Re: [R] table elemets testing
Emanuele Mazzola wrote: Hi everybody, i'm dealing with some percentage tables, of which i should test rowwise if the entries are sgnificantly equal or not. Namely, on row 1, test H0: element 1= element2, H0: element 1= element3...H0: element 2= element3...H0: element n-1= element n. The same on the other rows. Do you want to know how to write the code or which method to use? We cannot tackle the first question unless we have answered the second, which is much more difficult. Do you really want to a statistical test under H0: element 1 = element 2? Then you have to make some assumptions re. the *exact* distributions of element 1 and element 2 (are you assuming iid?). And if you assume the exact distribtion, you do not need to test on equality any more, but you want to know if element x is from this distribution, and you can simply use the quantiles themselves. Uwe Ligges Anybody knows how this can be done in quick way? I don't have large matrices, but it seems quite boring... Thank you very much in advance for your answering, Emanuele __ 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] equality constraint
I would like to optimize a (log-)likelihood function subject to linear equality constraints in parameters. My function has eight parameters. The first one, third and fourth are greater than zero, the second one must be less than zero. The problem is that the last four must sum zero. Function constrOptim only fits inequality constraints. Is there an alternative to lead with this problem? Ana Maria __ 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)
hi i created two files in excel with a dbf format in a similar way. the first is opened in R, however, when i try to open the second. i received the following message: sites.can - read.csv(SITES.csv) Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names The second file works with the same command larynx.can - read.csv(LARYNX.csv) SO, WHAT IS THE SOLUTIO Regards Ahmed - [[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] How to add a line on the boxplot
Hi, I have a data frame, df=rnorm(1000) dim(df)=c(100,10) And i can get the boxplot, boxplot(data.frame(df)) So how can add a line (aline) on the existing boxplot,eg, aline=apply(df,2,max) Thanks in advance. [[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] Putting x into the right subset
John Wiedenhoeft wrote:
Dear all,
I'm sorry I have to bother you with this newbie stuff.
Within a loop I obtain pairs of values x - c(a, b). An empty set M is
defined before the loop (as a list or whatever). Now I want to do the
following: if there is a vector y in M that contains at least one of
the values of x, then x shall be concatenated to y. If y doesn't contain
any of the values in x, then x shall be put into M as a new vector. I
first imagined it to be trivial but I'm having a hard time with the
if-statement. I tried to define a function contains(value, vector),
which returns FALSE or TRUE, but R complains that I tried to execute a
non-function...
Could anybody help a despaired newbie, please!
Example (maybe not efficient, but should do the trick):
M - list()
temp - NA
for(i in 1:20){
a - sample(1:10, 1)
b - sample(11:20, 1)
x - c(a, b)
if(i 1)
temp - which(sapply(M, function(y) any(x %in% y)))[1]
if(!is.na(temp))
M[[temp]] - c(M[[temp]], x)
else
M[[length(M) + 1]] - x
}
Thanks a lot,
John
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Re: [R] different csv files; was: (no subject)
ahmed el kenawy wrote: hi i created two files in excel with a dbf format in a similar way. the first is opened in R, however, when i try to open the second. i received the following message: sites.can - read.csv(SITES.csv) Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names The second file works with the same command larynx.can - read.csv(LARYNX.csv) SO, WHAT IS THE SOLUTIO 1. Please do not shout. 2. Please read the posting guide. 3. Please use a sensible subject. 4. Please read ?read.csv 5. You might want to check if the format of that csv files are really identical and check if the column names are strange (including comments or separators). If it still does not work, send us the first few lines of that file. We cannot look at it otherwise! Uwe Ligges Regards Ahmed - [[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] equality constraint
I would like to optimize a (log-)likelihood function subject to linear equality constraints in parameters. My function has eight parameters. The first one, third and fourth are greater than zero, the second one must be less than zero. The problem is that the last four must sum zero. Function constrOptim only fits inequality constraints. Is there an alternative to lead with this problem? - Any reason not to just replace e.g. parameter 8 with minus the sum of parameters 5, 6, and 7? best, Simon - Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY - +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/ __ 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 add a line on the boxplot
Jiantao Shi wrote: Hi, I have a data frame, df=rnorm(1000) dim(df)=c(100,10) And i can get the boxplot, boxplot(data.frame(df)) So how can add a line (aline) on the existing boxplot,eg, Thanks in advance. Example: df - rnorm(1000) dim(df) - c(100,10) boxplot(data.frame(df)) aline - apply(df, 2, max) # , now you might want either abline(h = aline, col = green, lty=dotted) # or segments(seq(along = aline) - 0.2, aline, seq(along = aline) + 0.2, aline, lwd = 2, col = red) Uwe Ligges [[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 add a line on the boxplot
Thanks The first method,i get many lines,using the second,i get segments.I actually need one line with y coordinate defined by aline,x along the boxplot. On 7/22/06, Uwe Ligges [EMAIL PROTECTED] wrote: Jiantao Shi wrote: Hi, I have a data frame, df=rnorm(1000) dim(df)=c(100,10) And i can get the boxplot, boxplot(data.frame(df)) So how can add a line (aline) on the existing boxplot,eg, Thanks in advance. Example: df - rnorm(1000) dim(df) - c(100,10) boxplot(data.frame(df)) aline - apply(df, 2, max) # , now you might want either abline(h = aline, col = green, lty=dotted) # or segments(seq(along = aline) - 0.2, aline, seq(along = aline) + 0.2, aline, lwd = 2, col = red) Uwe Ligges [[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] How to add a line on the boxplot
Jiantao Shi wrote: Thanks The first method,i get many lines,using the second,i get segments.I actually need one line with y coordinate defined by aline,x along the boxplot. Do you mean lines(aline)? If not, please explain in another way how you want to arrange those 10 values and make lines from it. Uwe Ligges On 7/22/06, Uwe Ligges [EMAIL PROTECTED] wrote: Jiantao Shi wrote: Hi, I have a data frame, df=rnorm(1000) dim(df)=c(100,10) And i can get the boxplot, boxplot(data.frame(df)) So how can add a line (aline) on the existing boxplot,eg, Thanks in advance. Example: df - rnorm(1000) dim(df) - c(100,10) boxplot(data.frame(df)) aline - apply(df, 2, max) # , now you might want either abline(h = aline, col = green, lty=dotted) # or segments(seq(along = aline) - 0.2, aline, seq(along = aline) + 0.2, aline, lwd = 2, col = red) Uwe Ligges [[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] R shutdown
Dear R Users, I run simulation that takes very long time (R 2.2.1, Win XP pro., Rgui SDI mode, editor Tinn-R). It's happened that R shuts down and Windows display the message: Rgui.exe makes an error and the application will shut down. Unfortunately everything I lost. Below I paste the message that is created when error appear. Maybe You as an expert will figure out what is happening to me. Best, Robert McFadden ?xml version=1.0 encoding=UTF-16? DATABASE EXE NAME=Rgui.exe FILTER=GRABMI_FILTER_PRIVACY MATCHING_FILE NAME=md5check.exe SIZE=15360 CHECKSUM=0x5685AC04 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows files checker FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x3CD5 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:59 UPTO_LINK_DATE=12/20/2005 13:17:59 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=R.dll SIZE=2201600 CHECKSUM=0xFC7E40D1 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows DLL FILE_VERSION=2.2.1(2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x2 MODULE_TYPE=WIN32 PE_CHECKSUM=0x21CDB3 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:16:00 UPTO_LINK_DATE=12/20/2005 13:16:00 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=R.exe SIZE=18432 CHECKSUM=0x4407B548 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows front-end FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x60D3 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:58 UPTO_LINK_DATE=12/20/2005 13:17:58 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rbitmap.dll SIZE=238592 CHECKSUM=0x861028AC MODULE_TYPE=WIN32 PE_CHECKSUM=0x457B3 LINKER_VERSION=0x1 LINK_DATE=12/20/2005 13:25:12 UPTO_LINK_DATE=12/20/2005 13:25:12 / MATCHING_FILE NAME=Rblas.dll SIZE=106496 CHECKSUM=0x9A1FC9D3 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows DLL FILE_VERSION=2.2.1(2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x2 MODULE_TYPE=WIN32 PE_CHECKSUM=0x28489 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:52 UPTO_LINK_DATE=12/20/2005 13:17:52 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rchtml.dll SIZE=6144 CHECKSUM=0x880344F MODULE_TYPE=WIN32 PE_CHECKSUM=0x4204 LINKER_VERSION=0x1 LINK_DATE=12/20/2005 13:17:52 UPTO_LINK_DATE=12/20/2005 13:17:52 / MATCHING_FILE NAME=Rcmd.exe SIZE=18432 CHECKSUM=0x19E72056 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows front-end FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x4A89 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:54 UPTO_LINK_DATE=12/20/2005 13:17:54 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rgui.exe SIZE=10240 CHECKSUM=0x96A0D31D BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows GUI front-end FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x6C46 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:53 UPTO_LINK_DATE=12/20/2005 13:17:53 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rlapack.dll SIZE=1184256 CHECKSUM=0x9FA3E37A BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R DLL for lapack FILE_VERSION=2.2.1(2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 2002-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x2 MODULE_TYPE=WIN32 PE_CHECKSUM=0x130713 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:18:52 UPTO_LINK_DATE=12/20/2005 13:18:52 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rproxy.dll SIZE=44544 CHECKSUM=0xDC26CFFF BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows terminal front-end FILE_VERSION=2.2.1
[R] ifelse command
Dear:
I try to revise the maximum likelihood function below using something
constrains. But it seems something wrong with it. Becasue R would not allow me
to edit the function like this. It is very appreciate if you can help.
function (parameters,y,x1,x2)
{
p-parameters[1]
alpha1-parameters[2]
beta1-parameters[3)]
delta1-parameters[4]
alpha2-parameters[5]
mu-alpha1*((x1)^beta1)*exp(-delta1*(x1^alpha2))
if(y0 x10 x2==1,
L-lgamma(y+p)+p*(log(p)-log(mu+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p)
)
else
if(y0 x10 x2==2,
L-lgamma(y+p)+p*(log(p)-log(mu+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p)
)
else
if(y0 x10 x2==3,
L-lgamma(y+p)+p*(log(p)-log(mu+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p)
)
else
L
}
Thanks a lot!
Xin Shi
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Re: [R] nested repeated measures in R
You can read the manual, read the FAQs, search the help functions and the archives. -Original Message- From: [EMAIL PROTECTED] on behalf of Eric C Merten Sent: Fri 7/21/2006 8:51 PM To: r-help@stat.math.ethz.ch Subject: [R] nested repeated measures in R R help, How would I input data, verify assumptions, and run a nested repeated measures ANOVA using R? I have STATION nested in SITE nested in BLOCK with measurements repeated for five YEARs. All are random variables and it's only slightly unbalanced. I'm trying to characterize spatiotemporal variation in stream habitat variables. Thanks for your help! Eric Merten __ 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] (no subject)
Check out this recent thread: https://www.stat.math.ethz.ch/pipermail/r-help/2006-July/109731.html On 7/22/06, ahmed el kenawy [EMAIL PROTECTED] wrote: hi i created two files in excel with a dbf format in a similar way. the first is opened in R, however, when i try to open the second. i received the following message: sites.can - read.csv(SITES.csv) Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names The second file works with the same command larynx.can - read.csv(LARYNX.csv) SO, WHAT IS THE SOLUTIO Regards Ahmed - [[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] Putting x into the right subset
Dear Uwe,
Many thanks for your help! Unfortunately, your function doesn't do
exactly what I need (I slightly modified it, but I don't think that
caused the problem):
M - list()
temp - NA
for (i in 1:length(deppat))
{
a - deppat[i]
b - deptest[i]
x - c(a, b)
if (i 1)
temp - which(sapply(M, function(y) any(x %in% y)))[1]
if(!is.na(temp))
M[[temp]] - c(M[[temp]], x)
else
M[[length(M) + 1]] - x
}
print(M)
print(length(M))
for (k in 1:length(M))
{
M[[k]] - sort(unique(M[[k]]))
print(M[[k]])
}
deppat and deptest are equal in length. Additionaly, they may contain
values more than once. At the end, M shall contain exactly
length(unique(c(deppat, deptest))) variables, but it doesn't. Also,
there are some matches that remained undetected:
M[[1]] 1 5 6 11 22 24 28 29 31 35 49 57 58 62 65 75 80 81 85 86
M[[2]] 2 7 11 12 25 30 31 32 36 50 53 58 59 63 66 69 82 87
11, 31 and 58 occur in two subsets (there are more examples for larger
k).
I've tried to do it more graphic, but for some reason the same failure
occures:
M - list()
for (j in 1:length(deppat))
{
for (listpos in 1:(length(M)+1))
{
if (listpos length(M))
{
M[[listpos]] - c(deppat[j], deptest[j])
break
}
else
{
if (deppat[j] %in% M[[listpos]] || deptest[j] %in%
M[[listpos]])
{
M[[listpos]] - c(M[[listpos]], deppat[j], deptest[j])
break
}
}
}
}
print(M)
for (k in 1:length(M))
{
M[[k]] - sort(unique(M[[k]]))
print(M[[k]])
}
There must be an error in reasoning, but I can't figure out where it
is...
Cheers,
John
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] R shutdown
On 7/22/2006 8:22 AM, Robert Mcfadden wrote: Dear R Users, I run simulation that takes very long time (R 2.2.1, Win XP pro., Rgui SDI mode, editor Tinn-R). It's happened that R shuts down and Windows display the message: Rgui.exe makes an error and the application will shut down. Unfortunately everything I lost. Below I paste the message that is created when error appear. Maybe You as an expert will figure out what is happening to me. I don't think there's any information below that is helpful to diagnose the reason for the crash. What I'd recommend is that you write out partial results as your simulation progresses. Then at least you'll have those partial results, but you may also have enough information to be able to be able to make the crash reproducible in a short script. If you can do that, and you can make the crash reproducible in a current version of R (version 2.2.1 is obsolete; you should be using 2.3.1 at a minimum, perhaps 2.3.1 patched), then there's a good chance someone will be able to track down the bug and fix it. Duncan Murdoch Best, Robert McFadden ?xml version=1.0 encoding=UTF-16? DATABASE EXE NAME=Rgui.exe FILTER=GRABMI_FILTER_PRIVACY MATCHING_FILE NAME=md5check.exe SIZE=15360 CHECKSUM=0x5685AC04 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows files checker FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x3CD5 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:59 UPTO_LINK_DATE=12/20/2005 13:17:59 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=R.dll SIZE=2201600 CHECKSUM=0xFC7E40D1 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows DLL FILE_VERSION=2.2.1(2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x2 MODULE_TYPE=WIN32 PE_CHECKSUM=0x21CDB3 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:16:00 UPTO_LINK_DATE=12/20/2005 13:16:00 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=R.exe SIZE=18432 CHECKSUM=0x4407B548 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows front-end FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x60D3 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:58 UPTO_LINK_DATE=12/20/2005 13:17:58 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rbitmap.dll SIZE=238592 CHECKSUM=0x861028AC MODULE_TYPE=WIN32 PE_CHECKSUM=0x457B3 LINKER_VERSION=0x1 LINK_DATE=12/20/2005 13:25:12 UPTO_LINK_DATE=12/20/2005 13:25:12 / MATCHING_FILE NAME=Rblas.dll SIZE=106496 CHECKSUM=0x9A1FC9D3 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows DLL FILE_VERSION=2.2.1(2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x2 MODULE_TYPE=WIN32 PE_CHECKSUM=0x28489 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:52 UPTO_LINK_DATE=12/20/2005 13:17:52 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rchtml.dll SIZE=6144 CHECKSUM=0x880344F MODULE_TYPE=WIN32 PE_CHECKSUM=0x4204 LINKER_VERSION=0x1 LINK_DATE=12/20/2005 13:17:52 UPTO_LINK_DATE=12/20/2005 13:17:52 / MATCHING_FILE NAME=Rcmd.exe SIZE=18432 CHECKSUM=0x19E72056 BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows front-end FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x4A89 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:54 UPTO_LINK_DATE=12/20/2005 13:17:54 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409] / MATCHING_FILE NAME=Rgui.exe SIZE=10240 CHECKSUM=0x96A0D31D BIN_FILE_VERSION=2.21.51220.0 BIN_PRODUCT_VERSION=3.0.0.0 FILE_DESCRIPTION=R for Windows GUI front-end FILE_VERSION=2.2.1 (2005-12-20) LEGAL_COPYRIGHT=R Development Core Team 1995-2005 VERFILEDATEHI=0x0 VERFILEDATELO=0x0 VERFILEOS=0x4 VERFILETYPE=0x1 MODULE_TYPE=WIN32 PE_CHECKSUM=0x6C46 LINKER_VERSION=0x1 UPTO_BIN_FILE_VERSION=2.21.51220.0 UPTO_BIN_PRODUCT_VERSION=3.0.0.0 LINK_DATE=12/20/2005 13:17:53 UPTO_LINK_DATE=12/20/2005 13:17:53 VER_LANGUAGE=Angielski (Stany Zjednoczone) [0x409]
[R] compile R with ACML support | RHEL 4
Greetings - I'm trying to compile R under GNU/Linux (RHEL 4) on a multi-Opteron box, with ACML support. First, I downloaded and installed ACML 3.5 - GNU version, although I'm not entirely sure what the differences are - from the AMD website. The ACML libraries were installed to /opt/acml3.5.0/ Second, I ran ./configure --with-blas='-lacml' The configure went fine, except that at the end of the output, it reports that readline is the only external library configured. External libraries: readline OK, so next, I try ./configure --with-lapack Same think - only readline is referenced. So, clearly, I'm missing a particular step. I'm guessing that I need to change some environment variable (or two), or tweak something at some other stage, to get R to properly reference the ACML libraries. I'm puzzled why --with-blas='-acml' doesn't do the trick? Suggestions? Pointers to the obvious mistake? Thanks... __ 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] mvpart
does anyone know of a tutorial that exists for the mvpart package other than the package documentation and De'ath's original article in Ecology? thanks, Helen Mills Poulos Yale School of Forestry __ 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] equality constraint
Dear Ana Maria, How about replacing the last of the four parameters with the negative of the sum of the others? I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, July 21, 2006 4:31 PM To: r-help@stat.math.ethz.ch Subject: [R] equality constraint I would like to optimize a (log-)likelihood function subject to linear equality constraints in parameters. My function has eight parameters. The first one, third and fourth are greater than zero, the second one must be less than zero. The problem is that the last four must sum zero. Function constrOptim only fits inequality constraints. Is there an alternative to lead with this problem? Ana Maria __ 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] Why the contrain does not work for selecting a particular range of data?
Dear:
Continuing the issue of 'ifelse'! I selecting the data whose 'x2'=1 for
maximizing likelihood. I used two way to do this but the results are different.
1.Way one I use the data for x2=1 and run the program. It works for me.
Tthe program is described as below:
function (parameters,y1,x11)
{
p-parameters[1]
alpha1-parameters[2]
beta1-parameters[3]
delta1-parameters[4]
lamda1-parameters[5]
mu-alpha1*((x11)^beta1)*exp(-delta1*(x11^lamda1))
ifelse(y10|x110,
L-lgamma(y1+p)+p*(log(p)-log(mu+p))+y1*(log(mu)-log(mu+p))-lfactorial(y1)-lgamma(p)
,Inf)
L
}
This is working for me.
2 Way two: I select the data whose x2=1 in the whole range of data. It works
but it is not right comparing the value of MLE. the program is:
function (parameters,y,x1,x2)
{
p-parameters[1]
alpha1-parameters[2]
beta1-parameters[3]
delta1-parameters[4]
alpha2-parameters[5]
mu-alpha1*((x1)^beta1)*exp(-delta1*(x1^alpha2))
if(x10 x2==1)
{
L-lgamma(y+p)+p*(log(p)-log(mu+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p)
}
else
L
}
The reason why I edit the program by the second way is I want to use one
program for getting results of the different range of data.
Anyone can help? Please!
Thanks!
Xin Shi
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[R] multcomp plotting Please help :)
I REALLY NEED HELP WITH THIS PLEASE I am using the multcomp package for doing multiple comparisons (R 2.3.1 windows). Since the data I am handling is huge the number of comparisons are also large. I am interested in: 1 Breaking down my plots to get rid of the clutter that happens when plotting the entire data set. How do I pass only part of the data to the plot function ? fungus.cirec-simint(Fungus.yield~Habitat, data=fungus,conf.level=0.95,type =c(Tukey)) plot(fungus.cirec) #This plots the entire data. I want to plot part of the data only 2I am also interested in getting rid of the field name associated with each categorical variable. Here is what the part of the data looks like Habitat Fungus.yield Birch 20.83829053 Birch 22.9718181 Birch 22.28216829 Birch 24.23136797 Birch 22.32147961 Birch 20.30783598 Oak 27.24047258 Oak 29.7730014 Oak 30.12608508 Oak 25.76088669 Oak 30.14750974 Hornbeam 17.05307949 Hornbeam 15.32805111 Hornbeam 18.26920177 Hornbeam 21.30987049 Hornbeam 21.7173223 When it plots labels it as HabitatBirch-HabitatOak for example. How do I get rid of the field name Habitat in the plot? 3 How do I tell the method to mark the significant comparisons? (i.e those that do not intersect the zero line). Thanks ../Murli __ 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] multcomp plotting Please help :)
On 7/22/06, Nair, Murlidharan T [EMAIL PROTECTED] wrote: I REALLY NEED HELP WITH THIS PLEASE [] __ 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. Suggest you follow the instructions to get better chance of a response. __ 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] Multcomp
Here it is again, hope this is more clear I am using the following data (only a small subset is given): Habitat Fungus.yield Birch 20.83829053 Birch 22.9718181 Birch 22.28216829 Birch 24.23136797 Birch 22.32147961 Birch 20.30783598 Oak 27.24047258 Oak 29.7730014 Oak 30.12608508 Oak 25.76088669 Oak 30.14750974 Hornbeam 17.05307949 Hornbeam 15.32805111 Hornbeam 18.26920177 Hornbeam 21.30987049 Hornbeam 21.7173223 I am using the multcomp package to do multiple comparisons as follows library(multcomp) # loads the package fungus-read.table(fungi.txt, Header=T)# Reads the data from file saved as fungi.txt fungus.cirec-simint(Fungus.yield~Habitat, data=fungus,conf.level=0.95,type =c(Tukey)) # Computes cimultaneous intervals using Tukey's method plot(fungus.cirec) # plots the data The plot function plots all the comparisons, I want to plot only part of the data since it clutters the graph. How do I plot only part of the data ? How do I tell it to mark the significant comparisons? How do I get rid of the field names in the plot? For eg. The plot labels are HabitatBirch-HabitatOak, I want it to be labeled as Birch-Oak. Hope I have posted it according to the guidelines, let me know otherwise. Cheers .../Murli __ 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] Multcomp
On 7/22/06, Nair, Murlidharan T [EMAIL PROTECTED] wrote: Here it is again, hope this is more clear I am using the following data (only a small subset is given): Habitat Fungus.yield Birch 20.83829053 Birch 22.9718181 Birch 22.28216829 Birch 24.23136797 Birch 22.32147961 Birch 20.30783598 Oak 27.24047258 Oak 29.7730014 Oak 30.12608508 Oak 25.76088669 Oak 30.14750974 Hornbeam 17.05307949 Hornbeam 15.32805111 Hornbeam 18.26920177 Hornbeam 21.30987049 Hornbeam 21.7173223 I am using the multcomp package to do multiple comparisons as follows library(multcomp) # loads the package fungus-read.table(fungi.txt, Header=T)# Reads the data from file saved as fungi.txt fungus.cirec-simint(Fungus.yield~Habitat, data=fungus,conf.level=0.95,type =c(Tukey)) # Computes cimultaneous intervals using Tukey's method plot(fungus.cirec) # plots the data The plot function plots all the comparisons, I want to plot only part of the data since it clutters the graph. How do I plot only part of the data ? Don't understand what part of the data means. Use data = fungus[1:10,] in the simint call to just process the first 10 data rows. To eliminate a portion of the plot note in ?plot.hmtest that there is a ... argument and its description is that its passed to plot which in turn passes them to plot.default so you could use ylim = 1:2, say, to show only part of the plot vertically. How do I tell it to mark the significant comparisons? # after your plot statement: pp - locator() # now click on a spot on the plot # and then right click and choose stop text(pp$x, pp$y, some text) How do I get rid of the field names in the plot? For eg. The plot labels are HabitatBirch-HabitatOak, I want it to be labeled as Birch-Oak. # change rownames of the estimates which has the effect # of changing the y axis labels rownames(fungus.cirec$estimate) - LETTERS[1:3] plot(fungus.cirec) __ 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] Random structure of nested design in lme
Have you considered the following: anova(lme(NA.1~soiltype*habitat,random=~1|destination/origin)) This seems more closely to match the 'aov' command in your original post. This model might be written in more detail as follows: NA.1[s, h, i,j,k] = b0 + ST[s] + H[h] + ST.H[s[i],j[j] j] + d[i] + o[i,j] + e[i,j,k] where b0 = a constant to be estimated, s = the soil type for that particular sample, h = the habitat for that sample, ST = soil type coefficients to be estimated subject to a constraint that they sum to 0, H = habitat coefficients to be estimated subject to the constraint that they sum to 0, ST.H = soil type by habitat interaction coefficients to be estimated subject to constraints that ST.H[s,.] sum to 0 and ST.H[., h] also sum to 0, d[i] = a random deviation associated with each destination, assuming the d's are all normal, independent, with mean 0 and unknown but constant variance s2.d o[i, j] = a random deviation associated with each destination / origin combination, assuming the o's are all normal, independent, with mean 0 and unknown variance s2.o, and e[i,j,j] = the standard unknown noise term, normal, independent with mean 0 and unknown variance s2.e. The model you wrote includes nested noise terms for soil type and habitat as well. These terms are not estimable, which makes the answers garbage, but the 'lme' function does not check for replicates and therefore sometimes gives garbage answers without warning. To get more information from the fit, I suggest you first try 'methods(class=lme)', and review help pages associated with what you see listed there. Have you looked at Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? This is my all-time favorite reference on Bates has been one of the leading original contributors in variance components analysis and nonlinear estimation more generally for over 25 years. The 'nlme' package is the product of his work and the work of many of his graduate students prior to 2000. The book, at least from my perspective, is very well written. Moreover, the standard R distribution includes files named ch01.R, ch02.R, ..., ch06.R, ch08.R with the R scripts accompanying each chapter in the book in ~\library\nlme\scripts under the R installation directory on your hard drive, e.g. D:\Program files\R\R-2.3.1\library\nlme\scripts, on my computer. There are minor changes in the syntax in a few places between the book and the current R implementation that make it impossible to get some of the published answers. Using these script files increases the likelihood that you will get essentially the book's answers and won't be defeated by subtle typographical errors or by the difference between x^2 and I(x^2), for example. If you would like further information from this listserver, please submit another post, preferably including a commented, minimal, self-contained, reproducible code, as suggested in the posting guide www.R-project.org/posting-guide.html. Hope this helps. Spencer Graves ESCHEN Rene wrote: Although I know it's not correct, this is what I tried in lme: anova(lme(NA.1~soiltype*habitat,random=~1|destination/habitat/origin/soiltype)) # numDF denDF F-value p-value #(Intercept) 1 130 12.136195 0.0007 #soiltype 1 130 15.099792 0.0002 #habitat 110 0.699045 0.4226 #soiltype:habitat 1 130 2.123408 0.1475 René. -Original Message- From: Doran, Harold [mailto:[EMAIL PROTECTED] Sent: Wed 2006-07-19 13:53 To: ESCHEN Rene; r-help@stat.math.ethz.ch Subject: RE: [R] Random structure of nested design in lme Can you provide an example of what you have done with lme so we might be able to evaluate the issue? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of ESCHEN Rene Sent: Wednesday, July 19, 2006 7:37 AM To: r-help@stat.math.ethz.ch Subject: [R] Random structure of nested design in lme All, I'm trying to analyze the results of a reciprocal transplant experiment using lme(). While I get the error-term right in aov(), in lme() it appears impossible to get as expected. I would be greatful for any help. My experiment aimed to identify whether two fixed factors (habitat type and soil type) affect the development of plants. I took soil from six random sites each of two types (arable and grassland) and transplanted them back into the sites of origin in such way that in each of the sites there were six pots containing arable soil and six pots of grassland soil, each containing a seedling. With aov(), I got the analysis as I expected, with habitat type tested against destination site, and soil type tested against origin site:
Re: [R] ifelse command
Dear Xin,
Although I have no idea what your function does, I believe it would be
formally correct in the following way:
foo - function (parameters,y,x1,x2)
{
p -parameters[1]
alpha1-parameters[2]
beta1-parameters[3]
delta1-parameters[4]
alpha2-parameters[5]
mu-alpha1*((x1)^beta1)*exp(-delta1*(x1^alpha2))
if(y0 x10 x2==1) return( lgamma(y+p)+p*(log(p)-log(mu
+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p) )
if(y0 x10 x2==2) return( lgamma(y+p)+p*(log(p)-log(mu
+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p) )
if(y0 x10 x2==3) return( lgamma(y+p)+p*(log(p)-log(mu
+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p) )
return( what then? )
}
Please, compare your code to mine. You will discover more than one error
in your code. See also where the if() parenthesis closes. I do not
believe your else's are necessary within a function. See also that the
code after your ifs is always the same.
Sincerely,
Carlos J. Gil Bellosta
http://www.datanalytics.com
http://www.data-mining-blog.com
El sáb, 22-07-2006 a las 13:25 +0100, Xin escribió:
Dear:
I try to revise the maximum likelihood function below using something
constrains. But it seems something wrong with it. Becasue R would not allow
me to edit the function like this. It is very appreciate if you can help.
function (parameters,y,x1,x2)
{
p-parameters[1]
alpha1-parameters[2]
beta1-parameters[3)]
delta1-parameters[4]
alpha2-parameters[5]
mu-alpha1*((x1)^beta1)*exp(-delta1*(x1^alpha2))
if(y0 x10 x2==1,
L-lgamma(y+p)+p*(log(p)-log(mu+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p)
)
else
if(y0 x10 x2==2,
L-lgamma(y+p)+p*(log(p)-log(mu+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p)
)
else
if(y0 x10 x2==3,
L-lgamma(y+p)+p*(log(p)-log(mu+p))+y*(log(mu)-log(mu+p))-lfactorial(y)-lgamma(p)
)
else
L
}
Thanks a lot!
Xin Shi
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Re: [R] Putting x into the right subset
Ahh, got it: There must be an error in reasoning, but I can't figure out where it is... Consider 3 pairs: (1, 2), (2, 3), (1, 3), first is put in the first line, second in the second, and third in the first, resulting in the 3 being contained in both. Simply folding lines together solves it. __ 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] fracdiff
Confidence intervals for the fracdiff parameter estimates shouldn't
be too difficult: the ?fracdiff help file says it returns a list with
components including 'd', 'ar' 'ma', and 'stderror.dpq'. From these one
should easily get the coeffecients, standard errors and naive, Wald
confidence intervals; for your convenience, I've embedded these in the
functions 'coef.fracdiff' and 'confint.fracdiff' given below.
By 'sigma2', I assume you mean the estimated variance of the whitened
residuals. That is not so obvious. For that, I might try
'arima(fitdiff(...))$sigma2', operating on a 'fracdiff' fit.
Hope this helps.
Spencer Graves
# coef and confint functions for output of fracdiff:
coef.fracdiff - function(object){
unlist(object[c(d, ar, ma)])
}
confint.fracdiff - function(object, parm, level=0.95, ...){
b - coef.fracdiff(object)
se - object$stderror.dpq
names(se) - names(b)
#
if(missing(parm))
parm - 1:length(b)
b. - b[parm]
se. - se[parm]
#
conf.c - (1-level)/2
conf2 - c(conf.c, 1-conf.c)
confNames - paste(100*conf2, %)
k. - length(b.)
CI - b+outer(se., qnorm(conf2))
dimnames(CI)[[2]] - confNames
CI
}
Melissa Ann Haltuch wrote:
Hi, I'm using the function fracdiff and can not
figure out how to get the estimated values for
sigma2 or confidence intervals for the parameter
estimates. Does anyone know how to obtain these
values?
Thanks,
Melissa
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] connection to X11 problem
(Ted Harding) [EMAIL PROTECTED] writes: On 21-Jul-06 Paquet, Agnes wrote: Dear List, I am a new Mac user and I am having problem generating png (or jpeg) using the GUI version of R. I installed R-2.3.1.dmg (custom install with everything selected) and X11User.pkg but I am still getting the following X11 connection error when I try to generate a png (or a jpeg): 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 '' I tried to set up the DISPLAY variable using the command: Sys.putenv(DISPLAY=:0) but I am still running into the same problem. Like Marc, I don't use a Mac either. But the underlying BSD OS is basically similar to Linux. On Linux, my primary X11 DISPLAY envvar would be :0.0, so (at a guess) I suggest you try Sys.putenv(DISPLAY=:0.0) Hoping this helps! Ted. A silly question must be asked: One thing is *installing* the X11 package on a Mac, but you do need to be actually *running* an X server. Are you? -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Multcomp
-Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Saturday, July 22, 2006 1:37 PM To: Nair, Murlidharan T Cc: R-help@stat.math.ethz.ch Subject: Re: [R] Multcomp On 7/22/06, Nair, Murlidharan T [EMAIL PROTECTED] wrote: Here it is again, hope this is more clear I am using the following data (only a small subset is given): Habitat Fungus.yield Birch 20.83829053 Birch 22.9718181 Birch 22.28216829 Birch 24.23136797 Birch 22.32147961 Birch 20.30783598 Oak 27.24047258 Oak 29.7730014 Oak 30.12608508 Oak 25.76088669 Oak 30.14750974 Hornbeam 17.05307949 Hornbeam 15.32805111 Hornbeam 18.26920177 Hornbeam 21.30987049 Hornbeam 21.7173223 I am using the multcomp package to do multiple comparisons as follows library(multcomp) # loads the package fungus-read.table(fungi.txt, Header=T)# Reads the data from file saved as fungi.txt fungus.cirec-simint(Fungus.yield~Habitat, data=fungus,conf.level=0.95,type =c(Tukey)) # Computes cimultaneous intervals using Tukey's method plot(fungus.cirec) # plots the data The plot function plots all the comparisons, I want to plot only part of the data since it clutters the graph. How do I plot only part of the data ? Don't understand what part of the data means. Use data = fungus[1:10,] in the simint call to just process the first 10 data rows. To eliminate a portion of the plot note in ?plot.hmtest that there is a ... argument and its description is that its passed to plot which in turn passes them to plot.default so you could use ylim = 1:2, say, to show only part of the plot vertically. I have to use all the data for my computation. Since the number of comparisons are many I want to plot it in different graphs so that the graph does not look cluttered. So part of the data means a subset of the comparisons in one graph and another subset in another and so on Can you give me an example of the ylim parameter. I tried plot(fungus.cirec, ylim=1:2) and it was not happy with it. I am not completely comfortable with the ... argument. I am trying to read up on it. How do I tell it to mark the significant comparisons? # after your plot statement: pp - locator() # now click on a spot on the plot # and then right click and choose stop text(pp$x, pp$y, some text) This is very useful How do I get rid of the field names in the plot? For eg. The plot labels are HabitatBirch-HabitatOak, I want it to be labeled as Birch-Oak. # change rownames of the estimates which has the effect # of changing the y axis labels rownames(fungus.cirec$estimate) - LETTERS[1:3] plot(fungus.cirec) This only labels it a A,B or C. What I wanted was to remove the field name Habitat in this case and out put the label as Birch-Oak. Thanks ../Murli __ 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] Multcomp
On 7/22/06, Nair, Murlidharan T [EMAIL PROTECTED] wrote: -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Saturday, July 22, 2006 1:37 PM To: Nair, Murlidharan T Cc: R-help@stat.math.ethz.ch Subject: Re: [R] Multcomp On 7/22/06, Nair, Murlidharan T [EMAIL PROTECTED] wrote: Here it is again, hope this is more clear I am using the following data (only a small subset is given): Habitat Fungus.yield Birch 20.83829053 Birch 22.9718181 Birch 22.28216829 Birch 24.23136797 Birch 22.32147961 Birch 20.30783598 Oak 27.24047258 Oak 29.7730014 Oak 30.12608508 Oak 25.76088669 Oak 30.14750974 Hornbeam 17.05307949 Hornbeam 15.32805111 Hornbeam 18.26920177 Hornbeam 21.30987049 Hornbeam 21.7173223 I am using the multcomp package to do multiple comparisons as follows library(multcomp) # loads the package fungus-read.table(fungi.txt, Header=T)# Reads the data from file saved as fungi.txt fungus.cirec-simint(Fungus.yield~Habitat, data=fungus,conf.level=0.95,type =c(Tukey)) # Computes cimultaneous intervals using Tukey's method plot(fungus.cirec) # plots the data The plot function plots all the comparisons, I want to plot only part of the data since it clutters the graph. How do I plot only part of the data ? Don't understand what part of the data means. Use data = fungus[1:10,] in the simint call to just process the first 10 data rows. To eliminate a portion of the plot note in ?plot.hmtest that there is a ... argument and its description is that its passed to plot which in turn passes them to plot.default so you could use ylim = 1:2, say, to show only part of the plot vertically. I have to use all the data for my computation. Since the number of comparisons are many I want to plot it in different graphs so that the graph does not look cluttered. So part of the data means a subset of the comparisons in one graph and another subset in another and so on Can you give me an example of the ylim parameter. I tried plot(fungus.cirec, ylim=1:2) and it was not happy with it. I am not completely comfortable with the ... argument. I am trying to read up on it. How do I tell it to mark the significant comparisons? # after your plot statement: pp - locator() # now click on a spot on the plot # and then right click and choose stop text(pp$x, pp$y, some text) This is very useful How do I get rid of the field names in the plot? For eg. The plot labels are HabitatBirch-HabitatOak, I want it to be labeled as Birch-Oak. # change rownames of the estimates which has the effect # of changing the y axis labels rownames(fungus.cirec$estimate) - LETTERS[1:3] plot(fungus.cirec) This only labels it a A,B or C. What I wanted was to remove the field name Habitat in this case and out put the label as Birch-Oak. See ?gsub __ 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] RfW 2.3.1: regular expressions to detect pairs of identical word-final character sequences
Dear all
I use R for Windows 2.3.1 on a fully updated Windows XP Home SP2 machine and I
have two related regular expression problems.
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.1
year 2006
month 06
day01
svn rev38247
language R
version.string Version 2.3.1 (2006-06-01)
I would like to find cases of words in elements of character vectors that end
in the same character sequences; if I find such cases, I want to add r to
both potentially rhyming sequences. An example:
INPUT:This is my dog.
DESIRED OUTPUT: Thisr isr my dog.
I found a solution for cases where the potentially rhyming words are adjacent:
text-This is my dog.
gsub((\\w+?)(\\W\\w+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
However, with another text vector, I came across two problems I cannot seem to
solve and for which I would love to get some input.
(i) While I know what to do for non-adjacent words in general
gsub((\\w+?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, This not is my dog,
perl=TRUE) # I know this is not proper English ;-)
this runs into problems with overlapping matches:
text-And this is the second sentence
gsub((\\w+?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
[1] Andr this is the secondr sentence
It finds the nd match, but since the is match is within the two nd's, it
doesn't get it. Any ideas on how to get all pairwise matches?
(ii) How would one tell R to match only when there are 2+ characters matching?
If the above expression is applied to another character string
text-this is an example sentence.
gsub((\\w+?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
it also matches the e's at the end of example and sentence. It's not possible
to get rid of that by specifying a range such as {2,}
text-this is an example sentence.
gsub((\\w{2,}?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
because, as I understand it, this requires the 2+ cases of \\w to be identical
characters:
text-doo yoo see mee?
gsub((\\w{2,}?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
Again, any ideas?
I'd really appreciate any snippets of codes, pointers, etc.
Thanks so much,
STG
--
Stefan Th. Gries
---
University of California, Santa Barbara
http://www.linguistics.ucsb.edu/faculty/stgries
__
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] Warning Messages using rq -quantile regressions
I am a new to using quantile regressions in R. I have estimated a set of coefficients using the method=br algorithm with the rq command at various quantiles along the entire distribution. My data set contains approximately 2,500 observations and I have 7 predictor variables. I receive the following warning message: Solution may be nonunique in: rq.fit.br(x, y, tau = tau, ...) There are 13 warnings of this type after I run a single model. My results are similiar to the results I received in other stat programs using quantile reg procedures. I am unclear what these warning messages imply and if there are problems with model fit/convergence that I may need to consider. Any help would be appreciated. Thanks! __ 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] RfW 2.3.1: regular expressions to detect pairs of identical word-final character sequences
The following requires more than just a single gsub but it does solve
the problem. Modify to suit.
The first gsub places ... around the first occurrence of any
duplicated suffixes. We use the (?=...) zero width regexp
to circumvent the nesting problem.
Then we use strapply from the gsubfn package to extract
the suffixes so marked and paste them together to pass
to a second gsub which locates them in the original
string appending an r to each. Uncomment the commented
pat if you only want to match 2+ character suffixes.
library(gsubfn)
# places ... around first occurrences of repeated suffixes
text - And this is the second sentence
pat - (\\w+)(?=\\b.+\\1\\b)
# pat - (\\w\\w+)(?=\\b.+\\1\\b)
out - gsub(pat, 1\\, text, perl = TRUE)
suff - strapply(out, ([^]+), function(x,y)y)[[1]]
gsub(paste((, paste(suff, collapse = |), )\\b, sep = ), \\1r, text)
On 7/22/06, Stefan Th. Gries [EMAIL PROTECTED] wrote:
Dear all
I use R for Windows 2.3.1 on a fully updated Windows XP Home SP2 machine and
I have two related regular expression problems.
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.1
year 2006
month 06
day01
svn rev38247
language R
version.string Version 2.3.1 (2006-06-01)
I would like to find cases of words in elements of character vectors that end
in the same character sequences; if I find such cases, I want to add r to
both potentially rhyming sequences. An example:
INPUT:This is my dog.
DESIRED OUTPUT: Thisr isr my dog.
I found a solution for cases where the potentially rhyming words are adjacent:
text-This is my dog.
gsub((\\w+?)(\\W\\w+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
However, with another text vector, I came across two problems I cannot seem
to solve and for which I would love to get some input.
(i) While I know what to do for non-adjacent words in general
gsub((\\w+?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, This not is my dog,
perl=TRUE) # I know this is not proper English ;-)
this runs into problems with overlapping matches:
text-And this is the second sentence
gsub((\\w+?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
[1] Andr this is the secondr sentence
It finds the nd match, but since the is match is within the two nd's,
it doesn't get it. Any ideas on how to get all pairwise matches?
(ii) How would one tell R to match only when there are 2+ characters
matching? If the above expression is applied to another character string
text-this is an example sentence.
gsub((\\w+?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
it also matches the e's at the end of example and sentence. It's not
possible to get rid of that by specifying a range such as {2,}
text-this is an example sentence.
gsub((\\w{2,}?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
because, as I understand it, this requires the 2+ cases of \\w to be
identical characters:
text-doo yoo see mee?
gsub((\\w{2,}?)(\\W.+?)\\1(\\W), \\1r\\2\\1r\\3, text, perl=TRUE)
Again, any ideas?
I'd really appreciate any snippets of codes, pointers, etc.
Thanks so much,
STG
--
Stefan Th. Gries
---
University of California, Santa Barbara
http://www.linguistics.ucsb.edu/faculty/stgries
__
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.
