Re: [R] avoiding a loop: cumsum-like
Hi
I have not seen any answer yet so I wil try (partly).
I believe that the loop can be vectorised but I am a little bit lost
in your fors and ifs. I found that first part of res is same as
cumsum(tab$x.jour) until about 81st value. However I did not decipher
how to compute the remaining part. I tried to add
cumsum(tab$posit.lat) (after changing NA to 0) what is not correct.
Probably some combination of logical operation and summing can do
what you want. I thought that something like
((cumsum(tab$posit.lat)*0.8)*(cumsum(tab$x.jour)30)+cumsum(tab$x.jour
))
can do it but the result is defferent from your computation.
Not much of help, but maybe you can do better with above suggestion.
Petr
On 2 Nov 2006 at 11:15, GOUACHE David wrote:
Date sent: Thu, 2 Nov 2006 11:15:49 +0100
From: GOUACHE David [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Subject:[R] avoiding a loop: cumsum-like
Hello Rhelpers,
I need to run the following loop over a large number of data-sets, and
was wondering if it could somehow be vectorized. It's more or less a
cumulative sum, but slightly more complex. Here's the code, and an
example dataset (called tab in my code) follows. Thanks in advance for
any suggestions!
res-0
for (i in min(tab$Date):max(tab$Date))
{
if (is.na(tab$posit.lat[tab$Date==i])==T)
{
res-c(res,res[length(res)]+tab$x.jour[tab$Date==i])
}
else
{
if (res[tab$posit.lat[tab$Date==i]+1]30)
{
res-c(res,res[length(res)]+tab$x.jour[tab$Date==i])
}
else
{
res-c(res,res[length(res)]+tab$x.jour[tab$Date==i]+0.8*res[tab$pos
it.lat[tab$Date==i]+1])
}
}
}
res[-1]
Date x.jour posit.lat
35804 0 NA
35805 0 NA
35806 0 NA
35807 0 NA
35808 0 NA
35809 2.97338883 NA
35810 2.796389915 NA
35811 0 NA
35812 0 NA
35813 1.000711886 NA
35814 0.894422571 NA
35815 0 NA
35816 0 NA
35817 0 NA
35818 0 NA
35819 0 NA
35820 0 NA
35821 0 NA
35822 0 NA
35823 0 NA
35824 0 NA
35825 0 NA
35826 0 NA
35827 0 NA
35828 0 NA
35829 0 NA
35830 0 NA
35831 0 NA
35832 0 NA
35833 0 NA
35834 0 NA
35835 0 NA
35836 0 NA
35837 0 NA
35838 0 NA
35839 0 NA
35840 2.47237455 NA
35841 0 2
35842 0 3
35843 0 4
35844 0 5
35845 0 6
35846 0 7
35847 4.842160488 8
35848 2.432125036 9
35849 0 10
35850 0 12
35851 0 14
35852 0 16
35853 3.739683882 18
35854 1.980214421 20
35855 0 22
35856 0 24
35857 5.953444078 27
35858 6.455722475 29
35859 0 31
35860 3.798690334 32
35861 6.222993364 34
35862 3.746243098 35
35863 0 35
35864 0 36
35865 0 37
35866 0 38
35867 0 38
35868 0 39
35869 0 40
35870 0 41
35871 0 42
35872 0 43
35873 0 44
35874 0 45
35875 0 46
35876 0 47
35877 1.951774892 48
35878 0 49
35879 0 50
35880 1.702837643 50
35881 0 52
35882 0 53
35883 0 54
35884 0 55
35885 5.953444078 57
35886 0 58
35887 5.737515358 59
35888 0 61
35889 6.215941227 63
35890 4.731576675 64
35891 0 66
35892 2.255448314 66
35893 3.782283008 67
35894 3.244474546 68
35895 1.808553193 69
35896 2.622680002 70
35897 0 71
35898 0 72
35899 0 72
35900 1.7084177 73
35901 1.28455982 74
35902 2.320013736 76
35903 0 77
35904 0 78
35905 0 79
35906 0 79
35907 0 80
35908 6.716812458 81
35909 0 82
35910 6.796571531 84
35911 5.573668337 85
35912 5.42513958 86
35913 3.774513877 86
35914 0 87
35915 0 89
35916 0 90
35917 4.208252725 91
35918 0 92
35919 0 93
35920 0 95
35921 5.70023661 97
35922 0 98
35923 0 100
35924 0 102
35925 0 103
35926 0 104
David Gouache
Arvalis - Institut du Végétal
Station de La Miničre
78280 Guyancourt
Tel: 01.30.12.96.22 / Port: 06.86.08.94.32
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented,
minimal, self-contained, reproducible code.
Petr Pikal
[EMAIL PROTECTED]
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[R] Installing a package - and making it work?
Dear list - Propoerly a beginner question, so bare with my frustration... I tried install the 'shapefiles' package into R 2.4.0 but it seems that the install had little effect... install.packages(c(shapefiles)) --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.dk.r-project.org/bin/windows/contrib/2.4/shapefiles_0.5.zip' Content type 'application/zip' length 42335 bytes opened URL downloaded 41Kb package 'shapefiles' successfully unpacked and MD5 sums checked The downloaded packages are in C:\TEMP\RtmpMz5Pqb\downloaded_packages updating HTML package descriptions dbf - read.dbf(test.dbf) Error: could not find function read.dbf Note thet the last line contains an error. Is the package installed or not? How do I get access to use the functionality it offers?? :-? Martin Hvidberg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Installing a package - and making it work?
On Fri, 3 Nov 2006, Hvidberg, Martin wrote: Dear list - Propoerly a beginner question, so bare with my frustration... I tried install the 'shapefiles' package into R 2.4.0 but it seems that the install had little effect... install.packages(c(shapefiles)) --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.dk.r-project.org/bin/windows/contrib/2.4/shapefiles_0.5.zip' Content type 'application/zip' length 42335 bytes opened URL downloaded 41Kb package 'shapefiles' successfully unpacked and MD5 sums checked The downloaded packages are in C:\TEMP\RtmpMz5Pqb\downloaded_packages updating HTML package descriptions library(shapefiles) dbf - read.dbf(test.dbf) Error: could not find function read.dbf Note thet the last line contains an error. Is the package installed or not? yes. The book (package) is in the library (is is installed). But you need to take it from the shelf and open it to read (load it into R via `library(pkgname)'). Best wishes, Torsten How do I get access to use the functionality it offers?? :-? Martin Hvidberg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Installing a package - and making it work?
On Fri, 3 Nov 2006, Hvidberg, Martin wrote: Dear list - Propoerly a beginner question, so bare with my frustration... Yes, and posting to R-help three minutes after posting to R-sig-geo, the correct list - raises the question about who's time is more important, doesn't it? What does help.search(read.dbf) tell you? (hint: read.dbf() in shapefiles calls read.dbf() in the recommended foreign package, which is certainly already present in your (unstated) Windows binary R 2.4.0 installation.) I tried install the 'shapefiles' package into R 2.4.0 but it seems that the install had little effect... install.packages(c(shapefiles)) --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.dk.r-project.org/bin/windows/contrib/2.4/shapefiles_0.5.zip' Content type 'application/zip' length 42335 bytes opened URL downloaded 41Kb package 'shapefiles' successfully unpacked and MD5 sums checked The downloaded packages are in C:\TEMP\RtmpMz5Pqb\downloaded_packages updating HTML package descriptions dbf - read.dbf(test.dbf) Error: could not find function read.dbf Note thet the last line contains an error. Is the package installed or not? How do I get access to use the functionality it offers?? :-? Martin Hvidberg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Compare linear regressios for significant differenc es of the slopes
Rainer M Krug wrote: I have (8 measures * 96 groups) = 768 datasets for which I did linear regressions using lm(). Now I want to compare the slopes for each of the 8 measures in each of the 96 groups. As I understand , I can not use anova(lm1, ..., lm8) as the lm1 ... lm8 are based on different datasets. Instead of doing this in two steps, you would better use lme in package nlme to test the hypothesis in one run. I don't understand the details of you design, but is looks like the oxboys example in Pinheiro/Bates (the book of nlme) could give you a first starter. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Installing a package - and making it work?
On Fri, 3 Nov 2006, Torsten Hothorn wrote: On Fri, 3 Nov 2006, Hvidberg, Martin wrote: Dear list - Propoerly a beginner question, so bare with my frustration... I tried install the 'shapefiles' package into R 2.4.0 but it seems that the install had little effect... install.packages(c(shapefiles)) --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.dk.r-project.org/bin/windows/contrib/2.4/shapefiles_0.5.zip' Content type 'application/zip' length 42335 bytes opened URL downloaded 41Kb package 'shapefiles' successfully unpacked and MD5 sums checked The downloaded packages are in C:\TEMP\RtmpMz5Pqb\downloaded_packages updating HTML package descriptions library(shapefiles) dbf - read.dbf(test.dbf) Error: could not find function read.dbf Note thet the last line contains an error. Is the package installed or not? yes. The book (package) is in the library (is is installed). But you need to take it from the shelf and open it to read (load it into R via `library(pkgname)'). Yes, rather a FAQ, and certainly the cause of the questioner's problem. Perhaps reading sections 5.2 and 5.3 of the R FAQ? Or looking at the Windows Packages menu a bit more carefully? Reading what sessionInfo() says? Roger Best wishes, Torsten How do I get access to use the functionality it offers?? :-? Martin Hvidberg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Prediction intervals for predict.gls
Spencer Jones ssj1364 at gmail.com writes: I am using R 2.3.0, Is there a way to get prediction intervals using predict.gls? A r-project site search (alway recommended) would have given you http://finzi.psych.upenn.edu/R/Rhelp02a/archive/42932.html Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 a deriv function in nlme
Hello,
I have a deriv function that I am feeding to nlme. It works, and I can use
it in nls, but when I try to use it in nlme I get Error: subscript out of
bounds. I can fit the model using SSasympOrig, instead of the deriv
function, but I am trying to reproduce an earlier analysis (done in Splus)
and I get slightly different results with SSasympOrig.
Here are my calls:
This does fit the nlme model:
L1.lis-nlsList(SSasympOrig,L1.gd)
L1.nlme-nlme(L1.lis)
Here is the derive function -it works for the nls call:
boundedexp-deriv(~100/(1+exp(-L))*(1-exp(-exp(logR)*x)),
c(L, logR), function(x,L,logR){} )
L1.nls-nls(ability ~ boundedexp(age,limit,lograte),
data=L1.gd, start=c(limit=2,lograte=-3))
summary(L1.nls)
. but here I run into problems
L1.nlme2-nlme(ability~boundedexp(age,limit,lograte),
data=L1.gd, fixed=limit+lograte~1,start=c(limit=2,lograte=-3))
Any suggestions would be well appreciated!
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] Forest plot
Need to modify ods ratios (like ods ratios from rmeta) so that they can line forest plot? How to do that? Branko! Branko Education inc. Brd. Icc. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] correaltion equal 1
Dear All, I wonder if this is a technical or an interpretation problem. I fitted an lme model including a random intercept and a random slope. The estimated correlation, from the lme, between the random intercept and the random slope is equal to 1. Does it mean that I should suppress one of the random effect from the model? Thanks a lot, Bernard - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] correaltion equal 1
or, it could mean you need to recenter your time variable. -Original Message- From: [EMAIL PROTECTED] on behalf of Marc Bernard Sent: Fri 11/3/2006 7:24 AM To: r-help@stat.math.ethz.ch Subject: [R] correaltion equal 1 Dear All, I wonder if this is a technical or an interpretation problem. I fitted an lme model including a random intercept and a random slope. The estimated correlation, from the lme, between the random intercept and the random slope is equal to 1. Does it mean that I should suppress one of the random effect from the model? Thanks a lot, Bernard - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Likelihood of multiple random processes
this way the problem is not well posed. You need to place an upper bound on the number of distributions in the mixture you want to estimate, for otherwise the likelihood is unbounded (take one normal distribution for each value in your data). - Original Message - Do you know which observations came from which process (you do in your example, but it whatever it is supposed to emulate)? No- I need to determine whether more than one process could have been involved. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Rank transformation and the linear mixed model
Hello, I am looking for references about mixed models built on rank transformed data. Did anybody ever consider this topic? Thank you, Bruno ~~ Bruno L. Giordano, Ph.D. CIRMMT Schulich School of Music, McGill University 555 Sherbrooke Street West Montréal, QC H3A 1E3 Canada http://www.music.mcgill.ca/~bruno/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Compare linear regressios for significant differences of the slopes
Dieter Menne wrote: Rainer M Krug wrote: I have (8 measures * 96 groups) = 768 datasets for which I did linear regressions using lm(). Sorry for my (probably incorrect) usage of group and measure. Here a (probably better) description of my design: I ran 96 different simulations (spread of a species along a transect) over four generations, based on different parameter sets. These resulted in 96 results (groups). Now I have 8 different ways to describe the result of one simulation based on x individuals further away then distance d, where x is replaced by 1, 5, 10, 50, 100, 500, 1000 and 5000 (measures). For each group / simulation, I did linear regressions for each measure lm.measure_1 - lm(distance ~ generation) ... resulting in lm.measure_1 to lm.measure_8 Within each group (based on one simulation), I get a different slope for each measure. What I want to know is if these resulting slopes differ within one group / simulation. Now I want to compare the slopes for each of the 8 measures in each of the 96 groups. As I understand , I can not use anova(lm1, ..., lm8) as the lm1 ... lm8 are based on different datasets. Instead of doing this in two steps, you would better use lme in package nlme to test the hypothesis in one run. I don't understand the details of you design, but is looks like the oxboys example in Pinheiro/Bates (the book of nlme) could give you a first starter. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation Biology (UCT) Department of Conservation Ecology and Entomology University of Stellenbosch Matieland 7602 South Africa Tel:+27 - (0)72 808 2975 (w) Fax:+27 - (0)21 808 3304 Cell: +27 - (0)83 9479 042 email: [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] difference in using with() and the data argument in glm call
Dear all,
I am dealing with the following (apparently simple problem):
For some reasons I am interested in passing variables from a dataframe
to a specific environment, and in fitting a standard glm:
dati-data.frame(y=rnorm(10),x1=runif(10),x2=runif(10))
KK-new.env()
for(i in 1:ncol(dati)) assign(names(dati[i]),dati[[i]],envir=KK)
#Now the following two lines work correctly:
coef(glm(y~x1+x2,data=KK))
with(KK,coef(glm(y~x1+x2)))
#However if I write the above code inside a function, with() does not
appear to work..
ff-function(Formula,Data,method=1){
KK-new.env()
for(i in 1:ncol(Data)) assign(names(Data[i]),Data[[i]],envir=KK)
o-if(method==1) glm(Formula,data=KK) else with(KK,glm(Formula))
o}
ff(y~x1+x2,dati,1) #it works
Call: glm(formula = Formula, data = KK)
..[SNIP]..
ff(y~x1+x2,dati,2) #it does not
Error in eval(expr, envir, enclos) : object y not found
Could anyone to explain such difference? I believed that
with(data,glm(formula)) and glm(formula,data) were equivalent.
Many thanks,
vito
--
Vito M.R. Muggeo
Dip.to Sc Statist e Matem `Vianelli'
Università di Palermo
viale delle Scienze, edificio 13
90128 Palermo - ITALY
tel: 091 6626240
fax: 091 485726/485612
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] rcompletion: TAB completion for the R command line
Just a quick follow-up. Thanks to Simon Urbanek and hints from Alexandre Aguiar, CRAN now has a version (0.0-10) of rcompletion that should work on more systems. If it still doesn't work when you think it should, please let me know. -Deepayan On 10/30/06, Deepayan Sarkar [EMAIL PROTECTED] wrote: CRAN now has a package called rcompletion that attempts to provide TAB completion for R using the GNU readline library, intended for R sessions run from a command line. From the package help page: ... ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Rank transformation and the linear mixed model
- Original Message - From: Frank E Harrell Jr [EMAIL PROTECTED] To: Bruno L. Giordano [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Friday, November 03, 2006 8:22 AM Subject: Re: [R] Rank transformation and the linear mixed model Bruno L. Giordano wrote: Hello, I am looking for references about mixed models built on rank transformed data. Did anybody ever consider this topic? Thank you, Bruno If you are speaking about the response variable, it's better to use a formal model such as the proportional odds model (generalization of the Wilcoxon test). That way you can do meaningful interaction tests and much more, plus handle ties elegantly with likelihood ratio tests. Some researchers have developed mixed effects prop. odds models (which I haven't used yet). Frank That's a nice start indeed!! However, I am referring both to rank transformation of response variables and covariates. The reference to this idea is the work by Conover and Iman (e.g., Conover and Iman - 1981 - Rank transformations as a bridge between parametric and nonparametric statistics). The need would be to handle robustly monotone and nonlinear response-covariates relationships. Bruno ~~ Bruno L. Giordano, Ph.D. CIRMMT Schulich School of Music, McGill University 555 Sherbrooke Street West Montréal, QC H3A 1E3 Canada http://www.music.mcgill.ca/~bruno/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] difference in using with() and the data argument in glm call
It looks into the data argument first and if not found there it looks into
environment(formula). Thus to pick it out of the 'with' try this:
with(KK, glm(fo, data = environment())
Also you could try this:
environment(fo) - KK
glm(fo)
On 11/3/06, vito muggeo [EMAIL PROTECTED] wrote:
Dear all,
I am dealing with the following (apparently simple problem):
For some reasons I am interested in passing variables from a dataframe
to a specific environment, and in fitting a standard glm:
dati-data.frame(y=rnorm(10),x1=runif(10),x2=runif(10))
KK-new.env()
for(i in 1:ncol(dati)) assign(names(dati[i]),dati[[i]],envir=KK)
#Now the following two lines work correctly:
coef(glm(y~x1+x2,data=KK))
with(KK,coef(glm(y~x1+x2)))
#However if I write the above code inside a function, with() does not
appear to work..
ff-function(Formula,Data,method=1){
KK-new.env()
for(i in 1:ncol(Data)) assign(names(Data[i]),Data[[i]],envir=KK)
o-if(method==1) glm(Formula,data=KK) else with(KK,glm(Formula))
o}
ff(y~x1+x2,dati,1) #it works
Call: glm(formula = Formula, data = KK)
..[SNIP]..
ff(y~x1+x2,dati,2) #it does not
Error in eval(expr, envir, enclos) : object y not found
Could anyone to explain such difference? I believed that
with(data,glm(formula)) and glm(formula,data) were equivalent.
Many thanks,
vito
--
Vito M.R. Muggeo
Dip.to Sc Statist e Matem `Vianelli'
Università di Palermo
viale delle Scienze, edificio 13
90128 Palermo - ITALY
tel: 091 6626240
fax: 091 485726/485612
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] Rank transformation and the linear mixed model
Bruno L. Giordano wrote: - Original Message - From: Frank E Harrell Jr [EMAIL PROTECTED] To: Bruno L. Giordano [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Friday, November 03, 2006 8:22 AM Subject: Re: [R] Rank transformation and the linear mixed model Bruno L. Giordano wrote: Hello, I am looking for references about mixed models built on rank transformed data. Did anybody ever consider this topic? Thank you, Bruno If you are speaking about the response variable, it's better to use a formal model such as the proportional odds model (generalization of the Wilcoxon test). That way you can do meaningful interaction tests and much more, plus handle ties elegantly with likelihood ratio tests. Some researchers have developed mixed effects prop. odds models (which I haven't used yet). Frank That's a nice start indeed!! However, I am referring both to rank transformation of response variables and covariates. The reference to this idea is the work by Conover and Iman (e.g., Conover and Iman - 1981 - Rank transformations as a bridge between parametric and nonparametric statistics). That has largely been replaced by flexible right-hand-side regression modeling (regression splines, gams, etc). These will handle any smooth shape and allow for modeling interactions. The problem with Conover and Iman's method is that when more than one X-variable is being ranked, interpretation of partial effects is difficult, and interpretation of interactions is nearly impossible. Frank The need would be to handle robustly monotone and nonlinear response-covariates relationships. Bruno ~~ Bruno L. Giordano, Ph.D. CIRMMT Schulich School of Music, McGill University 555 Sherbrooke Street West Montréal, QC H3A 1E3 Canada http://www.music.mcgill.ca/~bruno/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Error in X11(): Font Path?
Hy, I had the some problem. In my case an adjustment of the X11 font path, in the xorg.conf file did solve the problem. The fonts on my system were located in /usr/share/fonts and not in /usr/share/X11/fonts. Cheers Marc __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Rank transformation and the linear mixed model
Bruno L. Giordano bruno.giordano at music.mcgill.ca writes: I am looking for references about mixed models built on rank transformed data. To complement Frank H: Try lrm in package Design. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 a deriv function in nlme
Lisa Avery lisa_avery at sympatico.ca writes: Hello, I have a deriv function that I am feeding to nlme. It works, and I can use it in nls, but when I try to use it in nlme I get Error: subscript out of bounds. I can fit the model using SSasympOrig, instead of the deriv It might by a similar problem as in http://finzi.psych.upenn.edu/R/Rhelp02a/archive/4555.html Dieter Menne __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] read file problem
R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want Thanks in advance version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] identify extremes positions of values into matrix
Hi R-friends around world! I have a matrix that looks like bellow one. Each cell are filled with values 0, 1 or 2. In fact I have a lot of 512x512 matrices, with values varying from 0 to 999. I need to retrieve the left and right columns and the top and botton lines of the matrix where occours for example the value 2. Column and row labels are included at the example. 1234567890 1 00 2 011100 3 011100 4 00 5 002220 6 000222 7 002200 8 00 At this example, the right answer are: collumns 3 and 8 lines 5 and 7 Any idea of how can I solve this? Kind regards, Miltinho - Música para ver e ouvir: You're Beautiful, do James Blunt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] identify extremes positions of values into matrix
try this: # `mat' is your matrix apply(which(mat == 2, arr.ind = TRUE), 2, range) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Milton Cezar Ribeiro [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Friday, November 03, 2006 3:25 PM Subject: [R] identify extremes positions of values into matrix Hi R-friends around world! I have a matrix that looks like bellow one. Each cell are filled with values 0, 1 or 2. In fact I have a lot of 512x512 matrices, with values varying from 0 to 999. I need to retrieve the left and right columns and the top and botton lines of the matrix where occours for example the value 2. Column and row labels are included at the example. 1234567890 1 00 2 011100 3 011100 4 00 5 002220 6 000222 7 002200 8 00 At this example, the right answer are: collumns 3 and 8 lines 5 and 7 Any idea of how can I solve this? Kind regards, Miltinho - Música para ver e ouvir: You're Beautiful, do James Blunt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 CMD BATCH: unable to start device PNG
Dear r-helpers: Any ideas how to avoid problem described below? I am having the same problem when I run R remotly (not from cgi script); somehow png device wants to talk to X11 and X11 complains... Best regards, Ryszard error msg from batch R process (Linux/R-2.4.0) (executed on Apache server from cgi script): Error in X11(paste(png::, filename, sep = ), width, height, pointsize, : unable to start device PNG In addition: Warning message: unable to open connection to X11 display '' Execution halted [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 went away from top emacs window :-(
On 11/3/2006 12:02 AM, Spencer Graves wrote: This change has created problems for me using XEmacs 21.4.19 with ESS 5.3.1 ?help Error in print.help_files_with_topic(c:/progra~1/R/R-2.4.0/library/utils/chm/help) : CHM file could not be displayed sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 Can one of you ESS users track down what's going wrong? When I run Rterm at a command prompt with the --ess option, I have no trouble displaying CHMHELP. It looks to me like an Emacs bug, but I can't really see how it could cause that particular error message. Duncan Murdoch locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base Restoring the previous default with options(chmhelp=FALSE) eliminates this problem. From the time I first noticed this problem until just prior to reading this thread, I used RGui to get help. (It wasn't hard to think of this, because 'install.packages' under ESS goes waits for me to select a mirror -- but without asking me to select such! Result: I used RGui instead of Rterm under XEmacs to install.packages.) FYI. Thanks for all your great efforts on R. It has definitely made me much more productive, and I believe it is making substantive contributions to the improvement of people's quality of life all over the world. Best Wishes, Spencer Graves Richard M. Heiberger wrote: I agree with both Duncan and Martin. With Duncan, that this is not a Windows FAQ. With Martin, that it is an FAQ. I recommend that it go on the R FAQ page, prior to the current 7.24. Here is a draft of the question and an outline of the answer. 7.24 Why does the help information, for example when I type ?lm, show up in (a browser window, an emacs buffer in its own frame, an emacs buffer in the same frame as *R*, in a Windows-style help window, in a new frame inside the Rgui window, in a new frame on the computer screen)? I really want it in the (choose from the same list). The answer includes at least the following: On Windows, set options(chmhelp=TRUE/FALSE). With Java, use help.start() In emacs, set the emacs variable ess-help-frame On the correct default for ESS, I am not sure for myself. I can see a case both for help in emacs buffers and in the chmhelp window. This week I am tending to the chmhelp window, even when on emacs. Rich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 went away from top emacs window :-(
I located what might be the problem. There is a different misbehavior with Gnu emacs. I don't have Xemacs. I have an idea how to fix it but haven't worked out the details. ess-inf.el in the lines (defconst inferior-R-1-input-help (format ^ *help *(%s) ess-help-arg-regexp)) (defconst inferior-R-2-input-help (format ^ *\\? *%s ess-help-arg-regexp)) (defconst inferior-R-page (format ^ *page *(%s) ess-help-arg-regexp)) detects help requests from the commandline in the *R* buffer and redirects their output to an emacs *help[R] (whatever)* buffer. In gnu emacs on windows, with options(chmhelp=TRUE), the effect is an empty *help[R] (whatever)* buffer. What I think happened is that ESS trapped the request and created the buffer, then R never got the right content to send to that buffer because R thinks that chm is handling it. The fix probably requires ESS to check the value of the chmhelp option and suppress the interception of help requests if the option has the value TRUE. ESS also needs to monitor if that option has been changed. This might mean that ESS always intercepts help requests and checks the value of the option each time. Rich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 went away from top emacs window :-(
This change has created problems for me using XEmacs 21.4.19 with ESS 5.3.1 ?help Error in print.help_files_with_topic(c:/progra~1/R/R-2.4.0/library/utils/chm/help) : CHM file could not be displayed sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base Restoring the previous default with options(chmhelp=FALSE) eliminates this problem. From the time I first noticed this problem until just prior to reading this thread, I used RGui to get help. (It wasn't hard to think of this, because 'install.packages' under ESS goes waits for me to select a mirror -- but without asking me to select such! Result: I used RGui instead of Rterm under XEmacs to install.packages.) FYI. Thanks for all your great efforts on R. It has definitely made me much more productive, and I believe it is making substantive contributions to the improvement of people's quality of life all over the world. Best Wishes, Spencer Graves Richard M. Heiberger wrote: I agree with both Duncan and Martin. With Duncan, that this is not a Windows FAQ. With Martin, that it is an FAQ. I recommend that it go on the R FAQ page, prior to the current 7.24. Here is a draft of the question and an outline of the answer. 7.24 Why does the help information, for example when I type ?lm, show up in (a browser window, an emacs buffer in its own frame, an emacs buffer in the same frame as *R*, in a Windows-style help window, in a new frame inside the Rgui window, in a new frame on the computer screen)? I really want it in the (choose from the same list). The answer includes at least the following: On Windows, set options(chmhelp=TRUE/FALSE). With Java, use help.start() In emacs, set the emacs variable ess-help-frame On the correct default for ESS, I am not sure for myself. I can see a case both for help in emacs buffers and in the chmhelp window. This week I am tending to the chmhelp window, even when on emacs. Rich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 went away from top emacs window :-(
I located what might be the problem. There is a different misbehavior with Gnu emacs. I don't have Xemacs. I have an idea how to fix it but haven't worked out the details. ess-inf.el in the lines (defconst inferior-R-1-input-help (format ^ *help *(%s) ess-help-arg-regexp)) (defconst inferior-R-2-input-help (format ^ *\\? *%s ess-help-arg-regexp)) (defconst inferior-R-page (format ^ *page *(%s) ess-help-arg-regexp)) detects help requests from the commandline in the *R* buffer and redirects their output to an emacs *help[R] (whatever)* buffer. In gnu emacs on windows, with options(chmhelp=TRUE), the effect is an empty *help[R] (whatever)* buffer. What I think happened is that ESS trapped the request and created the buffer, then R never got the right content to send to that buffer because R thinks that chm is handling it. The fix probably requires ESS to check the value of the chmhelp option and suppress the interception of help requests if the option has the value TRUE. ESS also needs to monitor if that option has been changed. This might mean that ESS always intercepts help requests and checks the value of the option each time. Rich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 CMD BATCH: unable to start device PNG
[EMAIL PROTECTED] wrote: Dear r-helpers: Any ideas how to avoid problem described below? I am having the same problem when I run R remotly (not from cgi script); somehow png device wants to talk to X11 and X11 complains... Best regards, Ryszard error msg from batch R process (Linux/R-2.4.0) (executed on Apache server from cgi script): Error in X11(paste(png::, filename, sep = ), width, height, pointsize, : unable to start device PNG In addition: Warning message: unable to open connection to X11 display '' Execution halted Here's a snippet from the png help page: 'bitmap' provides an alternative way to generate PNG and JPEG plots that does not depend on accessing the X11 display but does depend on having GhostScript installed. (Device 'GDD' in 'GDD' is another alternative using several other additional pieces of software.) You can find GDD and another alternative Cairo here: http://www.rosuda.org/R Jeff -- http://biostat.mc.vanderbilt.edu/JeffreyHorner __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] read file problem
Hi If the file is tab delimited you could try something like this: a-read.delim(file, skip = 9, header=F, na.strings=NA) Are you sure you want to skip 10 lines? (Is there a blank line somewhere?) J --- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Luis Ridao Cruz Sent: 03 November 2006 14:03 To: r-help@stat.math.ethz.ch Subject: [R] read file problem R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want Thanks in advance version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] read file problem
You should pay attention to the argument na.string. na.strings: a character vector of strings which are to be interpreted as 'NA' values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields. On 11/3/06, Luis Ridao Cruz [EMAIL PROTECTED] wrote: R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want Thanks in advance version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ronggui Huang Department of Sociology Fudan University, Shanghai, China 黄荣贵 复旦大学社会学系 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] read file problem
On Fri, Nov 03, 2006 at 02:02:35PM +, Luis Ridao Cruz wrote: DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 read.table(file, skip = 10) To me it looks like your data is in a fixed-width format. If that is the case you should use read.fwf() instead of read.table(). cu Philipp -- Dr. Philipp PagelTel. +49-8161-71 2131 Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186 Technical University of Munich Science Center Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] read file problem
Luis Ridao Cruz wrote: R-help, I have the following file I want to import to R (some lines removed) Calibrated CTD data for station:00280001 Calibrated:23/8 2001, Salinity Unsmoothed, Fluorescence Uncalibrated Maximum observed depth:36 m QUAL has one digit for each of pressure, temp., sal. and fluor. QUAL=1:Uncal., QUAL=2:OK, QUAL=6:Interp., QUAL=9:No data DEPTH CTDPRS CTDTMP CTDSAL RAWFLU NUMB. QUAL MDBAR IPTS-68 PSS-78 OBS. *** *** *** *** 1 1.0 2999 2 2.0 5.9793 35.1629.10717 2221 3 3.0 5.9797 35.1631.10117 2221 4 4.0 5.9809 35.1631.11812 2221 5 5.1 5.9811 35.1629.11542 2221 6 6.1 5.9810 35.1631.11618 2221 7 7.1 5.9797 35.1631.11615 2221 8 8.1 5.9798 35.1630.10213 2221 9 9.1 5.9792 35.1629.11311 2221 ... . If I use : read.table(file, skip = 10) it works fine but sometimes the missing data are not only in line number 1 ( 1 1.0 2999) but in lines 1,2,3,,, and therefore R fails to import the data file How can I fix it? I have tried with the arguments strip.white = TRUE , fill = TRUE , blank.lines.skip = TRUE but still not get what I want This looks like a job for read.fwf... ?read.fwf -- --- Jeff NewmillerThe . . Go Live... DCN:[EMAIL PROTECTED]Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] maps. display hierararchical cluster analysis results on a map?
Besides symbols, size and color ramps come to mind Marsh Feldman -Original Message- From: David Farrar [mailto:[EMAIL PROTECTED] Sent: Thursday, November 02, 2006 9:37 PM To: R-help@stat.math.ethz.ch Subject: [R] maps. display hierararchical cluster analysis results on a map? All, I have done a cluster analysis analysis of some spatial locations, based on variables other than lat-long, and want to show the results on a map to see if my clusters have some geographic meaning. For kmeans (etc.) I would just use different symbols (etc.) to distinguish the clusters, but I am doing hierarchical CA. I am looking for ideas or (better) code. One idea would be to display the convex hull of each cluster on the map. Another would be to place some graph on the map, connecting the locations, with the same topology as my dendrogram. It seems like something useful would have been developed by biologists studying geographic variation of a species. Any ideas will be greatly appreciated. regards, Farrar [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] generic arrays in R
On Fri, Nov 03, 2006 at 07:20:34AM +, Prof Brian Ripley wrote: but a - array(list(f),c(2,2)) a[[2,1]] Thank you very much. Can you please tell me how to make apply generate arrays like this? Eg if a - array(1:16,rep(2,4)) then a apply(a,c(1,2,4), polynomial) will just give me a regular array of numbers, and apply(a,c(1,2,4),function(x) list(polynomial(x))) give me a generic array, but the polynomials I want are inside lists: I need constructs like [[1,1,1]][[1]] to access them. I would like to get a 3-way array with polynomials in it. It seems to work with function(x) splinefun(c(0,1),x) instead of polynomial, but array just converts polynomials into vectors... How can I protect them? Thank you, Tamas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Eilig Geschaftsvorschlag
Attn. Geschäftsvorschlag. Zuerst muß ich um Ihre Zuversicht in dieser verhandlung bitten. Das ist auf Grund seiner lage, als das sein total VERTRAULICH und Geheimnisvoll. Aber ich weiss, dass eine verhandlung dieses Ausmaßes irgendeinen Ängstlich und besorgt machen wird,aber ich versichre Ihnen, dass alles am Ende des tages in ordnung sein wird. Wir haben uns entschieden Sie durch eine E-mail sendung,wegen der Dringlichkeit diese verhandlung zu erreichen, als wir davon zuverlassig von seiner schnelligkeit und vertraulichkeit Überzeugt worden sind. Ich möchte mich nun vorstellen. Ich bin Herr Joseph Mbekulu (Rechnungprüfer bei der Chartered Bank von Süd Afrika). Ich kam zu ihrem kontakt in meiner persönlichen suche nach einer zuverlassigen und anstandige person, um eine sehr vertrauliche verhandlung zu erledigen, die Übertragung von einem fremden Konto das maximale zuversicht erfordert. Der vorschlag:Ein Ausländische,verstorbener Ingenieur Jurgen Rosenthal, ein Diamante-Handler/unternehmer mit der Republik Süd Afrika. Er war bis seinem Tod vor drei jahren in einem Flugzeug absturz,als unternehmer bei der Regierung tatig. Herr Rosenthal war unser kunde hier bei der Chartered Bank von Süd Afrika Johannesburg und hatte ein Konto guthaben von US$14.3 million (Vierzehnmilliondreihunderttausend United States Dollar). welches die Bank jetzt fraglos erwartet durch seine Verwandten das Sie sich melden, wenn Sie sich nicht melden wird alles zu einem Afrikanischen vertrauens fond für waffen und munitions besorgungen bei einer freiheitsbewegung hier in Africa gespendet. Leidenschaftliche wertvolle Anstrengungen werden durch die Chartered Bank gemacht,um einen kontakt mit jemanden von der Rosenthal familie oder Verwandten zu bekommen.Es hat aber bis jetzt keinen Erfolg gegeben. Es ist wegen der wahrgenommen moglichkeit keinen verwandten der Rosenthal zu finden (er hatte keine frau und kinder) dass eine Anordnung für den fond als nicht zubehaupten deklariert werden,sollte, und dann zum vertrauens-fond für waffen und munition bersorgung ausgeben,die dem kurs vom krieg in Afrika gespendet wird. Um dieser negative Entwicklung abzuwenden, haben ich und einige meiner bewährten kollegen in der Bank beschlossen das Geld nach Ihre zustimmung zu Überweisen und suchen jetzt Ihre Erlaubnis das Sie sich als verwandter des verstorbenen Ing.Jurgen Rosenthal deklarieren,damit der Fond in der höhe von USD$14.3m infolgen dessen als der Nutznießer(Verwandter des Rosenthal)auf Ihr Bank Konto Überwiesen werden. Alle beurkundungen und Beweist die Ihnen ermöglichen diese Fonds zu behaupten werden wir zu Ihrer verfügung stellen,damit alles gut verläuft und wir versicheren Ihnen ein 100% Risiko freie Verwicklung. Ihr Anteil wäre 30% von der totalen Gange, während die restlichen 70% ist für mich und meine kollege. Wenn dieser vorschlag für Sie OK ist und Sie Wünschen das vertrauen auszunutzen, das wir hoffen auf Ihnen und Ihrer Gesellschaft zu verleihen,dann senden sie mir netterweise sofort per meine personal E-mail Adresse, Ihre Voll Namen, Adresse, Telefonnummer, fax-nummer und Ihre vertraulicher E-mail adresse, damit ich Ihnen die relevanten details dieser verhandlung senden kann. Danke in voraus. Mit freundlichen Grüße. Joseph Mbekublu. Bitte schicken Sie Ihre Antwort auf meine Vertraulichen Email Adresse: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 CMD BATCH: unable to start device PNG
Whoops. I hit the wrong button! Here's the whole message:
And on that note, here is a function that I use to get around it:
startPNG - function(filename, width = 680, height = 990, ...)
{
nativePNG - capabilities(png)
if(nativePNG)
{
png(file = filename, width = width, height = height, ...)
} else {
bitmap(file = filename, width = width/72, height = height/72,
...)
}
invisible(NULL)
}
Max
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jeffrey Horner
Sent: Friday, November 03, 2006 10:01 AM
To: [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R CMD BATCH: unable to start device PNG
[EMAIL PROTECTED] wrote:
Dear r-helpers:
Any ideas how to avoid problem described below?
I am having the same problem when I run R remotly (not from cgi
script);
somehow png device wants to talk to X11 and X11 complains...
Best regards,
Ryszard
error msg from batch R process (Linux/R-2.4.0) (executed on Apache
server
from cgi script):
Error in X11(paste(png::, filename, sep = ), width, height,
pointsize,
:
unable to start device PNG
In addition: Warning message:
unable to open connection to X11 display ''
Execution halted
Here's a snippet from the png help page:
'bitmap' provides an alternative way to generate PNG and JPEG
plots that does not depend on accessing the X11 display but does
depend on having GhostScript installed. (Device 'GDD' in 'GDD' is
another alternative using several other additional pieces of
software.)
You can find GDD and another alternative Cairo here:
http://www.rosuda.org/R
Jeff
--
http://biostat.mc.vanderbilt.edu/JeffreyHorner
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD BATCH: unable to start device PNG
And on that note, here is a function that I use to get around it:
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jeffrey Horner
Sent: Friday, November 03, 2006 10:01 AM
To: [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R CMD BATCH: unable to start device PNG
[EMAIL PROTECTED] wrote:
Dear r-helpers:
Any ideas how to avoid problem described below?
I am having the same problem when I run R remotly (not from cgi
script);
somehow png device wants to talk to X11 and X11 complains...
Best regards,
Ryszard
error msg from batch R process (Linux/R-2.4.0) (executed on Apache
server
from cgi script):
Error in X11(paste(png::, filename, sep = ), width, height,
pointsize,
:
unable to start device PNG
In addition: Warning message:
unable to open connection to X11 display ''
Execution halted
Here's a snippet from the png help page:
'bitmap' provides an alternative way to generate PNG and JPEG
plots that does not depend on accessing the X11 display but does
depend on having GhostScript installed. (Device 'GDD' in 'GDD' is
another alternative using several other additional pieces of
software.)
You can find GDD and another alternative Cairo here:
http://www.rosuda.org/R
Jeff
--
http://biostat.mc.vanderbilt.edu/JeffreyHorner
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
__
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https://stat.ethz.ch/mailman/listinfo/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] CI -- fixed effects -- response -- mixed models
Dear Friends,
I have been following the discussions of mixed-effects models with
some confusion, and I realize that much of this is work in progress,
and that much of the discussion is beyond my knowledge of statistics.
My question is simple, though: Is there a set of commands that will
produce an output equivalent to the exceedingly useful
predict(bl.lm, newdata = bl.new, type = 'response', interval =
'confidence')
for (at least) gaussian mixed-effects model (but preferably for glmm
models)? I have looked at
predict.glmmPQL {MASS}
predict.lme {nlme}
and neither of them offer exactly what I need, and I just don't know
enough to go from what they do offer to what I need. I have Pinheiro
Bates as well as MASS, and both come tantalizingly close to what I
need, but I can't figure out the next step.
AFAIK, there's nothing of the sort for aov(. ~ ., Error(...) ...)
either.
In order to publish results of designed psychological experiments
(most of which are of the classic anova variety, with all the
predictors being factors), we need to plot error bars on our
interaction plots. I suspect (from the discussion on this list) that
my colleagues are using SPSS or SAS, and reporting incorrect CIs.
Not being a statistician I have hit a wall here. I'm not sure if the
transition to the results I need is staring me in the face, and I
don't know enough to take the next step, or if the tools aren't yet
available. In any event, I would be very grateful to you for guidance
on how to proceed.
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] R-help in Newsreader?
Dear list, I am new to this all and therefore have following Newbie question: How can I receive and read R-help mailings in a newsreader like thunderbird? Thanks Matthias _ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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-help in Newsreader?
On Fri, 2006-11-03 at 17:36 +0100, Matthias Voigt wrote: Dear list, I am new to this all and therefore have following Newbie question: How can I receive and read R-help mailings in a newsreader like thunderbird? Thanks Matthias If you go to the main R web site (http://www.r-project.org/) and click on the Mailing Lists link, then scroll down to Archives and Search Facilities, the second bullet indicates that the lists are available via Gmane, which mirrors the R lists (and many others) to an NNTP server. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Import problem with S-Plus 7.0 dataset
I am running R 2.3.1 on a Windows XP machine. I am trying to import some data into R that is stored as an S-Plus 7.0 .sdd file. When I run the following command, I get this error: library(foreign) d - read.S(file='H:\\Research\\data.sdd') Error in read.S(file = H:\\Research\\data.sdd) : not an S object The dataset is fairly large, roughly 13000 rows and 100 columns, but within S-Plus 7.0 it is stored as a normal dataframe (not a bd dataframe). Any ideas? Brant Inman [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] correaltion equal 1
On 11/3/06, Doran, Harold [EMAIL PROTECTED] wrote: or, it could mean you need to recenter your time variable. -Original Message- From: [EMAIL PROTECTED] on behalf of Marc Bernard Sent: Fri 11/3/2006 7:24 AM To: r-help@stat.math.ethz.ch Subject: [R] correaltion equal 1 Dear All, I wonder if this is a technical or an interpretation problem. I fitted an lme model including a random intercept and a random slope. The estimated correlation, from the lme, between the random intercept and the random slope is equal to 1. Does it mean that I should suppress one of the random effect from the model? It probably indicates that the estimate of the variance-covariance matrix for the random effects is singular. If you refit the model using lmer from the lme4 package and the estimate of the variance-covariance matrix is singular, you will get a warning to that effect. As Harold mentioned, you may be able to avoid the problem by re-centering the covariate. However, this may also be a characteristic of your data. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Translation of R code required
Dear All I am a complete novice when it comes to R. I have been sent some code which I need to run on a dataset. I have downloaded and installed R but I dont seem to be able to get the code to run. I was hoping someone on the list would be able to give me a 'translation' of what the code is trying to do and if there appears to be any errors in it. The code is; mental - read.csv(dataextract.csv) mental$Rx - factor(mental$Rx, levels=c(VS,IPS)) library(MASS) model.effect - glmmPQL(p~Benefit/Rx, ~1|Centre, data=mental, family=quasi(link=identity, variance=mu(1-mu)), weight=n) model.combined - glmmPQL(p~ Rx, ~1|Centre, data=mental, family=quasi(link=identity, variance=mu(1-mu)), weight=n) summary(model.effect) summary(model.combined) model.overall - glmmPQL(p~-1+Benefit, ~1|Centre, data=mental, family=quasi( link=identity,variance=mu(1-mu)), weight=n) model.overall.combined - glmmPQL(p~1, ~1|Centre, data=mental, family=quasi( link=identity,variance=mu(1-mu)), weight=n) summary(model.overall) summary(model.overall.combined) The dataset being read in has six variables, Centre, p, r, n, Rx and Benefit. I would really appreciate help with this. I am an experienced, SAS, SPSS, Stata user but never tried R before and I dont have the luxury of lots of time with which to master it currently. Sarah -- - Sarah White Biostatistician Research Resource Unit Division of Mental Health St George's, University of London Cranmer Terrace Tooting LONDON SW17 0RE Direct Line; 020 8725 3615 Fax; 020 8725 3538 Email; [EMAIL PROTECTED] -- believed to be clean. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Translation of R code required
I am a complete novice when it comes to R. I have been sent some code which I need to run on a dataset. I have downloaded and installed R but I dont seem to be able to get the code to run. It would be very helpful if you would tell us your OS, version of R, and if you would copy and paste the errors into your email so we can see what went wrong. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Translation of R code required
I am using Windows XP, R version 2.4. The code works until I get to the fourth line starting model.effect and I receive the following Error message. Error in eval(expr, envir, enclos) : object Centre not found When I say it works until the fourth line I mean I dont get an error message until then. It doesn't necessarily mean it has done what it should have done before then. Thanks for the help. Sarah Sarah Goslee wrote: I am a complete novice when it comes to R. I have been sent some code which I need to run on a dataset. I have downloaded and installed R but I dont seem to be able to get the code to run. It would be very helpful if you would tell us your OS, version of R, and if you would copy and paste the errors into your email so we can see what went wrong. Sarah -- - Sarah White Biostatistician Research Resource Unit Division of Mental Health St George's, University of London Cranmer Terrace Tooting LONDON SW17 0RE Direct Line; 020 8725 3615 Fax; 020 8725 3538 Email; [EMAIL PROTECTED] -- believed to be clean. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Translation of R code required
On 11/3/06, Sarah White [EMAIL PROTECTED] wrote: I am using Windows XP, R version 2.4. The code works until I get to the fourth line starting model.effect and I receive the following Error message. Error in eval(expr, envir, enclos) : object Centre not found It sounds like the variable names aren't what you think they are. Try this: mental - read.csv(dataextract.csv) colnames(mental) If the names don't match exactly, R won't know what you mean. Since this step works, mental$Rx - factor(mental$Rx, levels=c(VS,IPS)) I think that some of the names are right, but perhaps that one is spelled differently (Centre vs centre, maybe, since R is case-sensitive?). The easiest thing to do with no R knowledge is probably to change the name in the csv file to match your code, if that turns out to be the problem. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Import problem with S-Plus 7.0 dataset
From ?read.S 'read.S' can read the binary files produced in most recent versions of S-PLUS on either Windows (versions 3.x, 4.x, 2000) or Unix (version 3.x with 4 byte integers). It automatically detects whether the file was produced on a big- or little-endian machine and adapts itself accordingly. 'data.restore' can read a similar range of files produced by 'data.dump', for newer versions of S-PLUS, those from 'data.dump(., oldStyle=TRUE)'. Note: not S-PLUS 7.0. You need to dump with 'data.dump(., oldStyle=TRUE)' to have a chance of reading it. On Fri, 3 Nov 2006, Inman, Brant A. M.D. wrote: I am running R 2.3.1 on a Windows XP machine. I am trying to import some data into R that is stored as an S-Plus 7.0 .sdd file. When I run the following command, I get this error: library(foreign) d - read.S(file='H:\\Research\\data.sdd') Error in read.S(file = H:\\Research\\data.sdd) : not an S object The dataset is fairly large, roughly 13000 rows and 100 columns, but within S-Plus 7.0 it is stored as a normal dataframe (not a bd dataframe). Any ideas? Brant Inman [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Translation of R code required
Thank you for your help. Yes, it was a case-sensitive problem. I have run all the code now and have the requred output. Sarah Sarah Goslee wrote: On 11/3/06, Sarah White [EMAIL PROTECTED] wrote: I am using Windows XP, R version 2.4. The code works until I get to the fourth line starting model.effect and I receive the following Error message. Error in eval(expr, envir, enclos) : object Centre not found It sounds like the variable names aren't what you think they are. Try this: mental - read.csv(dataextract.csv) colnames(mental) If the names don't match exactly, R won't know what you mean. Since this step works, mental$Rx - factor(mental$Rx, levels=c(VS,IPS)) I think that some of the names are right, but perhaps that one is spelled differently (Centre vs centre, maybe, since R is case-sensitive?). The easiest thing to do with no R knowledge is probably to change the name in the csv file to match your code, if that turns out to be the problem. Sarah -- - Sarah White Biostatistician Research Resource Unit Division of Mental Health St George's, University of London Cranmer Terrace Tooting LONDON SW17 0RE Direct Line; 020 8725 3615 Fax; 020 8725 3538 Email; [EMAIL PROTECTED] -- believed to be clean. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Import problem with S-Plus 7.0 dataset
read.S is used to read S3 files (S-Plus 4 and older, not S-Plus 6 or newer) from the binary in the _Data directory. For example y - read.S(c:/HOME/rmh/503.f99/_Data/y) data.restore is used to read S3 .sdd data.dump files. The S3 part means that S-Plus 7 users must force the oldStyle data.dump. ## S-Plus 7 data.dump(y, oldStyle=TRUE) ## R data.restore(c:/HOME/hh-user/dumpdata) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Translation of R code required
Sarah Goslee wrote:
Since this step works,
mental$Rx - factor(mental$Rx, levels=c(VS,IPS))
I think that some of the names are right, but perhaps that
one is spelled differently (Centre vs centre, maybe, since
R is case-sensitive?).
How do you know that step works? If the dataframe 'mental' doesnt have
an 'Rx' column then mental$Rx will be 'NULL', and the factor() function
will make a factor out of that...
x=data.frame(foo=1:10)
so x is a data frame with one column, called 'foo'. Now lets make
levels from a non-existent column, 'bar':
x$bar=factor(x$bar,levels=c('x','y'))
No complaints... But try printing 'x' now (by typing x at the command
line)... Ick!
Try things one line at a time and check the objects created or
modified are sensible.
Barry
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] ssh and X11 forwarding
Everything is enabled, but still doesn't work. xeyes and xclock give errors (Error: Can't open display: localhost:10.0), R produces Rplots.ps I also have a windows box, and go to chena using PuTTY. I have cygwin with X server installed on it. If I enable X11 forwarding in PuTTY, start cygwin's X11 server on Windows and try to run xeyes or xclock, I see their windows on my local MS Windows desktop, R still produces Rplots.ps. Got it! It was long time ago, R (2.3.0) was compiled without X support, because development headers and libraries were not installed on that computer. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Translation of R code required
On 11/3/06, Barry Rowlingson [EMAIL PROTECTED] wrote: How do you know that step works? If the dataframe 'mental' doesnt have an 'Rx' column then mental$Rx will be 'NULL', and the factor() function will make a factor out of that... Good point. I rarely use factors and missed that one. Happily, my inaccurate solution turned out to solve the problem anyway. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] identify extremes positions of values into matrix
Oi Milton, Is this what you are after? x=read.table(miltondat.txt) x V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 1 1 0 0 3 0 0 0 0 0 1 1 1 0 0 4 0 0 0 0 0 0 0 0 0 0 5 0 0 2 2 2 0 0 0 0 0 6 0 0 0 2 2 2 0 0 0 0 7 0 0 2 2 2 2 2 2 0 0 8 0 0 0 0 0 0 0 0 0 0 idx=which(x==2,arr.ind=T) #Index of observations with values == 2 . Notice the use of arr.ind=t to get the rows and columns of the observations idx row col 5 5 3 7 7 3 5 5 4 6 6 4 7 7 4 5 5 5 6 6 5 7 7 5 6 6 6 7 7 6 7 7 7 7 7 8 range(idx[,row]) #gives you the min and max of the rows with x==2 [1] 5 7 range(idx[,col])#gives you the min and max of the columns with x==2 [1] 3 8 You can refine this and wrap it in a function to make reports in a more suitable form Regards Francisco Dr. Francisco J. Zagmutt College of Veterinary Medicine and Biomedical Sciences Colorado State University From: Milton Cezar Ribeiro [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject: [R] identify extremes positions of values into matrix Date: Fri, 3 Nov 2006 11:25:32 -0300 (ART) Hi R-friends around world! I have a matrix that looks like bellow one. Each cell are filled with values 0, 1 or 2. In fact I have a lot of 512x512 matrices, with values varying from 0 to 999. I need to retrieve the left and right columns and the top and botton lines of the matrix where occours for example the value 2. Column and row labels are included at the example. 1234567890 1 00 2 011100 3 011100 4 00 5 002220 6 000222 7 002200 8 00 At this example, the right answer are: collumns 3 and 8 lines 5 and 7 Any idea of how can I solve this? Kind regards, Miltinho - Música para ver e ouvir: You're Beautiful, do James Blunt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Try Search Survival Kits: Fix up your home and better handle your cash with Live Search! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 convert an existing package?
Dears, how could I convert an existing package to be able to modify it? Let s say, if I want to change the way how the results of the package are display (to see the oroginal code of the code). Thanks [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] identify extremes positions of values into matrix
Francisco, Thank you so much. It´s more than I need. You help was of great value. Kind regards, Miltinho Francisco J. Zagmutt [EMAIL PROTECTED] escreveu: Oi Milton, Is this what you are after? x=read.table(miltondat.txt) x V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 1 1 0 0 3 0 0 0 0 0 1 1 1 0 0 4 0 0 0 0 0 0 0 0 0 0 5 0 0 2 2 2 0 0 0 0 0 6 0 0 0 2 2 2 0 0 0 0 7 0 0 2 2 2 2 2 2 0 0 8 0 0 0 0 0 0 0 0 0 0 idx=which(x==2,arr.ind=T) #Index of observations with values == 2 . Notice the use of arr.ind=t to get the rows and columns of the observations idx row col 5 5 3 7 7 3 5 5 4 6 6 4 7 7 4 5 5 5 6 6 5 7 7 5 6 6 6 7 7 6 7 7 7 7 7 8 range(idx[,row]) #gives you the min and max of the rows with x==2 [1] 5 7 range(idx[,col])#gives you the min and max of the columns with x==2 [1] 3 8 You can refine this and wrap it in a function to make reports in a more suitable form Regards Francisco Dr. Francisco J. Zagmutt College of Veterinary Medicine and Biomedical Sciences Colorado State University From: Milton Cezar Ribeiro To: r-help@stat.math.ethz.ch Subject: [R] identify extremes positions of values into matrix Date: Fri, 3 Nov 2006 11:25:32 -0300 (ART) Hi R-friends around world! I have a matrix that looks like bellow one. Each cell are filled with values 0, 1 or 2. In fact I have a lot of 512x512 matrices, with values varying from 0 to 999. I need to retrieve the left and right columns and the top and botton lines of the matrix where occours for example the value 2. Column and row labels are included at the example. 1234567890 1 00 2 011100 3 011100 4 00 5 002220 6 000222 7 002200 8 00 At this example, the right answer are: collumns 3 and 8 lines 5 and 7 Any idea of how can I solve this? Kind regards, Miltinho - Música para ver e ouvir: You're Beautiful, do James Blunt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Try Search Survival Kits: Fix up your home and better handle your cash with Live Search! http://imagine-windowslive.com/search/kits/default.aspx?kit=improvelocale=en-USsource=hmtagline - Música para ver e ouvir: You're Beautiful, do James Blunt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] microarray analysis
__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] identify extremes positions of values into matrix
I am glad to help ;-) Cheers, Francisco Milton Cezar Ribeiro wrote: Francisco, Thank you so much. It´s more than I need. You help was of great value. Kind regards, Miltinho Francisco J. Zagmutt [EMAIL PROTECTED] escreveu: Oi Milton, Is this what you are after? x=read.table(miltondat.txt) x V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 1 1 1 0 0 3 0 0 0 0 0 1 1 1 0 0 4 0 0 0 0 0 0 0 0 0 0 5 0 0 2 2 2 0 0 0 0 0 6 0 0 0 2 2 2 0 0 0 0 7 0 0 2 2 2 2 2 2 0 0 8 0 0 0 0 0 0 0 0 0 0 idx=which(x==2,arr.ind=T) #Index of observations with values == 2 . Notice the use of arr.ind=t to get the rows and columns of the observations idx row col 5 5 3 7 7 3 5 5 4 6 6 4 7 7 4 5 5 5 6 6 5 7 7 5 6 6 6 7 7 6 7 7 7 7 7 8 range(idx[,row]) #gives you the min and max of the rows with x==2 [1] 5 7 range(idx[,col])#gives you the min and max of the columns with x==2 [1] 3 8 You can refine this and wrap it in a function to make reports in a more suitable form Regards Francisco Dr. Francisco J. Zagmutt College of Veterinary Medicine and Biomedical Sciences Colorado State University From: Milton Cezar Ribeiro To: r-help@stat.math.ethz.ch Subject: [R] identify extremes positions of values into matrix Date: Fri, 3 Nov 2006 11:25:32 -0300 (ART) Hi R-friends around world! I have a matrix that looks like bellow one. Each cell are filled with values 0, 1 or 2. In fact I have a lot of 512x512 matrices, with values varying from 0 to 999. I need to retrieve the left and right columns and the top and botton lines of the matrix where occours for example the value 2. Column and row labels are included at the example. 1234567890 1 00 2 011100 3 011100 4 00 5 002220 6 000222 7 002200 8 00 At this example, the right answer are: collumns 3 and 8 lines 5 and 7 Any idea of how can I solve this? Kind regards, Miltinho - Música para ver e ouvir: You're Beautiful, do James Blunt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Try Search Survival Kits: Fix up your home and better handle your cash with Live Search! http://imagine-windowslive.com/search/kits/default.aspx?kit=improvelocale=en-USsource=hmtagline - Música para ver e ouvir: You're Beautiful, do James Blunt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Microarray analysis
Dear List I am currently running a microarray analysis on the dataset schizo and would like to filter out all genes with a low variance. However, when running the code detailed below, I end up with 12,500 genes in my final set rather than the 10,000 I was looking for. Can anyone pinpoint where I am going wrong? ***reading in data** schizo-read.table(octassign_data.txt,header=T, sep=\t) dim(schizo) head(schizo) attach(schizo) ***creating matrix and calculating variance across probesets x-c(1:2) y-c(2:151) schizo.matrix-data.matrix(schizo[,y]) varprobe-c(var(schizo.matrix[x,])) hist(varprobe) **filter out low variance* top1 - which(rank(varprobe)1) schizo.sub-schizo[top1,] dim(schizo.sub) [1] 12500 151 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Import problem with S-Plus 7.0 dataset
As recommended, I have tried the following code to solve my problem
importing data to R from S-Plus 7.0. Unfortunately, I have not had
success.
In S-Plus:
data.dump('data', file='C:\\temp\\ddump.sdd', oldStyle=T)
This resulted in the production of a file called ddump.sdd that I can
import into S-Plus without any problem. However, when I use the
following code in R ...
In R:
d - data.restore(file='C:\\temp\\ddump.sdd')
d
[1] C:\\temp\\ddump.sdd
d - data.restore('C:\\temp\\ddump.sdd')
d
[1] C:\\temp\\ddump.sdd
I also tried the following:
d - read.S(file='C:\\temp\\ddump.sdd')
Error in read.S(file = C:\\temp\\ddump.sdd) :
not an S object
I thought that S-Plus might be doing something funny when I save as a
.sdd file, so I tried saving as ddump.dat but got exactly the same
results.
I have been able to save my original datafile as a csv and import it,
but I had hoped that it would be possible to keep my variable formats by
importing the S dataframe into R directly.
Brant Inman
[[alternative HTML version deleted]]
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Re: [R] Microarray analysis
Friederike - The program is doing exactly what you asked it to do, but please notice that varprobe-c(var(schizo.matrix[x,])) creates a vector containing all the elements of the variance-covariance matrix of schizo.matrix[x,], which is a 2x150 matrix, giving a variance-covariance matrix of 150x150 or 22500 elements. You then rank all of the elements of this variance-covariance matrix, and ask for the ones that are ranked higher than 1, leaving 22500-1=12500 elements. So now we should probably look at what you wanted to do: x - 1:2 y - 2:151 schizo.matrix-data.matrix(schizo[,y]) varprobe-apply(schizo.matrix[x,],1,var) # calculate the variance of each row # reorder the rows of schizo.matrix to correspond to varprobe and # select the top 1 schizo.sub = schizo.matrix[order(varprobe,decreasing=TRUE),][1:1,] There are other ways of extracting the top 1, but I think that this shows how to calculate what you really want. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley [EMAIL PROTECTED] On Fri, 3 Nov 2006, Friederike Barthel wrote: Dear List I am currently running a microarray analysis on the dataset schizo and would like to filter out all genes with a low variance. However, when running the code detailed below, I end up with 12,500 genes in my final set rather than the 10,000 I was looking for. Can anyone pinpoint where I am going wrong? ***reading in data** schizo-read.table(octassign_data.txt,header=T, sep=\t) dim(schizo) head(schizo) attach(schizo) ***creating matrix and calculating variance across probesets x-c(1:2) y-c(2:151) schizo.matrix-data.matrix(schizo[,y]) varprobe-c(var(schizo.matrix[x,])) hist(varprobe) **filter out low variance* top1 - which(rank(varprobe)1) schizo.sub-schizo[top1,] dim(schizo.sub) [1] 12500 151 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Import problem with S-Plus 7.0 dataset
It looks like it works. The result you printed is the name of the file that data.store read. The name of the variable is the same as the name you called it in S-Plus. type data[1:5,] and you should see your data.frame. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 went away from top emacs window :-(
I concur: Thanks very much for looking into this. Spencer Graves Duncan Murdoch wrote: Thanks for looking into this. On 11/3/2006 9:53 AM, Richard M. Heiberger wrote: I located what might be the problem. There is a different misbehavior with Gnu emacs. I don't have Xemacs. I have an idea how to fix it but haven't worked out the details. ess-inf.el in the lines (defconst inferior-R-1-input-help (format ^ *help *(%s) ess-help-arg-regexp)) (defconst inferior-R-2-input-help (format ^ *\\? *%s ess-help-arg-regexp)) (defconst inferior-R-page (format ^ *page *(%s) ess-help-arg-regexp)) detects help requests from the commandline in the *R* buffer and redirects their output to an emacs *help[R] (whatever)* buffer. In gnu emacs on windows, with options(chmhelp=TRUE), the effect is an empty *help[R] (whatever)* buffer. What I think happened is that ESS trapped the request and created the buffer, then R never got the right content to send to that buffer because R thinks that chm is handling it. The fix probably requires ESS to check the value of the chmhelp option and suppress the interception of help requests if the option has the value TRUE. ESS also needs to monitor if that option has been changed. This might mean that ESS always intercepts help requests and checks the value of the option each time. You should also look at options(htmlhelp) - a user might have chosen that style. Duncan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 went away from top emacs window :-(
Thanks for looking into this. On 11/3/2006 9:53 AM, Richard M. Heiberger wrote: I located what might be the problem. There is a different misbehavior with Gnu emacs. I don't have Xemacs. I have an idea how to fix it but haven't worked out the details. ess-inf.el in the lines (defconst inferior-R-1-input-help (format ^ *help *(%s) ess-help-arg-regexp)) (defconst inferior-R-2-input-help (format ^ *\\? *%s ess-help-arg-regexp)) (defconst inferior-R-page (format ^ *page *(%s) ess-help-arg-regexp)) detects help requests from the commandline in the *R* buffer and redirects their output to an emacs *help[R] (whatever)* buffer. In gnu emacs on windows, with options(chmhelp=TRUE), the effect is an empty *help[R] (whatever)* buffer. What I think happened is that ESS trapped the request and created the buffer, then R never got the right content to send to that buffer because R thinks that chm is handling it. The fix probably requires ESS to check the value of the chmhelp option and suppress the interception of help requests if the option has the value TRUE. ESS also needs to monitor if that option has been changed. This might mean that ESS always intercepts help requests and checks the value of the option each time. You should also look at options(htmlhelp) - a user might have chosen that style. Duncan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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)
From: Martin Maechler [EMAIL PROTECTED]
MIME-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
Message-ID: [EMAIL PROTECTED]
Date: Fri, 3 Nov 2006 22:26:20 +0100
To: Barry Rowlingson [EMAIL PROTECTED]
Cc: Sarah Goslee [EMAIL PROTECTED],
r-help@stat.math.ethz.ch,
Sarah White [EMAIL PROTECTED]
Subject: Re: [R] Translation of R code required
In-Reply-To: [EMAIL PROTECTED]
References: [EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
X-Mailer: VM 7.19 under Emacs 21.4.1
Reply-To: Martin Maechler [EMAIL PROTECTED]
BaRow == Barry Rowlingson [EMAIL PROTECTED]
on Fri, 03 Nov 2006 18:38:38 + writes:
BaRow Sarah Goslee wrote:
Since this step works,
mental$Rx - factor(mental$Rx, levels=c(VS,IPS))
I think that some of the names are right, but perhaps
that one is spelled differently (Centre vs centre, maybe,
since R is case-sensitive?).
BaRow How do you know that step works? If the dataframe
BaRow 'mental' doesnt have an 'Rx' column then mental$Rx
BaRow will be 'NULL', and the factor() function will make a
BaRow factor out of that...
x=data.frame(foo=1:10)
BaRow so x is a data frame with one column, called
BaRow 'foo'. Now lets make levels from a non-existent
BaRow column, 'bar':
x$bar=factor(x$bar,levels=c('x','y'))
BaRow No complaints... But try printing 'x' now (by
BaRow typing x at the command line)... Ick!
Hmm, what version of R would that be?
In any recent versions,
I get
x - data.frame(foo = 1:10)
x$bar - factor(x$bar,levels=c('x','y'))
Error in as.vector(x, mode) : invalid argument 'mode'
But I want to make another point:
For about a year now, for serious data-analysis using data frames,
I've been advocating to use the slightly more clumsy but much
more error-prone ``column indexing by name'' instead of the quick-and-dirty
$ selection :
x$bar
NULL
x[,bar]
Error in [.data.frame(x, , bar) : undefined columns selected
BaRow Try things one line at a time and check the objects
BaRow created or modified are sensible.
Indeed!
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Import problem with S-Plus 7.0 dataset
Thanks to Brian Ripley and Richard Heiberger for the solution to my
problem. I will spell it out below in steps so that (hopefully) nobody
else will need to ask the same question in the future (if they search
the R help archive).
HOW TO GET S-PLUS 7.0 DATA into R
__
STEP 0 (in S-Plus 7.0): Generation of a fake dataframe:
x - c(1:10)
y - rep(c(0,1),5)
mydata - data.frame(cbind(x,y))
mydata
x y
1 1 0
2 2 1
3 3 0
4 4 1
5 5 0
6 6 1
7 7 0
8 8 1
9 9 0
10 10 1
STEP 1 (in S-Plus 7.0): Save the dataframe as earlier versions of S-Plus
did
(note: I called the output file ddump.sdd instead of mydata.sdd to
demonstrate a point later on)
data.dump('mydata', file='C:\\temp\\ddump.sdd', oldStyle=T)
STEP 2 (In R): Restore the saved dataframe
data.restore('C:\\temp\\ddump.sdd')
[1] C:\\temp\\ddump.sdd
STEP 3 (In R): View/use the first few cases of dataset)
head(mydata)
x y
1 1 0
2 2 1
3 3 0
4 4 1
5 5 0
6 6 1
There are 2 important points to note:
1) The dataframe keeps the name it had in S-Plus, not the name of the
file you saved it in. Using the example above, R never creates an object
called ddump:
data.restore('C:\\temp\\ddump.sdd')
[1] C:\\temp\\ddump.sdd
ddump
Error: object ddump not found
2) Saving the data.restore result into a new variable is not that useful
because it will NOT contain your dataframe, only the name of the file
that contained your dataframe:
test - data.restore('C:\\temp\\ddump.sdd')
test
[1] C:\\temp\\ddump.sdd
Brant Inman
-Original Message-
From: Richard M. Heiberger [mailto:[EMAIL PROTECTED]
Sent: Friday, November 03, 2006 3:07 PM
To: Inman, Brant A. M.D.; Brian Ripley
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Import problem with S-Plus 7.0 dataset
It looks like it works. The result you printed is
the name of the file that data.store read. The name of the
variable is the same as the name you called it in S-Plus.
type
data[1:5,]
and you should see your data.frame.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] one row matrix
Hi, when I assign a one row matrix to another variable, then somehow R automatically convert that varaible into a list. For example: a = matrix (12, 3, 4) b = a[1,] b [1] 12 12 12 12 Is there a way to enable R automatically make b as a one row matrix , rather than explicitly assign like matrix (b, ncol=1). I have come across a couple of time, that when I try to check how many rows of the computed result matrix - nrow(,,,), because there is only one row, the program failed as R tried to interpret it as a list. Can some one help? -- Waverley @ Palo Alto [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] one row matrix
On Fri, 2006-11-03 at 14:12 -0800, Waverley wrote: Hi, when I assign a one row matrix to another variable, then somehow R automatically convert that varaible into a list. A 'vector', not a 'list' For example: a = matrix (12, 3, 4) b = a[1,] b [1] 12 12 12 12 Is there a way to enable R automatically make b as a one row matrix , rather than explicitly assign like matrix (b, ncol=1). I have come across a couple of time, that when I try to check how many rows of the computed result matrix - nrow(,,,), because there is only one row, the program failed as R tried to interpret it as a list. Can some one help? This is actually a FAQ: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-my-matrices-lose-dimensions_003f HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] one row matrix
On 11/3/06, Waverley [EMAIL PROTECTED] wrote:
Hi,
For example:
a = matrix (12, 3, 4)
b = a[1,]
b
[1] 12 12 12 12
It doesn't have anything to do with one-row matrices, at least in your example,
since that isn't what you made. Instead, you created a matrix with 3 rows,
4 columns, and all values equal to 12.
a - matrix(12, 3, 4)
a
[,1] [,2] [,3] [,4]
[1,] 12 12 12 12
[2,] 12 12 12 12
[3,] 12 12 12 12
a[1,]
[1] 12 12 12 12
You probably intended
a - matrix(c(12, 3, 4), nrow=1)
a
[,1] [,2] [,3]
[1,] 1234
But to solve what I think you were actually asking, even though it
wasn't reflected in your example... By default, R drops unused
dimensions when subsetting. You can override this behavior
b - a[1, ,drop=FALSE]
b
[,1] [,2] [,3]
[1,] 1234
See:
?subset
help('[')
?matrix
Sarah
--
Sarah Goslee
http://www.functionaldiversity.org
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and provide commented, minimal, self-contained, reproducible code.
[R] question of one matrix column being treated as list rather than vector
Hi, I have one matrix derived from my function. It is as following: Browse[1] each.uaa.data [,1] [,2] [1,] 33 152.3530 [2,] 33 264.7059 [3,] 51 583. [4,] 33 323. [5,] 50 292.549 [6,] 33 300 [7,] 56 104.1176 [8,] 52 246.6667 [9,] 53 242.5490 [10,] 33 212.9412 when I tried to get each.uaa.data[,2], it gave me a list, when I expect a vector so that I can find the max(each.uaa.data[,2]), this max() failed. I have checked is.matrix (each.uaa.data) and it is TRUE. I have a created a = matrix (12, 12, 2), a[,2] give me a vector of 12 of 12s which is what I have expected. Can someone help as how to prevent it becomes a list? I am new and thanks much for the help. Browse[1] (each.uaa.data[,2]) [[1]] [1] 152.3530 [[2]] [1] 264.7059 [[3]] [1] 583. [[4]] [1] 323. [[5]] [1] 292.549 [[6]] [1] 300 [[7]] [1] 104.1176 [[8]] [1] 246.6667 [[9]] [1] 242.5490 [[10]] [1] 212.9412 -- Waverley @ Palo Alto [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] finding significant change points after fitting GAM using TPRS
Does anybody know if code or functions exist for determining significant change points after fitting GAM in 'mgcv' using thin plate regression spline and 'ts' bases? I would like to identify years where the curvature or change in trajectory of a longterm annual population curve is significant. Thank you. Deahn DonnerWright email: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] as.zoo behavior (
hi all : the code pasted below runs but then, a dput on
rollmeandifflogbidask gives me what is below the code. the structure of
rollmeandifflogbidask is a zoo object but with a frequency
so it's not the same structure as the original actual diff and this
really causes things to blow up in later code. i'm sure gabor and achim
know what to do but in the case that they
are not around, would someone else know ? the code for ewma is below the
structure of rollmeandifflogbidask in the case that someone wants
to run it themselves. thanks a lot.
#---
---
actualdiff-structure(c(-1.45571955822987e-06, -7.27862957994319e-06,
-0.000109185801586698,
-0.000134158878632995, -9.98463614099165e-06, 0.000128544569886202,
5.33190241842618e-05, 1.5881826502806e-06, -2.23230209073222e-05,
-6.66190921299048e-05, -5.95638733376092e-05, -3.5740027046316e-05,
-0.000211818969710897, 0.000241006754088779, 5.89686385294996e-05,
-9.88290397652136e-05, 2.45716680487007e-05, -2.18414528943001e-05,
2.18414528943001e-05, 0, -2.18414528943001e-05, 1.45610216018000e-05,
-8.55490383084856e-05, -1.63825656738226e-05, 0.000101931603982308,
-1.45610216018000e-05, 2.18414528943001e-05, 0, -2.18414528943001e-05,
-6.5527221122963e-05), index = structure(c(1151884920, 1151884980,
1151885040, 1151885100, 1151885160, 1151885220, 1151885280, 1151885340,
1151885400, 1151885460, 1151885520, 1151885580, 1151885640, 1151885700,
1151885760, 1151885820, 1151885880, 1151885940, 1151886060, 1151886120,
1151886180, 1151886240, 1151886300, 1151886360, 1151886420, 1151886480,
1151886540, 1151886600, 1151886660, 1151886720), class = c(POSIXt,
POSIXct)), class = zoo)
temp-ewma(actualdiff,.05),
rollmeandifflogbidask-as.zoo(temp,index(actualdiff))
resulting structure of rollmeandifflogbidask
#---
-
structure(c(-7.27859779114937e-08, -4.33078158013078e-07,
-5.8707143294473e-06,
-1.22851225446247e-05, -1.21700982244430e-05, -5.13436481891078e-06,
-2.21169536875215e-06, -2.02170146780051e-06, -3.0367674397766e-06,
-6.21588367428301e-06, -8.88328315744932e-06, -1.02261203518926e-05,
-2.03057628198429e-05, -7.24013697441177e-06, -3.9296981992162e-06,
-8.67466527751607e-06, -7.01234861120523e-06, -7.75380382535997e-06,
NA, 0, 0, -1.09207264471500e-06, -3.09417932389255e-07,
-4.57139895119407e-06,
-5.1619572873255e-06, 1.92720776156187e-07, -5.4496634274162e-07,
5.74354619110464e-07, 5.45636888154941e-07, -5.73717600967809e-07,
-3.82139277706757e-06), index = c(1151884920, 1151884980, 1151885040,
1151885100, 1151885160, 1151885220, 1151885280, 1151885340, 1151885400,
1151885460, 1151885520, 1151885580, 1151885640, 1151885700, 1151885760,
1151885820, 1151885880, 1151885940, 1151886000, 1151886060, 1151886120,
1151886180, 1151886240, 1151886300, 1151886360, 1151886420, 1151886480,
1151886540, 1151886600, 1151886660, 1151886720), frequency =
0.0167, class = c(zooreg,
zoo))
it seems to be a zoo object but with a frequency that i think comes from
the fact that the ewma function produces a series of class ts.
I need the structure to be the EXACT same structure as the original
actual diff so i must be doing something wrong.
EWMA function
#---
ewma-function(x,lambda = 1, init = 0) {
filter(lambda*x,filter=(1-lambda),method=recursive,init=init)
}
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[R] How to obtain the estimate of baseline survival function?
Hi, If I fit a Cox model using coxph, is there a R function so that I could obtain the estimate of baseline survival function? Thank you. Zheng -- Zheng Yuan Ph.D student Department of Biostatistics University of Michigan Ann Arbor, MI 48109 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] question of one matrix column being treated as list rather than vector
On Fri, Nov 03, 2006 at 02:47:37PM -0800, Waverley wrote: Hi, You probably created that matrix from a list. Eg a - matrix(list(1,2,3,4),2,2) a [,1] [,2] [1,] 13 [2,] 24 a[,2] [[1]] [1] 3 [[2]] [1] 4 b - matrix(1:4,2,2) b[,2] [1] 3 4 Both a and b are matrices, but note: is.recursive(a) [1] TRUE is.recursive(b) [1] FALSE Possible solutions: generate the matrix like b above, or use as.vector before calling max. Read ?[ and ?[[. HTH, Tamas Browse[1] each.uaa.data [,1] [,2] [1,] 33 152.3530 [2,] 33 264.7059 [3,] 51 583. [4,] 33 323. [5,] 50 292.549 [6,] 33 300 [7,] 56 104.1176 [8,] 52 246.6667 [9,] 53 242.5490 [10,] 33 212.9412 when I tried to get each.uaa.data[,2], it gave me a list, when I expect a vector so that I can find the max(each.uaa.data[,2]), this max() failed. I have checked is.matrix (each.uaa.data) and it is TRUE. I have a created a = matrix (12, 12, 2), a[,2] give me a vector of 12 of 12s which is what I have expected. Can someone help as how to prevent it becomes a list? I am new and thanks much for the help. Browse[1] (each.uaa.data[,2]) [[1]] [1] 152.3530 [[2]] [1] 264.7059 [[3]] [1] 583. [[4]] [1] 323. [[5]] [1] 292.549 [[6]] [1] 300 [[7]] [1] 104.1176 [[8]] [1] 246.6667 [[9]] [1] 242.5490 [[10]] [1] 212.9412 -- Waverley @ Palo Alto [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 convert an existing package?
On Fri, Nov 03, 2006 at 07:59:37PM +0100, rasti matus wrote: Dears, how could I convert an existing package to be able to modify it? Let s say, if I want to change the way how the results of the package are display (to see the oroginal code of the code). Hi, Could you be more specific about what you are trying to achieve? To see the source, just type the name of the function, or if that doesn't work, getAnywhere(functionname) Then you can modify that (copy into your editor, or edit(functionname)). You can also look at the package sources. Tamas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] plotting residuals
Does anyone know how to obtain a plot of residuals by predicted values for a main-effects aov? I want to check that the residuals are distributed equally across treatment means. Thanks, Jeff [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Chronbach's Alpha
Dear all experts, Can anyone help me to find information on how to calculate the Chronbach's Alpha Coefficient (sometimes called Crombach or even just Alpha coefficient) Thanks in advance Ralf Finne SYH University of Applied Science Wolffskavägen 33 P.O.Box 6 FIN-65201 VASA, Finland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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)
On 03-Nov-06 Martin Maechler wrote: [...] But I want to make another point: For about a year now, for serious data-analysis using data frames, I've been advocating to use the slightly more clumsy but much more error-prone ``column indexing by name'' instead of the quick-and-dirty $ selection : x$bar NULL x[,bar] Error in [.data.frame(x, , bar) : undefined columns selected Your point is well made, Martin, but I'd like to present a different view of the same issue. Suppose you are working on a somewhat flexibly structured computation in which columns get adjoined to a dataframe (by name) according (e.g.) as they become available at some (unforeseeable) point in the pathway through the computation. This could also arise in real time if bar is the output from some measuring device, not yet available, yet the computation can get on with other things until it is available. Then a test based on is.null(x$bar) could divert the computation round some path suitable for a case where x$bar has not yet been defined and adjoined, as opposed to a case where x$bar has already been adjoined. The use of x[,bar], however, would generate an error and cause the computation to slide through a hole in the floor. Horses for courses, I suppose! Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 04-Nov-06 Time: 00:29:03 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Chronbach's Alpha
On 11/04/06 02:25, Ralf Finne wrote: Dear all experts, Can anyone help me to find information on how to calculate the Chronbach's Alpha Coefficient (sometimes called Crombach or even just Alpha coefficient) And even more often called Cronbach. It is in the psy package. And there is some discussion of it in http://www.psych.upenn.edu/~baron/rpsych/rpsych.html Jon __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Ridge for logistic regression
Dear all experts, Does anyone know if there is a R function which can perform Ridge regression for logistic models? Thank in advance. Ying Yuan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] as.zoo behavior (
Mark:
temp-ewma(actualdiff,.05),
ok, because ewma() is a wrapper for filter() this returns an object of
class ts. Therefore you want to add the index again, but:
rollmeandifflogbidask-as.zoo(temp,index(actualdiff))
is not the right thing to do. as.zoo() is a coercion generic and its ts
method ignores all arguments except the first. Thus, index(actualdiff) is
*not* added and a zooreg object created (which is appropriate because
you supply an object of class ts, a regular series. See
zoo:::as.zoo.ts
for the actual code).
You want to create a zoo series from scratch using the data from temp
and the index from actualdiff. Hence, the appropriate command is
zoo(coredata(temp), index(actualdiff))
But let's go back to the ewma() function. The NA in temp looks suspicious
(and stems from another implicit coercion from zoo to ts). I guess you
want:
ewma - function(x, lambda = 1, init = 0) {
rval - filter(lambda * coredata(x),
filter = (1-lambda),
method = recursive,
init = init)
rval - zoo(coredata(rval), index(x))
rval
}
And then you can do
ewma(actualdiff, 0.05)
and already get a nicely formatted zoo object back.
Z
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[R] multiple plots in the same graph
I'd like to plot y vs x according to the third variable group which has three levels. I am wondering how can I put the three plots in one graph? Thank you (http://groups.yahoo.com) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 Error: Subscript out of bounds
I can't begin to guess. If your example were self contained (and preferably simple), it would be easier to diagnose. When I have problems like this, I often try to find a simple example that produced the same error message. That process often leads me to a solution. If it doesn't it often produces a sufficiently simple example that I can describe it easily in a few lines of a question to r-help. I might also use the 'debug' function (in the 'base' package. I have not used the 'debug' package, which may be more powerful but possibly harder to use.). To access a chain of earlier recommendations on debug, I tried 'RSiteSearch(graves debug), then 'RSiteSearch(graves debug lme)'. The fifth hit from the latter is http://finzi.psych.upenn.edu/R/Rhelp02a/archive/77298.html;. Hope this helps. Spencer Graves Lisa Avery wrote: Hello, I am new to non-linear growth modelling in R and I am trying to reproduce an analysis that was done (successfully) in S-Plus. I have a simple non-linear growth model, with no nesting. I have attempted to simplify the call as much as possible (by creating another grouped object, instead of using subset= and compacting the fixed and random expressions.) This is a what the grouped data object looks like: levelI.data[1:2,] Grouped Data: GMAE ~ AGE | STUDYID STUDYID TIMESCORE INCURVES MOST FIRST AGE 1910051 ACTUAL (unaided) in JAMA curves Level I Level I 49.11301 2010052 ACTUAL (unaided) in JAMA curves Level I Level I 56.53745 GMFM GMFCS GMAE YRS 19 91.03394 1 74.16 4.092751 20 95.35018 1 84.05 4.711454 Here is the nlme model: cp.grad-deriv(~ (100/(1+exp(-L)))*(1-exp(-exp(logR)*x)), c(L, logR), function(x=0:100,L,logR) NULL) levelI.nlme-nlme(GMAE~cp.grad(AGE,limit,lograte), data=levelI.data, fixed = limit+lograte~1, random = limit+lograte~1, start = c(2.0, -3.0)) I get a subscript out of bounds error - which I am not finding very helpful because I don't know where things are going wrong. Bill Shipley posted a similar problem with nlme called with a self-starting function - but here I don't use a self-starting function and I give the starting values explicitly so I assume that this is not the same problem he is having. What am I doing wrong? Any insights would be very much appreciated. Kind Regards, Lisa Avery [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] multiple plots in the same graph
See ?points and ?lines for adding new groups of points or lines to an existing graph created by plot. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Li Zhang Sent: Friday, November 03, 2006 9:55 PM To: R-help@stat.math.ethz.ch Subject: [R] multiple plots in the same graph I'd like to plot y vs x according to the third variable group which has three levels. I am wondering how can I put the three plots in one graph? Thank you (http://groups.yahoo.com) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 obtain the estimate of baseline survival function?
See ?basehaz in 'survival' package. -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zheng Yuan Sent: Friday, November 03, 2006 6:20 PM To: r-help@stat.math.ethz.ch Subject: [R] How to obtain the estimate of baseline survival function? Hi, If I fit a Cox model using coxph, is there a R function so that I could obtain the estimate of baseline survival function? Thank you. Zheng -- Zheng Yuan Ph.D student Department of Biostatistics University of Michigan Ann Arbor, MI 48109 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
