Re: [R] Zipping Rdata Files
On Thu, 7 Apr 2005 [EMAIL PROTECTED] wrote: Saving Rdata files in a zip archive form can in some cases save a considerable amount of disk space. Not if they were saved with compress=TRUE: it is likely to increase the size of compressed saved images. R has the zip.file.extract function to extract files from zip archives, but appears not to have any corresponding function to save in zipped form. (At least I have not been able to find anything in the help files or through searching the mail archives.) That is true, but I think you are looking for gzip format. If you want zip format, just use a system call to zip (if you have it). zip.file.extract is provided only because R for Windows needs to unzip on systems without unzip. (On other platforms it calls unzip.) The system function can be used to call gzip or some other utility, but perhaps there is a more direct method. Yes, for gzip (not zip). gzfile() connections, as used by save(compress=TRUE) and by load(). Also, when I use gzip to zip a file, I get an error message when using That's because gzip gzips a file, not zips a file. gzip and zip are different formats. zip.file.extract to extract the file as follows: save(trips, file=trips.Rdata) system(gzip trips.Rdata) # saves trips.Rdata in an archive named trips.Rdata.gz load(zip.file.extract(trips.Rdata, trips.Rdata.gz)) [1] trips.Rdata Warning message: error 1 in extracting from zip file Setting options(unzip=gunzip) or options(unzip=gunzip.exe) does not solve the error. load(zip.file.extract(trips.Rdata, trips.Rdata.gz)) Error in open.connection(con, rb) : unable to open connection In addition: Warning message: cannot open compressed file `trips.Rdata' Of course I could reverse the process with, system(gunzip trips.Rdata.gz) load(trips.Rdata) but perhaps there is a simpler solution. P.S. I'm running R 2.0.1 on a Windows XP computer. -- 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
Re: [R] hex format
David == David Forrest [EMAIL PROTECTED]
on Thu, 7 Apr 2005 16:19:33 -0500 (CDT) writes:
David I think R has the hex to decimal OK, but might be
David lacking in the decimal to hex case
David zz-function(x){ x-as.numeric(sub(#,'0x',x));
David c(x%/%256^2, x%/%256%%256, x%%256) }
zz('#0f0e0d')
David [1] 15 14 13
zz('#ff0080')
David [1] 255 0 128
I think you have overlooked the col2rgb() function
which does this (and more).
David If you already have the 3 byte triplet in read in as
David a binary, the same integer arithmetic does the
David extraction.
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Re: [R] /bin/exec/R: No such file or directory
Jarmila Bohmanova wrote: I have just installed R-2.0.1 from R-2.0.1.tar.gz on SUSe 9.1 64bit. When I am trying to launch R: R_HOME_DIR/bin/R; I am getting following message: ./R: line 151: /R_HOME_DIR/bin/exec/R: No such file or directory ./R: line 151: exec: /R_HOME_DIR/bin/exec/R: cannot execute: No such file or directory I do not have exec directory in bin directory. Does anybody know what went wrong? Looks like make failed. What was the error message from ./configure and/or make? Uwe Ligges Thank you. Jarmila. Jarmila Bohmanova University of Georgia Department of Animal and Dairy Science Athens, GA __ 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 __ 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
Re: [R] Adapt Function Examples
[EMAIL PROTECTED] wrote: I have read the help file for Adapt, but I cannot create a functn that works. I believe this is because I do not understand how to do this, and I have not found any working examples posted in the help. I have recieved many different errors in my attempts. Please post a simple but working use of the adapt function in 2 dimensions other than the one in the help(adapt) or explain it differently. So we are talking about function adapt() in package adapt? PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Please specify a simple example of what you are going to do and specify a non-working piece of code. Nobody wants to rephrase a help page not knowing whether it will help or not. Uwe Ligges Thank you __ 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 __ 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
Re: [R] NA in table with integer types
NaN only applies to double values: there is no integer NaN (nor Inf nor -Inf). The difference is clear from factor(x, exclude=NaN) [1] 1233NA Levels: 1 2 3 NA factor(as.integer(x), exclude=NaN) [1] 1233NA Levels: 1 2 3 If you read ?factor it says exclude: a vector of values to be excluded when forming the set of levels. This should be of the same type as 'x', and will be coerced if necessary. and as.integer(NaN) is integer NA. So factor(as.integer(x), exclude=NaN) is the same as factor(as.integer(x), exclude=NA). On Thu, 7 Apr 2005, Paul Rathouz wrote: Hi -- I am having the following problem with table() when applied to vectors of type (mode) integer. When I use the table() command, I can *only obtain an entry in the table for NA values by using exclude=NULL*. Just issuing exclude=NaN will not do it. See below, where x is double at first, and then coerced to integer and notice the difference. Is this a bug or is there something that I do not understand about the integer data type? That is, is there some other value besides NA and NaN that missing integers take? Thanks -- pr -- x - c(1,2,3,3,NA) is.double(x) [1] TRUE table(x,exclude=NA) x 1 2 3 1 1 2 table(x,exclude=NaN) x 123 NA 1121 table(x,exclude=NULL) x 123 NA 1121 x - as.integer(x) x [1] 1 2 3 3 NA is.na(x) [1] FALSE FALSE FALSE FALSE TRUE is.integer(x) [1] TRUE table(x,exclude=NA) x 1 2 3 1 1 2 table(x,exclude=NaN) x 1 2 3 1 1 2 table(x,exclude=NULL) x 123 NA 1121 -- 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
[R] weird results w/ prcomp-princomp
I am doing a Principal Component Analaysis (PCA) on a 44x19 matrix. with princomp(x,cor=TRUE,scores=TRUE) and prcomp(x,scale=TRUE,center=TRUE) The resulted eigenv. and rotated matrix are the same (as expected), however the sum of eigenvalues is lower than 19 (number of variables). With a commercial stat software it worked correctly, with the same dataset. Am I doing something wrong? Thanks Alex -- No virus found in this outgoing message. Checked by AVG Anti-Virus. -- No virus found in this outgoing message. Checked by AVG Anti-Virus. __ 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
Re: [R] weird results w/ prcomp-princomp
On Fri, 2005-04-08 at 11:12 +0200, Alessandro Bigi wrote: I am doing a Principal Component Analaysis (PCA) on a 44x19 matrix. with princomp(x,cor=TRUE,scores=TRUE) and prcomp(x,scale=TRUE,center=TRUE) The resulted eigenv. and rotated matrix are the same (as expected), however the sum of eigenvalues is lower than 19 (number of variables). What about the sum of squared sdev? (Hint, the prcomp help page says that the returned sdev are the square root of the eigenvalues. While princomp help does not say this explicitly, it says that sdev are standard deviations). cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061 email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ 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
[R] Can't get function to run iteratively
Trying to do something very simple...
numerical.grad
function(func,x, eps=1e-12) {
# very simple (crude) numerical approximation
f -func(x)
df -1:length(x)
for (i in 1:length(x)) {
dx - x
dx[i] - dx[i] +eps
df[i] - (func(dx)-f)/eps
}
df
}
test-function(x){x^2}
y-seq(0.1,0.5,0.1)
numerical.grad(test,y)
[1] 0.197 0.000 0.000 0.000 0.000
Warning messages:
1: number of items to replace is not a multiple of replacement length
2: number of items to replace is not a multiple of replacement length
3: number of items to replace is not a multiple of replacement length
4: number of items to replace is not a multiple of replacement length
5: number of items to replace is not a multiple of replacement length
Any thoughts why this doesn't seem to be working ?
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Re: [R] Can't get function to run iteratively
R is a vectorized language, look at this:
fd - function(b, gn, ..., eps=sqrt(.Machine$double.neg.eps)){
n - length(b)
g0 - gn(b, ...)
out - numeric(n)
b. - b + eps*max(abs(b), 1)
c(gn(b., ...) - g0) / (b. - b)
}
##
test - function(x) x*x
fd(seq(0.1, 0.5, 0.1), test)
2*seq(0.1, 0.5, 0.1)
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: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Uzuner, Tolga [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Sent: Friday, April 08, 2005 12:08 PM
Subject: [R] Can't get function to run iteratively
Trying to do something very simple...
numerical.grad
function(func,x, eps=1e-12) {
# very simple (crude) numerical approximation
f -func(x)
df -1:length(x)
for (i in 1:length(x)) {
dx - x
dx[i] - dx[i] +eps
df[i] - (func(dx)-f)/eps
}
df
}
test-function(x){x^2}
y-seq(0.1,0.5,0.1)
numerical.grad(test,y)
[1] 0.197 0.000 0.000 0.000 0.000
Warning messages:
1: number of items to replace is not a multiple of replacement
length
2: number of items to replace is not a multiple of replacement
length
3: number of items to replace is not a multiple of replacement
length
4: number of items to replace is not a multiple of replacement
length
5: number of items to replace is not a multiple of replacement
length
Any thoughts why this doesn't seem to be working ?
==
This message is for the sole use of the intended recipient. If you
received
this message in error please delete it and notify us. If this
message was
misdirected, CSFB does not waive any confidentiality or privilege.
CSFB
retains and monitors electronic communications sent through its
network.
Instructions transmitted over this system are not binding on CSFB
until they
are confirmed by us. Message transmission is not guaranteed to be
secure.
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Re: [R] off-topic question: Latex and R in industries
Donald Ingram wrote: ( Is there a universal vector format I could use ? ) If there were one, you can be sure that Microsoft would take steps to corrupt their implementation of the ``universal'' format so that material produced by non-Microsoft software would be unusable by Microsoft software. Microsoft's goal is to create an effective ***monopoly*** for themselves. People being the idiots that they are, Microsoft is succeeding admirably. My problems - are not R but with general UNIX - PC interoperability This terminology is incorrect and misleading. It is not a ``PC'' problem --- the PC is the hardware on which any software/operating system can run. UNIX (in the guise of Linux) runs on PCs. The problem is the Micrsoft Windoze operating system, which goes out of its way to be incompatible with everything else. cheers, Rolf Turner [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
RE: [R] /bin/exec/R: No such file or directory
Make gives me following error message: R_HOME_DIR/src/main/array.c:504: undefined reference to `zgemm' array.o(.text+0x2526): In function `do_matprod': R_HOME_DIR/src/main/array.c:472: undefined reference to `dsyrk' array.o(.text+0x2601):R_HOME_DIR/src/main/array.c:487: undefined reference to `dgemm' array.o(.text+0x2667):R_HOME_DIR/src/main/array.c:432: undefined reference to `zgemm' array.o(.text+0x27f0):R_HOME_DIR/src/main/array.c:405: undefined reference to `dgemm' registration.o(.data+0xb8): undefined reference to `cg' registration.o(.data+0xe0): undefined reference to `ch' registration.o(.data+0x108): undefined reference to `rg' registration.o(.data+0x130): undefined reference to `rs' ../appl/libappl.a(bakslv.o)(.text+0x12a): In function `bakslv': R_HOME_DIR/src/appl/bakslv.c:108: undefined reference to `dtrsm' ../appl/libappl.a(uncmin.o)(.text+0x15e5): In function `secunf': R_HOME_DIR/src/appl/uncmin.c:1187: undefined reference to `dnrm2' ../appl/libappl.a(uncmin.o)(.text+0x15fd):R_HOME_DIR/src/appl/uncmin.c:1188: undefined reference to `dnrm2' ../appl/libappl.a(uncmin.o)(.text+0x1abb): In function `secfac': R_HOME_DIR/src/appl/uncmin.c:1271: undefined reference to `dnrm2' ../appl/libappl.a(uncmin.o)(.text+0x1ade):R_HOME_DIR/src/appl/uncmin.c:1272: undefined reference to `dnrm2' ../appl/libappl.a(uncmin.o)(.text+0x3859): In function `optdrv': R_HOME_DIR/src/appl/uncmin.c:970: undefined reference to `dnrm2' ../appl/libappl.a(uncmin.o)(.text+0x3bb6):R_HOME_DIR/src/appl/uncmin.c:1016: more undefined references to `dnrm2' follow ../appl/libappl.a(blas.o)(.text+0x21e0): In function `DGBMV': R_HOME_DIR/src/appl/blas.f:357: undefined reference to `XERBLA' ../appl/libappl.a(blas.o)(.text+0x41c6): In function `DGEMM': R_HOME_DIR/src/appl/blas.f:682: undefined reference to `XERBLA' ../appl/libappl.a(blas.o)(.text+0x642e): In function `DGEMV': R_HOME_DIR/src/appl/blas.f:940: undefined reference to `XERBLA' ../appl/libappl.a(blas.o)(.text+0x7ab2): In function `DGER': R_HOME_DIR/src/appl/blas.f:1171: undefined reference to `XERBLA' ../appl/libappl.a(blas.o)(.text+0xaf29): In function `DSBMV': R_HOME_DIR/src/appl/blas.f:1794: undefined reference to `XERBLA' ../appl/libappl.a(blas.o)(.text+0xda14):R_HOME_DIR/src/appl/blas.f:2177: more undefined references to `XERBLA' follow collect2: ld returned 1 exit status make[3]: *** [R.bin] Error 1 make[3]: Leaving directory `R_HOME_DIR/src/main' make[2]: *** [R] Error 2 make[2]: Leaving directory `R_HOME_DIR/src/main' make[1]: *** [R] Error 1 make[1]: Leaving directory `R_HOME_DIR/src' make: *** [R] Error 1 -Original Message- From: Uwe Ligges [mailto:[EMAIL PROTECTED] Sent: Friday, April 08, 2005 3:19 AM To: [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] /bin/exec/R: No such file or directory Jarmila Bohmanova wrote: I have just installed R-2.0.1 from R-2.0.1.tar.gz on SUSe 9.1 64bit. When I am trying to launch R: R_HOME_DIR/bin/R; I am getting following message: ./R: line 151: /R_HOME_DIR/bin/exec/R: No such file or directory ./R: line 151: exec: /R_HOME_DIR/bin/exec/R: cannot execute: No such file or directory I do not have exec directory in bin directory. Does anybody know what went wrong? Looks like make failed. What was the error message from ./configure and/or make? Uwe Ligges Thank you. Jarmila. Jarmila Bohmanova University of Georgia Department of Animal and Dairy Science Athens, GA __ 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 __ 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
[R] is there any function to do oblique rotation in factor analysis?
splus has many different rotation methods,but i can only find 2 in R.i want to do oblique rotation .has any function for this? i have search the web,but can not find. __ 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
[R] TR: The results of your email commands
Hi,
I try to minimize the sum of the sum of sce. The following program has
been
created but it only takes in consideration the last kinetic and not the
first ones. I think that I have forget a subscrib but I don't know
where. so
if you can help me, it will be great
I have try an other program where y and x are directly calculate in sce
function but the time of running was to long.
Thanks in advance,
Anne KERVAHU
rm(list=ls())
nbr=10
#list of data
x_a-c(0,0.5,1,1.5,2,3,4,6,8,15,20,40,60,80,120)
y_a-c(5.4771213,5.0791812,4.8450980,4.3010300,4,2.30103,1.5563025,1.30103,1
,1.6434527,0.60206,0.60206,0.30103,0,0.4771213)
x_b-c(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14)
y_b-c(5.3424227,4.9867717,4.6627578,4.0606978,3.07182,3.4771213,2.7993405,2
.9395193,2.69897,2.6127839,1.9777236,1.3222193,1.4149733,0.7781513,1.322219)
x_c-c(0,3,6,10,12,14,16,18,20,24,26,28,30,34)
y_c-c(5.5185139,5.1461280,4.3617278,3.771513,3.20412,3.0413927,2.7781513,2.
5682017,2.255272,1.7823917,1.447158,1.3222193,1.2787536,0.69897)
#number of kinetics
nb=3
#complete data set
x-c(x_a,x_b,x_c)
y-c(y_a,y_b,y_c)
#cumulative length
long-c(0,15,30,44)
coeff-matrix(nrow=1,ncol=(nb*2)+2)
#function to minimise
sce-function(param){
return(sum(sum((yy-(param[i+nb]-(xx/param[i])^param[(nb*2)+1]))^2)))
}
#initial value for optim function
ninit-vector(length=nb)
for(i in 1:nb){
ninit[i]-x[long[i]+1]
}
pinf=c(rep(0.01,nb),rep(3,nb),0.5)
psup=c(rep(10,nb),rep(8,nb),4)
pinit=c(runif(nb,min=0.1,max=5),ninit,runif(1,min=0.5,max=4))
print(pinit)
for (i in 1:nb)
{
yy-y[((long[i]+1):long[i+1])]
for( k in 1:length(yy)){
ifelse((yy[k]=log10(nbr)),(yy-yy[1:(min(which(yy=log10(nbr),arr.ind=FALSE
))-1)]),(yy-yy))
}
vv-x[((long[i]+1):long[i+1])]
xx-x[((long[i]+1):((long[i]+1)+(length(vv)=length(yy))-1))]
fl-optim(p=pinit,sce,method=L-BFGS-B,lower=pinf,upper=psup,
control=list(maxit=20,temp=200))
co-fl$par
coe-fl$value
coeff-c(co,coe)
}
coeff
#graphical verification
plot(x_b,y_b)
y_est-coeff[6]-(x_b/coeff[2])^coeff[7]
points(x_b,y_est)
---BeginMessage---
Hi,
I try to minimize the sum of the sum of sce. The following program has been
created but it only takes in consideration the last kinetic and not the
first ones. I think that I have forget a subscrib but I don't know where. so
if you can help me, it will be great
I have try an other program where y and x are directly calculate in sce
function but the time of running was to long.
Thanks in advance,
Anne KERVAHU
rm(list=ls())
nbr=10
#list of data
x_a-c(0,0.5,1,1.5,2,3,4,6,8,15,20,40,60,80,120)
y_a-c(5.4771213,5.0791812,4.8450980,4.3010300,4,2.30103,1.5563025,1.30103,1
,1.6434527,0.60206,0.60206,0.30103,0,0.4771213)
x_b-c(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14)
y_b-c(5.3424227,4.9867717,4.6627578,4.0606978,3.07182,3.4771213,2.7993405,2
.9395193,2.69897,2.6127839,1.9777236,1.3222193,1.4149733,0.7781513,1.3222193
)
x_c-c(0,3,6,10,12,14,16,18,20,24,26,28,30,34)
y_c-c(5.5185139,5.1461280,4.3617278,3.771513,3.20412,3.0413927,2.7781513,2.
5682017,2.255272,1.7823917,1.447158,1.3222193,1.2787536,0.69897)
#number of kinetics
nb=3
#complete data set
x-c(x_a,x_b,x_c)
y-c(y_a,y_b,y_c)
#cumulative length
long-c(0,15,30,44)
coeff-matrix(nrow=1,ncol=(nb*2)+2)
#function to minimise
sce-function(param){
return(sum(sum((yy-(param[i+nb]-(xx/param[i])^param[(nb*2)+1]))^2)))
}
#initial value for optim function
ninit-vector(length=nb)
for(i in 1:nb){
ninit[i]-x[long[i]+1]
}
pinf=c(rep(0.01,nb),rep(3,nb),0.5)
psup=c(rep(10,nb),rep(8,nb),4)
pinit=c(runif(nb,min=0.1,max=5),ninit,runif(1,min=0.5,max=4))
print(pinit)
for (i in 1:nb)
{
yy-y[((long[i]+1):long[i+1])]
for( k in 1:length(yy)){
ifelse((yy[k]=log10(nbr)),(yy-yy[1:(min(which(yy=log10(nbr),arr.ind=FALSE
))-1)]),(yy-yy))
}
vv-x[((long[i]+1):long[i+1])]
xx-x[((long[i]+1):((long[i]+1)+(length(vv)=length(yy))-1))]
fl-optim(p=pinit,sce,method=L-BFGS-B,lower=pinf,upper=psup,
control=list(maxit=20,temp=200))
co-fl$par
coe-fl$value
coeff-c(co,coe)
}
coeff
#graphical verification
plot(x_b,y_b)
y_est-coeff[6]-(x_b/coeff[2])^coeff[7]
points(x_b,y_est)
---End Message---
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RE: [R] 'skewing' a normal random variable
Hi: Thank you and sorry for getting back late. Your input helped me a lot. I particularly liked using box.cox. Regards, Ashraf __ 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
Re: [R] NA in table with integer types
OK. Thanks. So, if you use table() on a factor that contains NA's, but for which NA is not a level, is there any way to get table to generate an entry for the NAs? For example, in below, even exclude=NULL will not give me an entry for NA on the factor y: x - c(1,2,3,3,NA) y - factor(x) y [1] 1233NA Levels: 1 2 3 table(y,exclude=NA) y 1 2 3 1 1 2 table(y,exclude=NaN) y 1 2 3 1 1 2 table(y,exclude=NULL) y 1 2 3 1 1 2 On Fri, 8 Apr 2005, Prof Brian Ripley wrote: NaN only applies to double values: there is no integer NaN (nor Inf nor -Inf). The difference is clear from factor(x, exclude=NaN) [1] 1233NA Levels: 1 2 3 NA factor(as.integer(x), exclude=NaN) [1] 1233NA Levels: 1 2 3 If you read ?factor it says exclude: a vector of values to be excluded when forming the set of levels. This should be of the same type as 'x', and will be coerced if necessary. and as.integer(NaN) is integer NA. So factor(as.integer(x), exclude=NaN) is the same as factor(as.integer(x), exclude=NA). [rest deleted] == Paul Rathouz, Assoc. Professor ph 773-834-1970 Dept. of Health Studies, Rm. W-264 fax 773-702-1979 University of Chicago[EMAIL PROTECTED] 5841 S. Maryland Ave. MC 2007 Chicago, IL 60637 __ 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
Re: [R] NA in table with integer types
On Apr 8, 2005 9:05 AM, Paul Rathouz [EMAIL PROTECTED] wrote: OK. Thanks. So, if you use table() on a factor that contains NA's, but for which NA is not a level, is there any way to get table to generate an entry for the NAs? For example, in below, even exclude=NULL will not give me an entry for NA on the factor y: x - c(1,2,3,3,NA) y - factor(x) y [1] 1233NA Levels: 1 2 3 summary(y) __ 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
Re: [R] NA in table with integer types
On Fri, 8 Apr 2005, Paul Rathouz wrote: OK. Thanks. So, if you use table() on a factor that contains NA's, but for which NA is not a level, is there any way to get table to generate an entry for the NAs? For example, in below, even exclude=NULL will not give me an entry for NA on the factor y: I think this very clear from the help page: exclude: values to use in the exclude argument of 'factor' when interpreting non-factor objects; if specified, levels to remove from all factors in Only when 'exclude' is specified (i.e., not by default), will 'table' drop levels of factor arguments potentially. and you cannot remove a level that is not there. You seem to be persisting in not understanding: 'exclude' is supposed to be the same type as x (or its levels), and you have given logical and numeric values, not character ones. x - c(1,2,3,3,NA) y - factor(x) y [1] 1233NA Levels: 1 2 3 table(y,exclude=NA) y 1 2 3 1 1 2 table(y,exclude=NaN) y 1 2 3 1 1 2 table(y,exclude=NULL) y 1 2 3 1 1 2 On Fri, 8 Apr 2005, Prof Brian Ripley wrote: NaN only applies to double values: there is no integer NaN (nor Inf nor -Inf). The difference is clear from factor(x, exclude=NaN) [1] 1233NA Levels: 1 2 3 NA factor(as.integer(x), exclude=NaN) [1] 1233NA Levels: 1 2 3 If you read ?factor it says exclude: a vector of values to be excluded when forming the set of levels. This should be of the same type as 'x', and will be coerced if necessary. and as.integer(NaN) is integer NA. So factor(as.integer(x), exclude=NaN) is the same as factor(as.integer(x), exclude=NA). [rest deleted] == Paul Rathouz, Assoc. Professor ph 773-834-1970 Dept. of Health Studies, Rm. W-264 fax 773-702-1979 University of Chicago[EMAIL PROTECTED] 5841 S. Maryland Ave. MC 2007 Chicago, IL 60637 == -- 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
[R] anova with gam?
Hello. In SPLUS I am used to comparing nested models in gam using the anova function. When I tried this in R this doesn't work (the error message says that anova() doesn't recognise the gam fit). What must I do to use anova with gam? To be clear, I want to do the following: fFit1-gam(y~x,.) fit1-fam(y~s(x),.) anova(fit2,fit1,test=F) Thanks. Bill Shipley [[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
Re: [R] NA in table with integer types
On 8 Apr 2005 at 14:20, Prof Brian Ripley wrote: On Fri, 8 Apr 2005, Paul Rathouz wrote: OK. Thanks. So, if you use table() on a factor that contains NA's, but for which NA is not a level, is there any way to get table to generate an entry for the NAs? For example, in below, even exclude=NULL will not give me an entry for NA on the factor y: Hi Use exclude in factor not in table x-sample(1:3, 10, replace=T) x[5:6]-NA table(x) x 1 2 3 5 2 1 y-factor(x) y [1] 1123NA NA 1121 Levels: 1 2 3 table(y) # no entry for NA y 1 2 3 5 2 1 factor(y,exclude=NULL) #make NA a level in factor y [1] 1123NA NA 1121 Levels: 1 2 3 NA table(y) # shows you entry for NA y 123 NA 5212 I think this very clear from the help page: exclude: values to use in the exclude argument of 'factor' when interpreting non-factor objects; if specified, levels to remove from all factors in Only when 'exclude' is specified (i.e., not by default), will 'table' drop levels of factor arguments potentially. and you cannot remove a level that is not there. You seem to be persisting in not understanding: 'exclude' is supposed to be the same type as x (or its levels), and you have given logical and numeric values, not character ones. x - c(1,2,3,3,NA) y - factor(x) y [1] 1233NA Levels: 1 2 3 table(y,exclude=NA) y 1 2 3 1 1 2 table(y,exclude=NaN) y 1 2 3 1 1 2 table(y,exclude=NULL) y 1 2 3 1 1 2 On Fri, 8 Apr 2005, Prof Brian Ripley wrote: NaN only applies to double values: there is no integer NaN (nor Inf nor -Inf). The difference is clear from factor(x, exclude=NaN) [1] 1233NA Levels: 1 2 3 NA factor(as.integer(x), exclude=NaN) [1] 1233NA Levels: 1 2 3 If you read ?factor it says exclude: a vector of values to be excluded when forming the set of levels. This should be of the same type as 'x', and will be coerced if necessary. and as.integer(NaN) is integer NA. So factor(as.integer(x), exclude=NaN) is the same as factor(as.integer(x), exclude=NA). [rest deleted] == Paul Rathouz, Assoc. Professor ph 773-834-1970 Dept. of Health Studies, Rm. W-264 fax 773-702-1979 University of Chicago[EMAIL PROTECTED] 5841 S. Maryland Ave. MC 2007 Chicago, IL 60637 == -- 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 Petr Pikal [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
RE: [R] anova with gam?
Dear Bill, There are anova.gam methods in both the mgcv and gam packages -- perhaps you have an older version of one of these packages. 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 Bill Shipley Sent: Friday, April 08, 2005 8:31 AM To: R help list Subject: [R] anova with gam? Hello. In SPLUS I am used to comparing nested models in gam using the anova function. When I tried this in R this doesn't work (the error message says that anova() doesn't recognise the gam fit). What must I do to use anova with gam? To be clear, I want to do the following: fFit1-gam(y~x,.) fit1-fam(y~s(x),.) anova(fit2,fit1,test=F) Thanks. Bill Shipley [[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 __ 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
[R] error on install Rmpi packages
Dear Sir/Madam, I need to install Rmpi Package on my linux debian like, but I get some errors. I try to instal it using install.packages or after download and save it on my local dir and run R CMD INSTALL packagename and, both, I get these errors: checking mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no Try to find mpi.h ... Cannot find mpi header file. Please use --with-mpi=/path/to/mpi ERROR: configuration failed for package 'Rmpi' I search on archivies help but dont get any issues. I use Rmpi_0.4-9.tar.gz. What I to do to fiz it? Thanks Marcelo __ 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
Re: [R] /bin/exec/R: No such file or directory
Jarmila Bohmanova wrote: Make gives me following error message: R_HOME_DIR/src/main/array.c:504: undefined reference to `zgemm' array.o(.text+0x2526): In function `do_matprod': R_HOME_DIR/src/main/array.c:472: undefined reference to `dsyrk' array.o(.text+0x2601):R_HOME_DIR/src/main/array.c:487: undefined reference to `dgemm' [SNIP] So this is probably a problem with a BLAS installation choosen by ./configure. Uwe Ligges -Original Message- From: Uwe Ligges [mailto:[EMAIL PROTECTED] Sent: Friday, April 08, 2005 3:19 AM To: [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] /bin/exec/R: No such file or directory Jarmila Bohmanova wrote: I have just installed R-2.0.1 from R-2.0.1.tar.gz on SUSe 9.1 64bit. When I am trying to launch R: R_HOME_DIR/bin/R; I am getting following message: ./R: line 151: /R_HOME_DIR/bin/exec/R: No such file or directory ./R: line 151: exec: /R_HOME_DIR/bin/exec/R: cannot execute: No such file or directory I do not have exec directory in bin directory. Does anybody know what went wrong? Looks like make failed. What was the error message from ./configure and/or make? Uwe Ligges Thank you. Jarmila. Jarmila Bohmanova University of Georgia Department of Animal and Dairy Science Athens, GA __ 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 __ 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 __ 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
[R] restrict namespace inside functions?
Is there a way to exclude from the namespace all
variables other than function arguments and local
variables? For example, I would like the following
code
a = 2.0
mult - function(x)
{
pi = 3.14
return(pi*a*x)
}
print(mult(10.0))
to say a not found rather than using a = 2.0 inside
function mult. Thanks.
Vivek Rao
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Re: [R] restrict namespace inside functions?
On Friday 08 April 2005 09:50, Vivek Rao wrote:
Is there a way to exclude from the namespace all
variables other than function arguments and local
variables? For example, I would like the following
code
a = 2.0
mult - function(x)
{
pi = 3.14
return(pi*a*x)
}
print(mult(10.0))
to say a not found rather than using a = 2.0 inside
function mult. Thanks.
Depending on why you want to do this, it might be enough to say
environment(mult) - new.env(parent = NULL)
HTH,
Deepayan
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[R] DLL Memory Problem
Hello,
I have created a .dll file using G77 and MinGW on my PC (Windows
2000). After using dyn.load to bring it into R2.0.1, I then call the .dll
through the function ccprox shown below. It returns the correct
values. If I run it a second time though it returns different values, so
it seems something is being placed oddly in memory.
If I unload and reload the .dll it works again the first time.
It does the same if I copy the compiled .dll over to my Windows XP machine.
Thank you for any help,
Brian Habing
[EMAIL PROTECTED]
The Fortran subroutine beings with:
subroutine ccprox(nexmn,nitem,respmat2,covmatr,covmatt,
$ cormatr,cormatt)
!c This subroutine will calculate all the pairwise
!c conditional covariances. An ending r means for
!c rest score, an ending t means for total score.
parameter (maxitem=100,maxexmn=1,maxcats=10,ncells=1001)
!c ncells must be maxitem*maxcats+1
integer nexmn,nitem,scoretemp,mscore
integer respmat(maxexmn,maxitem)
integer tscore(maxexmn) /maxexmn*0/
integer tstemp(maxexmn) /maxexmn*0/
integer natscore(ncells) /ncells*0/
integer natemp(ncells) /ncells*0/
integer i,j,k,l
integer tcountt,tcountr,tcountt2,tcountr2
real*8 respmat2(maxexmn,maxitem)
real*8 pisum(ncells),plsum(ncells),pilsum(ncells)
real*8 qisum(ncells),qlsum(ncells),qilsum(ncells)
real*8 pi2sum(ncells),pl2sum(ncells)
real*8 qi2sum(ncells),ql2sum(ncells)
real*8 covmatr(maxitem,maxitem),cormatr(maxitem,maxitem)
real*8 covmatt(maxitem,maxitem),cormatt(maxitem,maxitem)
real*8 sisl
The R function that is calling it is as follows (inputdata is a 400x10
matrix of 0's and 1's
in the example I have been trying).
ccprox-function(inputdata){
nexmn-length(inputdata[,1])
nitem-length(inputdata[1,])
covmatr-matrix(0,100,100)
covmatt-matrix(0,100,100)
cormatr-matrix(0,100,100)
cormatt-matrix(0,100,100)
respmat2-matrix(0,nrow=1,ncol=100)
respmat2[1:nexmn,1:nitem]-as.matrix(inputdata)
if (is.loaded(ccprox_)==TRUE){
x-(.C(ccprox_,as.integer(nexmn),as.integer(nitem),respmat2,
covmatr,covmatt,cormatr,cormatt))
list(covmatr=x[[4]][1:nitem,1:nitem],covmatt=x[[5]][1:nitem,1:nitem],
cormatr=x[[6]][1:nitem,1:nitem],cormatt=x[[7]][1:nitem,1:nitem],)
}
else{
warning(ccprox.dll was not loaded)
NULL
}
}
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[R] kunamorph@web.de
Hello, how can I use the function cor() with x and y in function aggregate() or by()? The data are like this: x y group 1 4 B 2 4 B 3 5 C I would like obtain the correlation between x and y for each subset. I don't want to use the workaround with the function subset(), because I have many groups. Thanks in advance. Christfried Kunath KC __ 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
Re: [R] hex format
Thomas Lumley [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Yes, and convertColor in R-devel does quite a few of these (XYZ tristimulus space; CIE Lab and Luv; sRGB, Apple RGB and roll-your-own RGB based on chromaticities of the primaries; and chromatic adaptation for changing the white point). The colorspace package has a more elegant implementation of a somewhat different set of color space computations, and R-devel also has hcl() for specifying colors based on hue, chroma, and luminance (polar coordinates in Luv space). Thank you for this info. I struggle to keep up with what is on CRAN and in Bioconductor, so I haven't looked at the newer packages in R-devel. Both convertColor and colorspace look interesting and I'll definitely investigate them. I see the latest (first?) version of colorspace was introduced in January 2005 and provides functions hex, hex2RGB, readhex and writehex, and these functions seem to address my color concerns. But I was using color manipulations as an example of a need for more general capapabilities in R to do these hex conversions when needed, and without a special package. I recently discovered R's writeBin and readBin functions. readBin, in particular, looks like an extremely powerful tool for loading external files. This might be an easier way to perform some one-time data manipulations instead of writing a separate C, Perl or Delphi program to manipulate data before bringing it into R for analysis. readBin returns a raw data type that looks like an array of bytes that R displays in hex. That's where my problem begins and why I joined this hex format thread. I'd love to manipulate this raw hex data, but R makes using these hex bytes quite difficult to use (or more difficult than I think it should be based on how easy it is in other languages). I might want to interpret a byte, or a string of bytes, as characters. Or, I might want to interpret pairs of bytes as 2-byte unsigned (or possibly signed) integers. Or, I might want to interpret 3-bytes at a time as RGB values (in either RGB or BGR order). Or, I might want to interpret 8-bytes at a type as a IEEE754 floating point number. Every time someone wants to manipulate this raw data in R, as far as I can tell now, one must start from scratch and do all sorts of manipulations on these hex byte values to get characters, or integers, or doubles. And because it's not that easy (but it's not that hard either, more of an annoyance), I guess many just go back to C to get that job done there and then return to R. Perhaps I've missed some R functions that do this conversion, but if not, I suggest some new functions that take an array of raw bytes like this, and return either a single value, or an array of values, under a given interpretation would be a useful addition to R for working with raw data (like flow cytometery data -- http://www.softflow.com/sf_www/fcap/Fcsformt.htm, or even TIFF files, or other forms of scientific data). Examples of writeBin/readBin: # Integers IntegerSize - 4# How do I get this value from R? i - -2:2 i [1] -2 -1 0 1 2 writeBin(i, big.bin, endian=big) big - readBin(big.bin, raw, length(i)*IntegerSize) big [1] ff ff ff fe ff ff ff ff 00 00 00 00 00 00 00 01 00 00 00 02 typeof(big) [1] raw writeBin(i, little.bin, endian=little) little - readBin(little.bin, raw, length(i)*IntegerSize) little [1] fe ff ff ff ff ff ff ff 00 00 00 00 01 00 00 00 02 00 00 00 #Doubles DoubleSize - 8 x - 10^(-2:2) x [1] 1e-02 1e-01 1e+00 1e+01 1e+02 writeBin(x, big.bin, endian=big) big - readBin(big.bin, raw, length(x)*DoubleSize) big [1] 3f 84 7a e1 47 ae 14 7b 3f b9 99 99 99 99 99 9a 3f f0 00 00 00 00 00 00 40 24 00 00 00 00 00 00 40 59 00 00 00 00 00 00 writeBin(x, platform.bin, endian=.Platform$endian) platform - readBin(platform.bin, raw, length(x)*DoubleSize) platform [1] 7b 14 ae 47 e1 7a 84 3f 9a 99 99 99 99 99 b9 3f 00 00 00 00 00 00 f0 3f 00 00 00 00 00 00 24 40 00 00 00 00 00 00 59 40 y - readBin(platform.bin, double, length(x)*DoubleSize) y [1] 1e-02 1e-01 1e+00 1e+01 1e+02 efg __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] DLL Memory Problem - Solved
At 11:04 AM 4/8/2005, you wrote: Hello, I have created a .dll file using G77 and MinGW on my PC (Windows 2000). After using dyn.load to bring it into R2.0.1, I then call the .dll through the function ccprox shown below. It returns the correct values. If I run it a second time though it returns different values, so it seems something is being placed oddly in memory. The Fortran subroutine beings with: integer tscore(maxexmn) /maxexmn*0/ integer tstemp(maxexmn) /maxexmn*0/ integer natscore(ncells) /ncells*0/ integer natemp(ncells) /ncells*0/ These are only reset to zero the first time when its loaded. Putting the reset manually in the Fortran code fixes it. Thanks to anyone who had been thinking about it! -Brian [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] axis colors in pairs plot
Thanks Bill and Deepayan for the panel function idea. Somehow I've always associated the panel functions with lattice -- not sure why, but thanks for pointing out their more universal applicability. Anne On Thu, 7 Apr 2005, Deepayan Sarkar wrote: DS On Thursday 07 April 2005 17:51, Anne York wrote: DS The following command produces red axis line in a pairs DS plot: DS DS pairs(iris[1:4], main = Anderson's Iris Data -- 3 species, DS pch = +, col = c(red, green3, blue)[unclass(iris$Species)]) DS DS DS Trying to fool pairs in the following way produces the DS same plot as above: DS DS pairs(iris[1:4], main = Anderson's Iris Data -- 3 species,pch = DS +, col = c(black, red, green3, blue)[ 1+ DS unclass(iris$Species)]) DS DS One very kludgy work-around is to define a new level 1, say DS foo in the first row of iris: DS DS iris2=iris DS iris2$Species = as.character(iris2$Species) DS iris2$Species[1]=foo DS iris2$Species = factor(iris2$Species) DS DS pairs(iris2[1:4], main = Anderson's Iris Data -- 3 DS species, pch = +, DS col = c( black,red, green3,blue)[ unclass(iris2$Species)]) DS DS However, if any other row is redefined, the red-axis DS persists. For example: DS DS iris2=iris DS iris2$Species = as.character(iris2$Species) DS iris2$Species[3]=foo DS iris2$Species = factor(iris2$Species) DS DS DS pairs(iris2[1:4], main = Anderson's Iris Data -- 3 DS species, pch = +, DS col = c( black,red, green3,blue)[ unclass(iris2$Species)]) DS DS I'd appreciate suggestions for a simpler work-around. DS DS One possibility is something along the lines of DS DS pairs(iris[1:4], DSpanel = function(...) DSpoints(..., DS col = c(red, green3, blue) DS [unclass(iris$Species)] )) DS DS Deepayan DS DS __ 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
[R] BUG in RODBC with OS X?
This is my second posting on this topic, the first recieved no replies. Has anyone successfully used RODBC on the OS X platform? I've tested the ODBC drivers I'm using with two other applications and I've had no problems. I begining to think the problem is with R/RODBC and not the drivers. Here are the specifics: I'm having a problem connecting to an MS SQL Database via RODBC on OS X. If I try to connect through the GUI using chan - odbcConnect(drewdb, uid=user, pwd =pwd) it simply crashes R with the following crash report: Date/Time: 2005-03-28 12:30:48 -0600 OS Version: 10.3.8 (Build 7U16) Report Version: 2 Command: R Path:/Applications/R.app/Contents/MacOS/R Version: 1.01 (1.01) PID: 507 Thread: 0 Exception: EXC_BAD_ACCESS (0x0001) Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x01fc However, if I try it through an xterm (command line), I get the following: Warning messages: 1: [RODBC] ERROR: state IM004, code 0, message [iODBC][Driver Manager]Driver's SQLAllocEnv() failed 2: ODBC connection failed in: odbcDriverConnect(st, case = case, believeNRows = believeNRows) I'm reasonably sure the DSN is okay because I can use it to connect to the DB with other applications. Any suggestions? -Drew Specific Info: Machine Model:PowerBook5,6 CPU Type: PowerPC G4 (1.2) Number Of CPUs: 1 CPU Speed:1.67 GHz L2 Cache (per CPU): 512 KB Memory: 2 GB Bus Speed:167 MHz System Version: Mac OS X 10.3.8 (7U16) Kernel Version: Darwin 7.8.0 Boot Volume: Macintosh HD R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0 __ 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
Re: [R] weird results w/ prcomp-princomp
R2.0.1 x-matrix(rnorm(44*19),nrow=44) princomp(x,cor=TRUE,scores=TRUE) Call: princomp(x = x, cor = TRUE, scores = TRUE) Standard deviations: Comp.1Comp.2Comp.3Comp.4Comp.5Comp.6Comp.7Comp.8 1.5874672 1.4652217 1.3088833 1.2339949 1.1697727 1.1402570 1.0774402 1.0458567 Comp.9 Comp.10 Comp.11 Comp.12 Comp.13 Comp.14 Comp.15 Comp.16 1.0152164 0.9403912 0.8854087 0.8433314 0.7918201 0.7454395 0.6680463 0.6240805 Comp.17 Comp.18 Comp.19 0.5752994 0.4873633 0.4205193 19 variables and 44 observations. sum(princomp(x,cor=TRUE,scores=TRUE)$sdev^2) [1] 19 it seems ok. On Fri, 08 Apr 2005 11:12:26 +0200 Alessandro Bigi [EMAIL PROTECTED] wrote: I am doing a Principal Component Analaysis (PCA) on a 44x19 matrix. with princomp(x,cor=TRUE,scores=TRUE) and prcomp(x,scale=TRUE,center=TRUE) The resulted eigenv. and rotated matrix are the same (as expected), however the sum of eigenvalues is lower than 19 (number of variables). With a commercial stat software it worked correctly, with the same dataset. Am I doing something wrong? Thanks Alex -- No virus found in this outgoing message. Checked by AVG Anti-Virus. -- No virus found in this outgoing message. Checked by AVG Anti-Virus. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
correlation by group (was Re: [R] kunamorph@web.de)
Christfried Kunath wrote on 4/8/2005 10:39 AM: Hello, how can I use the function cor() with x and y in function aggregate() or by()? The data are like this: x y group 1 4 B 2 4 B 3 5 C I would like obtain the correlation between x and y for each subset. I don't want to use the workaround with the function subset(), because I have many groups. Thanks in advance. Christfried Kunath KC (Please use an informative subject as the posting guide recommends.) Your example is not very useful, but perhaps you need something like: tmp - data.frame(x = rnorm(100), y = rnorm(100), group = rep(letters[1:5], each = 20)) sapply(split(tmp, tmp[group]), function(z) cor(z$x, z$y)) # OR rbind(by(tmp, tmp[group], function(z) cor(z$x, z$y))) --sundar __ 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
Re: [R] hex format
Earl F. Glynn wrote: I recently discovered R's writeBin and readBin functions. readBin, in particular, looks like an extremely powerful tool for loading external files. This might be an easier way to perform some one-time data manipulations instead of writing a separate C, Perl or Delphi program to manipulate data before bringing it into R for analysis. readBin returns a raw data type that looks like an array of bytes that R displays in hex. That's where my problem begins and why I joined this hex format thread. That's only one possibility. readBin can return a number of different types. I'd love to manipulate this raw hex data, but R makes using these hex bytes quite difficult to use (or more difficult than I think it should be based on how easy it is in other languages). I might want to interpret a byte, or a string of bytes, as characters. A simple solution to this would be to implement a raw connection, that takes a raw variable and lets you read it using readBin. Or, I might want to interpret pairs of bytes as 2-byte unsigned (or possibly signed) integers. Or, I might want to interpret 3-bytes at a time as RGB values (in either RGB or BGR order). Or, I might want to interpret 8-bytes at a type as a IEEE754 floating point number. Every time someone wants to manipulate this raw data in R, as far as I can tell now, one must start from scratch and do all sorts of manipulations on these hex byte values to get characters, or integers, or doubles. And because it's not that easy (but it's not that hard either, more of an annoyance), I guess many just go back to C to get that job done there and then return to R. Currently you can do it by writing the raw data out to a temporary file and reading it back in. It would be nice to allow this to happen without the temporary file. Duncan Murdoch __ 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
[R] Princomp$Scores
Hi all, I was hoping that someone could verify this for me- when I run princomp() on a matrix, it is my understanding that the scores slot of the output is a measure of how well each row correlates (for lack of a better word) with each principal component. i.e. say I have a 300x6 log2 scaled matrix, and I run princomp(). I would get back a $scores slot that is also 300x6, where each value can be negative or positive. I'd assume that the negative values correspond to rows that are negatively correlated with that particular PC, and vice-versa for positives. Thanks in advance for the help, Ken __ 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
[R] EEG, ERP, ERF analysis with boot or bootstrap package
Does anyone have experience in using boot or bootstrap for ERP data analysis? Event-related potentials (ERPs) are electrical recordings from the human scalp during the presentation of stimulus events. They are a timeseries with msec resolution. They are essentially a timeseries that are defined relative to an event onset. They contain data prior to the event and after the event. They might be considered similar to a stock-market timeseries, defined in relation to some socio-political event. I want to evaluate whether a group of points after the event are significantly different from all the points before the event. There are several publications on using randomization or bootstrap analysis to do this. I wonder if the packages in R called boot and bootstrap can be used for this purpose. Best, Darren [[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
[R] Using Flexible Discriminant Analysis (fda) in mda
Greetings everyone, I was wondering if anyone had experience in using fda (flexible discriminant analysis) in the mda package. Specifically, I can run the model but I cant locate/produce much of anything beyond the predicted values and confusion matrix. I've been searching for more examples or documentation but cant seem to locate any specific to the program itself. I need to be able to find the Discriminant function coefficients (DFC) and Correlations between the DFC's and the variables (I believe these are referred to as the total canonical structure in SAS I ultimately want to graph the total canonical structure coefficients for the first 2 discriminant variables along with the groups scores calculated by putting in variable means into the discriminant functions. Any help or advice would be greatly appreciated, Thanks very much, Joe Retzer - Show us what our next emoticon should look like. Join the fun. [[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
[R] subset arg lmList
I'm having trouble understanding how functions in the subset argument for
lmList search for the objects they need. This trivial example produces
Error in rownames(fakedf) : Object fakedf not found:
library(nlme)
fitbyID - function() {
fakedf - data.frame(ID = gl(5, 10, 50),
A = sample(1:100, 50),
B = rnorm(50))
mycoefs - lmList(B ~ A | ID,
data = fakedf,
subset = !is.element(rownames(fakedf),
c(3, 10)))
coef(mycoefs)
}
fitbyID()
If fakedf is already in the workspace, then the function runs fine, so
rownames seems to be looking for it in the global environment, although
I'd expect it to search locally first. I suspect this shows some gaps in
my understanding of environments and related concepts. I'd be grateful for
some advice on this.
Best wishes,
--
Sebastian P. Luque
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[R] R-generated animation of a polynomiograph
Hi, people. Two days ago, I sent to this list a little toy for exploring polynomiographs (yet, the mathematical formulas were not polynomials anymore, so the name is not really appropriate). After studying R calls, expressions and functions a bit more, I gave myself the homework of producing an animation out of my recent toy. The resulting animation, and also the sources, are available at: http://pinard.progiciels-bpi.ca/plaisirs/nr-anim-01.html P.S. - My intent was studying R, much more than producing art :-). I'm sure anyone could do nicer, playing a few hours with this! -- François Pinard http://pinard.progiciels-bpi.ca __ 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
[R] Plotting principle components against individual variables
Dear R I am trying to plot some Principle component scores against the individual variables that made the first biplot. First I need to identify some points in the plot as follows running2 - running[c(USA, New Zealand, Dominican Republic, Western Samoa, Cook Islands),] this works fine, I then ask to do a plot plot(running$X100m, running.pca$scores[,1]) this works fine also I then need to specify points to highlight the countries of running2 And this is where I get stuck points(running2$X100m, running.pca$scores, col=red) Error in xy.coords(x, y) : x and y lengths differ What am I doing wrong here Brett Stansfield __ 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
[R] Journal of Statistical Software, Volume 12
This volume now has extensive documentation on the following R packages. Issue 8: EbayesTresh (Johnstone/Silverman) Issue 6: spatstat (Baddeley/Turner) Issue 5: drc (Ritz/Streibig) Issue 4: normalp (Mineo/Ruggieri) Issue 3: R2WinBugs (Sturtz, Ligges, Gelman) Issue 1: BradleyTerry (Firth) Package writers are encouraged to submit to JSS. === Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] .mac: jdeleeuw ++ aim: deleeuwjan ++ skype: j_deleeuw homepages: http://gifi.stat.ucla.edu ++ http://www.cuddyvalley.org - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ 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
[R] advice on crafting examples for packages
Folks- I have developed a package which I am planning on posting to CRAN. I include examples for each of the 40 or so functions in the package. However, since the examples are non-trivial and the package is using MCMC simulation methods, it takes about 20 minutes to run the complete set of examples on a 2.8 Ghz windows PC. The R process reaches a high water mark of about 100 MB of memory as well. I would appreciate some guidance on this. many thanks! peter Peter E. Rossi [EMAIL PROTECTED] WWW: http://ChicagoGsb.edu/fac/peter.rossi SSRN: http://ssrn.com/author=22862 QME: http://www.kluweronline.com/issn/1570-7156 __ 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
