rv = rnorm(1000), I plot its density curve and calculate some quantiles: plot(density(rv)) P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) I would like to color the area between P10 and P90 and under the curve and mark the P50 on the curve. rv = rnorm(1000) plot(density(rv)) P10P50P90 = = quantile(rv,probs = c(10,50,90)/100) Could you please teach me how to do these using R? Thanks, -james see ?polygon Here after is an example of the use of polygon to solve your problem: rv - rnorm(1000) drv - density(rv) plot(drv) # further steps: # 1. compute quantiles # 2. determine the x and y of the area that must be drawn # 3. drawn # 4. add q.5 info qrv - quantile(rv, prob=c(0.1, 0.9)) select - qrv[1] = drv$x drv$x = qrv[2] polygon(x = c(qrv[1], drv$x[select], qrv[2]), y = c(0, drv$y[select], 0, col='blue') abline(v= quantile(rv, p=0.5), lty=2) Hope this will help. Matthieu __ 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] ordering
A) I predict that if you apply the str function to the second test that you will find that con is not numeric but rather of class character or factor. And the second test is probably not a matrix but rather a dataframe. Matrices in R need to have all their elements of the same class. B) Read the FAQ ... find the one that tells you how to convert factors to numeric. -- David Winsemius On Mar 10, 2009, at 3:29 PM, aaron wells wrote: Hello, I would like to order a matrix by a specific column. For instance: test [,1] [,2] [,3] [1,]1 100 21 [2,]23 22 [3,]3 100 23 [4,]4 60 24 [5,]5 55 25 [6,]6 45 26 [7,]7 75 27 [8,]8 12 28 [9,]9 10 29 [10,] 10 22 30 test[order(test[,2]),] [,1] [,2] [,3] [1,]23 22 [2,]9 10 29 [3,]8 12 28 [4,] 10 22 30 [5,]6 45 26 [6,]5 55 25 [7,]4 60 24 [8,]7 75 27 [9,]1 100 21 [10,]3 100 23 This works well and good in the above example matrix. However in the matrix that I actually want to sort (derived from a function that I wrote) I get something like this: test[order(as.numeric(test[,2])),] ### First column is row.names f con f.1 cov f.2 minimum f.3 maximum f.4 cl asahi* 100 * 1 * 0.1 * 2 * test castet * 100 * 2 * 0.1 * 5 * test clado* 100 * 1 * 0.7 * 2 * test aulac* 33 * 0 * 0.1 * 0.1 * test buell* 33 * 0 * 0.1 * 0.1 * test camlas * 33 * 0 * 0.1 * 0.1 * test carbig * 33 * 1 * 1 * 1 * test poaarc * 67 * 0 * 0.1 * 0.1 * test polviv * 67 * 0 * 0.1 * 0.1 * test where R interprets 100 to be the lowest value and orders increasing from there. is.numeric(test[,2]) [1] FALSE is.double(test[,2]) [1] FALSE is.integer(test[,2]) [1] FALSE is.real(test[,2]) [1] FALSE My questions are: Why is this happening? and How do I fix it? Thanks in advance! Aaron Wells _ cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ordering
Thanks Peter, that did the trick. I'll modify my function so that the numeric conversion is done automatically thus saving me the extra step of converting later on. Aaron Wells Subject: RE: [R] ordering Date: Wed, 11 Mar 2009 08:41:50 +1300 From: palsp...@hortresearch.co.nz To: awell...@hotmail.com; r-help@r-project.org Kia ora Aaron As you have identified, test[,2] is not numeric - it is probably factor. Your function must have made the conversion, so you may want to modify that. Alternative, try: test[order(as.numeric(as.character(test[,2]))),] BTW, str(test) is a good way to find out more about the structure of your object. HTH Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of aaron wells Sent: Wednesday, 11 March 2009 8:30 a.m. To: r-help@r-project.org Subject: [R] ordering Hello, I would like to order a matrix by a specific column. For instance: test [,1] [,2] [,3] [1,] 1 100 21 [2,] 2 3 22 [3,] 3 100 23 [4,] 4 60 24 [5,] 5 55 25 [6,] 6 45 26 [7,] 7 75 27 [8,] 8 12 28 [9,] 9 10 29 [10,] 10 22 30 test[order(test[,2]),] [,1] [,2] [,3] [1,] 2 3 22 [2,] 9 10 29 [3,] 8 12 28 [4,] 10 22 30 [5,] 6 45 26 [6,] 5 55 25 [7,] 4 60 24 [8,] 7 75 27 [9,] 1 100 21 [10,] 3 100 23 This works well and good in the above example matrix. However in the matrix that I actually want to sort (derived from a function that I wrote) I get something like this: test[order(as.numeric(test[,2])),] ### First column is row.names f con f.1 cov f.2 minimum f.3 maximum f.4 cl asahi * 100 * 1 * 0.1 * 2 * test castet * 100 * 2 * 0.1 * 5 * test clado * 100 * 1 * 0.7 * 2 * test aulac * 33 * 0 * 0.1 * 0.1 * test buell * 33 * 0 * 0.1 * 0.1 * test camlas * 33 * 0 * 0.1 * 0.1 * test carbig * 33 * 1 * 1 * 1 * test poaarc * 67 * 0 * 0.1 * 0.1 * test polviv * 67 * 0 * 0.1 * 0.1 * test where R interprets 100 to be the lowest value and orders increasing from there. is.numeric(test[,2]) [1] FALSE is.double(test[,2]) [1] FALSE is.integer(test[,2]) [1] FALSE is.real(test[,2]) [1] FALSE My questions are: Why is this happening? and How do I fix it? Thanks in advance! Aaron Wells _ cns!503D1D86EBB2B53C!2285.entry?ocid=TXT_TAGLM_WL_UGC_Contacts_032009 [[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. The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited. _ [[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] Nesting order for mixed models
Hello, I am confused about the order of nesting in mixed models using functions like aov(), lme(), lmer(). I have the following data: n subjects in either condition A or B each subject tested at each of 3 numerical values (distance = 40,50,60), repeated 4 times for each of the 3 numerical values (trial = 1,2,3,4) Variable summary: Condition: 2 level factor Distance: numerical (but only 3 values) in the same units as y Trial: 4 level factor I expect the subjects' data to differ due to condition and distance, and am doing repeated measurements to reduce any variability due to measurement error. Currently I'm using this model: lme(y ~ Condition + Distance, random = ...) the question is how do I organize the random statement? Is it: random = ~1 | Subject random = ~1 | Subject/Trial random = ~1 | Trial/Subject random = ~1 | Condition/Distance/Subject/Trial ...etc, or something else entirely? Mostly I'm unclear about whether the Trials should be grouped under subject because I expect the trials to be more similar within a subject than across subjects, or whether subjects should be grouped under trials because the trials are going to differ depending on the subject. If trials should be grouped under subjects, then do the condition or distance belong as well, since the trials will be most similar within each distance within each subject? Thanks in advance! - Jon -- Jon Zadra Department of Psychology University of Virginia P.O. Box 400400 Charlottesville VA 22904 (434) 982-4744 email: za...@virginia.edu http://www.google.com/calendar/embed?src=jzadra%40gmail.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] How to color certain area under curve
Just a small typo. I forgot a ) in the polygon function. The code must be: polygon(x = c(qrv[1], drv$x[select], qrv[2]), y = c(0, drv$y[select], 0), col='blue') __ 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] Sparse PCA in R
Take a look at the elasticnet package. -Christos -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of joris meys Sent: Tuesday, March 10, 2009 3:43 PM To: R-help Mailing List Subject: [R] Sparse PCA in R Dear all, I would like to perform a sparse PCA, but I didn't find any library offering me this in R. Is there one available, or do I have to write the functions myself? Kind regards Joris Meys [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] system() not accepting strings from cat()
Hi again R-ists, How do you construct a string that you can pass to system()? For instance. Say I do system(echo Hello!) Hello! That works. Now the alternative: I need to construct the string like this a - echo b - Hello! c - \n cat(a, b, c) echo Hello! Looks nice... but see what happens when I try to use it system(cat(a, b, c)) echo Hello! Error in system(command, intern) : non-empty character argument expected I have googled extensively in and out of r-lists but I can't find a solution. Can anybody help? __ 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] help structuring mixed model using lmer()
Hi Simon, Have a look at Chap. 11 of An Introduction to R (one of R's manuals), which explains the different ways of specifying models using formulae. Briefly, y ~ x1 * x2 expands to y ~ x1 + x2 + x1:x2, where the last term (interaction term) amounts to a test of slope. Normally you would read its significance from F/chisq/p-value. Many practitioners consider the L.Ratio test to be a better option. For the fixed effects part in lmer() do: mod1 - y ~ x1 + x2 == y ~ x1 + x2 mod2 - y ~ x1 * x2 == y ~ x1 + x2 + x1:x2 anova(mod1, mod2) This will tell you if you need to worry about interaction or whether slopes are parallel. Regards, Mark. Simon Pickett-4 wrote: Cheers, Actually I was using quasipoisson for my models, but for the puposes of my example, it doesnt really matter. I am trying to work out a way of quantifying whether the slopes (for years) are covary with habitat scores. The more I think about it, the more I am convinced that it isnt possible do to that using a glm approach. I think I have to run separate models for each site, calculate the gradient, then do a lm with gradient explained by habitat score Thanks, Simon. On Tue, Mar 10, 2009 at 10:15 AM, Simon Pickett simon.pick...@bto.org wrote: This is partly a statistical question as well as a question about R, but I am stumped! I have count data from various sites across years. (Not all of the sites in the study appear in all years). Each site has its own habitat score habitat that remains constant across all years. I want to know if counts declined faster on sites with high habitat scores. I can construct a model that tests for the effect of habitat as a main effect, controlling for year model1-lmer(count~habitat+yr+(1|site), family=quasibinomial,data=m) model2-lmer(count~yr+(1|site), family=quasibinomial,data=m) anova(model1,model2) I'm curious as to why you use the quasibinomial family for count data. When you say count data do you mean just presence/absence or an actual count of the number present? Generally the binomial and quasibinomial families are used when you have a binary response, and the poisson or quasipoisson family are used for responses that are counts. __ 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://www.nabble.com/help-structuring-mixed-model-using-lmer%28%29-tp22436596p22441985.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.
