Re: [R] deSolve question
In-Sun,
It is very simple. You define your state variables in the following order:
y <- c(Agi = 0,Alu = 0, Abr = 0, Ah = 0, Ali = 0, Ak = 0, Am = 0, Ask =
0, Aad = 0, Apa = 0, Asp = 0, Aar = 0, Ave = 0)
and your rates of change in another order:
dy = c(dAar, dAve, dAlu, dAli, dAbr, dAh, dApa, dAsp, dAgi, dAk,
dAm, dAad, dAsk)
So, The solver uses the rate of change of Aar to update Agi etc... and you
get nonsense in the end.
I hope correcting this will solve your problem.
I have seen this multiple times; it is definitely the most common type of
mistake in using R for solving differential equations.
Btw, why use daspk ? It is really meant for solving DAEs, not ODEs.
lsoda or lsode or vode might be a better choice.
Cheers,
Karline
insun nam wrote:
>
> Dear All,
>
> I like to simulate a physiologically based pharmacokinetics model using R
> but am having a problem with the daspk routine.
>
> The same problem has been implemented in Berkeley madonna and Winbugs so
> that I know that it is working. However, with daspk it is not, and the
> numbers are everywhere!
>
> Please see the following and let me know if I am missing something...
>
> Thanks a lot in advance,
> In-Sun
>
> #---
>
> library("deSolve")
>
> y <- c(Agi = 0,Alu = 0, Abr = 0, Ah = 0, Ali = 0, Ak = 0, Am = 0, Ask
> =
> 0, Aad = 0, Apa = 0, Asp = 0, Aar = 0, Ave = 0)
> times = seq(0, 100, length=100)
>
> pars <- c(
> dose = 80 * 0.26,
> doseduration = 10,
> Vmax = 1.44,
> Km = 0.96,
> s = 1.33,
> fp = 0.236,
> Kpfgi=0.324,
> Kpflu = 1.092,
> Kpfbr= 0.155 ,
> Kpfh=0.767,
> Kpfli = 0.551,
> Kpfk=0.537,
> Kpfm=0.339,
> Kpfsk=0.784,
> Kpfad=0.465,
> Kpfpa=0.595,
> Kpfsp=0.410,
> Qar = 51.9,
> Qve = 51.9,
> Qgi = 12.3,
> Qlu = 51.9,
> Qbr = 3.2,
> Qh = 6.4,
> Qli = 16.5,
> Qk = 12.8,
> Qm = 7.6,
> Qsk = 5.0,
> Qad = 0.4,
> Qpa = 1.0,
> Qsp = 1.0,
> Var = 7.0,
> Vve = 14.1,
> Vgi = 12.4,
> Vlu = 1.3,
> Vbr = 1.3,
> Vh = 1.2,
> Vli = 12.4,
> Vk = 2.2,
> Vm = 140.0,
> Vsk = 49.0,
> Vad = 11.2,
> Vpa = 1.0,
> Vsp = 1.0
> )
>
> Fun_ODE <- function(t,y, pars){
> with (as.list(c(y, pars)), {
> It <- dose/doseduration
> Car <- Aar/Var
> Cve <- Ave/Vve
> Clu <- Alu/Vlu
> Cli <- Ali/Vli
> Cbr <- Abr/Vbr
> Ch <- Ah/Vh
> Cpa <- Apa/Vpa
> Csp <- Asp/Vsp
> Cgi <- Agi/Vgi
> Ck <- Ak/Vk
> Cm <- Am/Vm
> Cad <- Aad/Vad
> Csk <- Ask/Vsk
>
> Kpbbr <- s*fp*Kpfbr
> Kpbli <- s*fp*Kpfli
> Kpbh <- s*fp*Kpfh
> Kpbpa <- s*fp*Kpfpa
> Kpbsp <- s*fp*Kpfsp
> Kpbgi <- s*fp*Kpfgi
> Kpbk <- s*fp*Kpfk
> Kpbm <- s*fp*Kpfm
> Kpbad <- s*fp*Kpfad
> Kpbsk <- s*fp*Kpfsk
> Kpblu <- s*fp*Kpflu
>
> dAar <- (Clu/Kpblu - Car)*Qar
> dAve <- if (t < 10) It + Cbr*Qbr/Kpbbr + Ch *Qh/Kpbh + Cli*Qli/Kpbli +
> Ck*Qk/Kpbk + Cm*Qm/Kpbm + Csk * Qsk /Kpbsk + Cad*Qad/Kpbad - Cve*Qve
>
> else Cbr*Qbr/Kpbbr + Ch *Qh/Kpbh + Cli*Qli/Kpbli + Ck*Qk/Kpbk +
> Cm*Qm/Kpbm + Csk * Qsk /Kpbsk + Cad*Qad/Kpbad - Cve*Qve
> dAlu <- (Cve-Clu/Kpblu)*Qlu
>
> dAli <- ((Qli - Qgi- Qpa-Qsp)*Car + Cgi*Qgi/Kpbgi + Csp*Qsp/Kpbsp +
> Cpa*Qpa/Kpbpa - Cli*Qli/Kpbli) - Vmax*Cli/Kpfli/(Km + Cli/Kpfli)
> dAbr <- (Car - Cbr/Kpbbr)*Qbr
> dAh <- (Car - Ch/Kpbh)*Qh
> dApa <- (Car - Cpa/Kpbpa)*Qpa
> dAsp <- (Car - Csp/Kpbsp)*Qsp
> dAgi <- (Car - Cgi/Kpbgi)*Qgi
> dAk <- (Car - Ck/Kpbk)*Qk
> dAm <- (Car - Cm/Kpbm)*Qm
> dAad <- (Car - Cad/Kpbad)*Qad
> dAsk <- (Car - Csk/Kpbsk)*Qsk
>
> return(list(dy = c(dAar, dAve, dAlu, dAli, dAbr, dAh, dApa, dAsp, dAgi,
> dAk,
> dAm, dAad, dAsk),
> Car = Car, Cve=Cve, Clu=Clu, Cli=Cli, Cbr=Cbr, Ch=Ch, Cpa=Cpa,
> Csp=Csp, Cgi=Cgi, Ck=Ck, Cm=Cm, Cad=Cad, Csk=Csk))
> })
> }
>
> ODE <- as.data.frame(daspk(y = y, times = times, func = Fun_ODE,
> parms = pars, atol = 1e-10, rtol = 1e-10))
>
>
>
>
> --
> Dr In-Sun Nam Knutsson
> Research Associate
> The Centre for Applied Pharmacokinetic Research (CAPKR)
> School of Pharmacy and Pharmaceutical Sciences
> University of Manchester
> Stopford Building
> Oxford Road
> Manchester
> U.K.
> Phone: +44 161 275 2355
> Email: in-sunnam.knuts...@manchester.ac.uk
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
--
View this message in context:
http://www.nabble.com/deSolve-question-tp23985008p23994033.html
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[R] Sending a function as an argument to C code.
Hi the list,
I am writing a function (myFunc) that is using an other function (let
say distance).
+++
dist1 <- function(x,y)dist(rbind(x,y))
dist2 <- function(x,y)y2
myFunc <- function(x,distance){
cat("...\n")
cat(distance(1,x))
}
myFunc(x=3,distance=dist1)
myFunc(x=3,distance=dist2)
In order to optimize the code, I would like to write myFunc in C. Is it
possible, in the C code, to call a function define in R (dist1 or dist2)
that will be send to myFunc as an argument ?
Christophe
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Re: [R] gfortran command not found?
Hi Alon,
It works for me.
According to YAST I got libgfortran4.3, gcc-43fortran and gcc-fortran
installed
Kees
Marc Schwartz wrote:
> On Jun 11, 2009, at 12:34 PM, Alon Ben-Ari wrote:
>
>> Hello, I have openSUSE 11.1
>> Trying to install randomForest
>> as SU after invoking R install.packages("randomForest")
>>
>> and I get this
>>
>> * Installing *source* package ‘randomForest’ ...
>> ** libs
>> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c
>> classTree.c -o classTree.o
>> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c
>> regTree.c -o regTree.o
>> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c
>> regrf.c -o regrf.o
>> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c
>> rf.c -o rf.o
>> gfortran -fpic -O2 -c rfsub.f -o rfsub.o
>> make: gfortran: Command not found
>> make: *** [rfsub.o] Error 127
>> ERROR: compilation failed for package ‘randomForest’
>> * Removing ‘/usr/lib/R/library/randomForest’
>>
>> The downloaded packages are in
>> ‘/tmp/RtmpLEyfgR/downloaded_packages’
>> Updating HTML index of packages in '.Library'
>> Warning message:
>> In install.packages("randomForest") :
>> installation of package 'randomForest' had non-zero exit status
>>>
>>
>>
>> I checked that I have th fortran library
>>
>> S | Name | Summary | Type
>> --+---+--+
>> i | libgfortran41 | The GNU Fortran Compiler Runtime Library | package
>> i | libgfortran43 | The GNU Fortran Compiler Runtime Library | package
>>
>> Any ideas how to solve this impass?
>
>
>
> I have not worked on SUSE, but check to see where gfortran is located:
>
> $ which gfortran
>
> and be sure that it returns the path to the executable and that the
> path to it is in your $PATH.
>
> You might also want to review:
>
> http://cran.r-project.org/doc/manuals/R-admin.html#Using-FORTRAN
>
> HTH,
>
> Marc Schwartz
>
> __
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Re: [R] removing elements from a "unit" vector
Paul Murrell wrote: Hi The bug is now fixed in the development version (thanks to Duncan for the diagnosis and suggested fix). Paul Thank you both for your help and dedication! Best regards, baptiste -- _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Changing CRAN package compile option defaults?
Is there an easy way to override the compile options when installing packages from CRAN on Unix-style systems? I tried setting CFLAGS, CXXFLAGS, and FFLAGS but they are not picked up. For example (with a random package and adding -mtune only to try to get rid of the default) export CFLAGS="-march=native -mtune=native" export CXXFLAGS="-march=native -mtune=native" R CMD INSTALL gstat_0.9-60.tar.gz [...] gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c block.c -o block.o [...] I am building a custom system and I'd like to get rid of '-g' (won't debug on that system) and change '-mtune=generic' to '-march=native' (don't need compatibility with other systems). Is there an easy way of doing this for all packages I build? Allan (Currently re-compiling BLAS and friends with -march=native.) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to trigger variable creation?
Hello R users,
i'm wondering how to trigger variable creation.
Whenever a variable is created i want my own function myFun(...) to be
started.
if (exists("x")) {rm(x)} # after removal of x
# any of these calls
x<-10# should call myFun
x=10 # should call myFun
assign(x,10) # should call myFun
etc.
# afterwards, each of the calls
x<-15# should not call myFun
x=15 # should not call myFun
assign(x,15) # should not call myFun
etc.
Has anyone an idea? Unfortunately, this feature is also missing in the
library trackObjs.
regards,
Thomas
--
Thomas Liebig
Fraunhofer-Institut für Intelligente Analyse- und
Informationssysteme (IAIS)
Schloss Birlinghoven, D-53754 Sankt Augustin, Germany
Email: thomas.lie...@iais.fraunhofer.de
Phone: +49 2241 142050
Fax:+49 2241 142072
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Re: [R] Automatically placing legend in location of most whitespace.
Jason Rupert wrote: Just read the following: https://stat.ethz.ch/pipermail/r-help/2003-October/039940.html Is the labcurve function, really the putKey function, in the Hmisc package the best way the to go about automatically placing legend in location of most whitespace? Hi Jason, I wasn't aware of the largest.empty function (thanks), and the code is packed away in a Fortran routine, so I couldn't compare it to the emptyspace function in the plotrix package. However, I suspect that largest.empty is a more sophisticated way of finding space for a legend. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (kein Betreff)
Hi all,
first of all: Sorry for my bad englis, and now the Question:
I have some problems with running R from Java. First i tried using rJava (JRI).
But the examples didnt work properly.
Now im trying to establish a connection by using Rserve and JRclient (RF503).
I have the following code, which i`ve found:
public class RTester {
public static void main(String[] args) {
Rconnection c = getLocalRconnection();
if (c != null) {
try {
double[] d = c.eval("rnorm(10)").asDoubleArray();
for (double n : d)
System.out.println(n);
} catch (RSrvException e) {
e.printStackTrace();
}
}
}
private static Rconnection getLocalRconnection() {
try {
return new Rconnection();
} catch (RSrvException e) {
//If we get this kind of error, it may be because Rserve is not
running
if (e.getMessage().equals("Cannot connect: Connection refused")) {
try {
String rserveStartCommand = "R CMD Rserve --vanilla";
//do a blocking call to the shell command for starting
Rserve
int exitValue =
Runtime.getRuntime().exec(rserveStartCommand).waitFor();
//if it returned success, try connecting again
if (exitValue == 0)
return new Rconnection();
//otherwise, Rserve is probably not installed
else
System.err.println("Could not start Rserve - is it
installed properly? Shell command \""+rserveStartCommand+"\" exited with exit
value "+exitValue+".");
} catch (Exception e1) {
e1.printStackTrace();
}
}
else
e.printStackTrace();
}
return null;
}
-
The Problem ist, that i get the following Exception:
org.rosuda.JRclient.RSrvException: Handshake failed: The server uses more
recent protocol than this client.
at org.rosuda.JRclient.Rconnection.(Rconnection.java:113)
at org.rosuda.JRclient.Rconnection.(Rconnection.java:58)
at org.rosuda.JRclient.Rconnection.(Rconnection.java:42)
at tester.RTester.getLocalRconnection(RTester.java:28)
at tester.RTester.main(RTester.java:14)
Well, i understand, that tehre seems to be a version problem, but i dont
understand what kind of. Im using the most recent Versions of RServe and
JRclient which i could find on the page.
btw. im using Windows XP Pro and Eclipse ganimed (recent Version) as IDE.
Java jdk is at version 1.6.
Thx in advance for any help!
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[R] How to plot hyperbolic iso-lines of a cost function?
Hi R-specialists!
I would like to draw some hyperbolic (iso-)lines of a cost function in a
bi-dimensional space ( =shapes of a cost function ), based on (the
general form):
C(x) = c1*Ce + c2*Oe + c3*{ 1 - [ (1 - Ce)^a * (1 - Oe)^b ] }
where:
- Oe/Ce are Omission/Commission (ranging between 0 and 1 ) values in a
bi-dimensional space ( see example of Oe/Ce values [1])
- c1, c2, c3, a and b are some parameters which determine "sensitivity"
of the function
Is there a ready-to-use plotting - function?
Kind regards, Nikos
---
[1] Omission/ Commission errors
0.0.42497404
0.010124160.35377707
0.031503210.30218908
0.061586110.26031315
0.101884180.21955793
0.155588280.17899955
0.225111560.14204273
0.316631640.10425152
0.427280350.06922038
0.584208960.03561727
0.903683970.
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[R] Function for AIC or logLIK for nlsList object
Dear R users, Does anybody have a function to calculate logLik or AIC for nlsList objects? After receiving error messages, another user helped me ascertain that this function is not currently written into R. Many thanks Lindsay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] JRclient.RSrvException Exception: Handshake
Hi all,
first of all: Sorry for my bad englis, and now the Question:
I have some problems with running R from Java. First i tried using rJava (JRI).
But the examples didnt work properly.
Now im trying to establish a connection by using Rserve and JRclient (RF503).
I have the following code, which i`ve found:
public class RTester {
public static void main(String[] args) {
Rconnection c = getLocalRconnection();
if (c != null) {
try {
double[] d = c.eval("rnorm(10)").asDoubleArray();
for (double n : d)
System.out.println(n);
} catch (RSrvException e) {
e.printStackTrace();
}
}
}
private static Rconnection getLocalRconnection() {
try {
return new Rconnection();
} catch (RSrvException e) {
//If we get this kind of error, it may be because Rserve is not
running
if (e.getMessage().equals("Cannot connect: Connection refused")) {
try {
String rserveStartCommand = "R CMD Rserve --vanilla";
//do a blocking call to the shell command for starting
Rserve
int exitValue =
Runtime.getRuntime().exec(rserveStartCommand).waitFor();
//if it returned success, try connecting again
if (exitValue == 0)
return new Rconnection();
//otherwise, Rserve is probably not installed
else
System.err.println("Could not start Rserve - is it
installed properly? Shell command \""+rserveStartCommand+"\" exited with exit
value "+exitValue+".");
} catch (Exception e1) {
e1.printStackTrace();
}
}
else
e.printStackTrace();
}
return null;
}
-
The Problem ist, that i get the following Exception:
org.rosuda.JRclient.RSrvException: Handshake failed: The server uses more
recent protocol than this client.
at org.rosuda.JRclient.Rconnection.(Rconnection.java:113)
at org.rosuda.JRclient.Rconnection.(Rconnection.java:58)
at org.rosuda.JRclient.Rconnection.(Rconnection.java:42)
at tester.RTester.getLocalRconnection(RTester.java:28)
at tester.RTester.main(RTester.java:14)
Well, i understand, that tehre seems to be a version problem, but i dont
understand what kind of. Im using the most recent Versions of RServe and
JRclient which i could find on the page.
btw. im using Windows XP Pro and Eclipse ganimed (recent Version) as IDE.
Java jdk is at version 1.6.
Thx in advance for any help!
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[R] Comparing model fits for NLME when models are not nested
Hi there, I am looking to compare nonlinear mixed effects models that have different nonlinear functions (different types of growth curve)embedded. Most of the literature I can find focuses on comparing nested models with likelihood ratios and AIC. Is there a way to compare model fits when models are not nested, i.e. when the nonlinear functions are not the same? Many thanks in advance! Lindsay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Replacing 0s with NA
Hello I have a dataset in which I would like to replace 0s with NAs. There is a lot of information on how to replace NAs with 0, but I have struggled to find anything with regards to doing the reverse. Any recommendations would be great. Cheers Christine __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replacing 0s with NA
On 6/12/2009 4:55 AM, Christine Griffiths wrote:
> Hello
>
> I have a dataset in which I would like to replace 0s with NAs. There is
> a lot of information on how to replace NAs with 0, but I have struggled
> to find anything with regards to doing the reverse. Any recommendations
> would be great.
X <- as.data.frame(matrix(sample(0:9, 100, replace=TRUE), ncol=10))
X
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
1 7 5 8 9 6 6 4 8 5 8
2 6 2 9 6 8 5 9 1 1 3
3 4 1 5 8 9 5 3 2 1 4
4 4 8 7 7 4 1 1 4 9 8
5 9 2 5 8 4 8 4 8 6 0
6 3 4 2 8 2 0 6 4 8 5
7 3 5 0 2 7 7 9 9 3 1
8 7 3 3 4 8 3 9 2 7 1
9 4 7 9 1 5 4 8 2 1 9
10 7 7 6 1 0 9 0 5 7 0
X[] <- lapply(X, function(x){replace(x, x == 0, NA)})
X
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
1 7 5 8 9 6 6 4 8 5 8
2 6 2 9 6 8 5 9 1 1 3
3 4 1 5 8 9 5 3 2 1 4
4 4 8 7 7 4 1 1 4 9 8
5 9 2 5 8 4 8 4 8 6 NA
6 3 4 2 8 2 NA 6 4 8 5
7 3 5 NA 2 7 7 9 9 3 1
8 7 3 3 4 8 3 9 2 7 1
9 4 7 9 1 5 4 8 2 1 9
10 7 7 6 1 NA 9 NA 5 7 NA
> Cheers
> Christine
>
> __
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> PLEASE do read the posting guide
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[R] replacing zeros by NAs
something like ... > x<-c(1,2,3,0,5,6,0) > is.na(x[x==0])<-T > x [1] 1 2 3 NA 5 6 NA Robert Kinley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing Rmpi on Fedora Linux [was: Re: help installing Rmpi]
On 11/06/09 22:46, ALAN SMITH wrote:
Hello R users and developers,
I would like to install Rmpi so that I may take advantage of all of
the CPUs in my computer
Package "multicore" *may* be easier for this.
, but I cannot get it to install [...]
The configuration file for Rmpi is, unfortunately, completely
brain-damaged with hard-coded assumptions about which subdirectories
should contain header and library files and no way of overriding it.
This is what I did:
[...]
#I have tried two different ways to install openMPI in fedora in the linux shell
In any recent version of Fedora don't do any of what you suggest; instead do
# yum install openmpi openmpi-devel openmpi-libs
Then *download* the Rmpi package and unpack it using something like
$ tar xvf Rmpi_0.5-7.tar.gz
(version number may be different).
Then go into the Rmpi directory and change configure.ac. If you are on
a x86_64 platform, the following hack should work (for 32 bit try
s/64/32/g):
+++[cut here]+++
Process this file with autoconf to produce a configure script.
AC_INIT(DESCRIPTION)
AC_PROG_CC
MPI_LIBS=`pkg-config --libs openmpi-1.3.1-gcc-64`
MPI_INCLUDE=`pkg-config --cflags openmpi-1.3.1-gcc-64`
MPITYPE="OPENMPI"
MPI_DEPS="-DMPI2"
AC_CHECK_LIB(util, openpty, [ MPI_LIBS="$MPI_LIBS -lutil" ])
AC_CHECK_LIB(pthread, main, [ MPI_LIBS="$MPI_LIBS -lpthread" ])
PKG_LIBS="${MPI_LIBS} -fPIC"
PKG_CPPFLAGS="${MPI_INCLUDE} ${MPI_DEPS} -D${MPITYPE} -fPIC"
AC_SUBST(PKG_LIBS)
AC_SUBST(PKG_CPPFLAGS)
AC_SUBST(DEFS)
AC_OUTPUT(src/Makevars)
---[cut here]---
The number 1.3.1 may change in future updates to Fedora, I guess
Now (still in Rmpi directory) do
$ autoconf
$ cd ..
$ tar zcvf Rmpi-0.5-7-F1.tar.gz Rmpi
$ R CMD INSTALL Rmpi-0.5-7-F1.tar.gz
Which more-or-less works in R:
> library("Rmpi")
> mpi.spawn.Rslaves(nslaves=2)
2 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 3 is running on: server
slave1 (rank 1, comm 1) of size 3 is running on: server
slave2 (rank 2, comm 1) of size 3 is running on: server
> x=c(10,20)
> mpi.apply(x,runif)
[[1]]
[1] 0.25142616 0.93505554 0.03162852 0.71783194 0.35916139 0.85082154
[7] 0.35404191 0.14221315 0.60063773 0.71805190
[[2]]
[1] 0.84157864 0.63481773 0.38217188 0.67839089 0.27827728 0.35429266
[7] 0.04898744 0.96601584 0.25687905 0.77381186 0.69011927 0.37391028
[13] 0.19017369 0.51196594 0.51970563 0.15791524 0.21358237 0.69642478
[19] 0.12690207 0.44177656
>
Hope this helps!
Allan.
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Re: [R] Replacing 0s with NA
On Fri, 2009-06-12 at 09:55 +0100, Christine Griffiths wrote:
> Hello
>
> I have a dataset in which I would like to replace 0s with NAs. There is a
> lot of information on how to replace NAs with 0, but I have struggled to
> find anything with regards to doing the reverse. Any recommendations would
> be great.
Here is one way:
## some dummy data
set.seed(123)
dat <- matrix(rnorm(100), ncol = 10)
## add some 0's
dat[sample(100, 20)] <- 0
## convert to df
dat <- data.frame(dat)
dat
## now replace 0 with NA
## replacement function
foo <- function(x) {
x[x == 0] <- NA
x
}
## lapply it, and force back to df
dat2 <- data.frame(lapply(dat, foo))
dat2
HTH
G
>
> Cheers
> Christine
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
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Re: [R] Replacing 0s with NA
Also try this:
X[X == 0] <- NA
or
X2 <- replace(X, X == 0, NA)
On Fri, Jun 12, 2009 at 5:54 AM, Chuck Cleland wrote:
> On 6/12/2009 4:55 AM, Christine Griffiths wrote:
>> Hello
>>
>> I have a dataset in which I would like to replace 0s with NAs. There is
>> a lot of information on how to replace NAs with 0, but I have struggled
>> to find anything with regards to doing the reverse. Any recommendations
>> would be great.
>
> X <- as.data.frame(matrix(sample(0:9, 100, replace=TRUE), ncol=10))
>
> X
> V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
> 1 7 5 8 9 6 6 4 8 5 8
> 2 6 2 9 6 8 5 9 1 1 3
> 3 4 1 5 8 9 5 3 2 1 4
> 4 4 8 7 7 4 1 1 4 9 8
> 5 9 2 5 8 4 8 4 8 6 0
> 6 3 4 2 8 2 0 6 4 8 5
> 7 3 5 0 2 7 7 9 9 3 1
> 8 7 3 3 4 8 3 9 2 7 1
> 9 4 7 9 1 5 4 8 2 1 9
> 10 7 7 6 1 0 9 0 5 7 0
>
> X[] <- lapply(X, function(x){replace(x, x == 0, NA)})
>
> X
> V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
> 1 7 5 8 9 6 6 4 8 5 8
> 2 6 2 9 6 8 5 9 1 1 3
> 3 4 1 5 8 9 5 3 2 1 4
> 4 4 8 7 7 4 1 1 4 9 8
> 5 9 2 5 8 4 8 4 8 6 NA
> 6 3 4 2 8 2 NA 6 4 8 5
> 7 3 5 NA 2 7 7 9 9 3 1
> 8 7 3 3 4 8 3 9 2 7 1
> 9 4 7 9 1 5 4 8 2 1 9
> 10 7 7 6 1 NA 9 NA 5 7 NA
>
>> Cheers
>> Christine
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Chuck Cleland, Ph.D.
> NDRI, Inc. (www.ndri.org)
> 71 West 23rd Street, 8th floor
> New York, NY 10010
> tel: (212) 845-4495 (Tu, Th)
> tel: (732) 512-0171 (M, W, F)
> fax: (917) 438-0894
>
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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Re: [R] Changing CRAN package compile option defaults?
On Fri, 12 Jun 2009, Allan Engelhardt wrote: Is there an easy way to override the compile options when installing packages from CRAN on Unix-style systems? I tried setting CFLAGS, CXXFLAGS, and FFLAGS but they are not picked up. For example (with a random package and adding -mtune only to try to get rid of the default) export CFLAGS="-march=native -mtune=native" export CXXFLAGS="-march=native -mtune=native" R CMD INSTALL gstat_0.9-60.tar.gz [...] gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c block.c -o block.o [...] I am building a custom system and I'd like to get rid of '-g' (won't debug on that system) and change '-mtune=generic' to '-march=native' (don't need compatibility with other systems). Is there an easy way of doing this for all packages I build? Yes: read 'R Installation and Administration' section 6.3.3 (at least of the version on CRAN). Also, it seems likely that you should be building R itself with the options you want for packages: how to do that is discussed in the same manual. (Looks like this may be a pre-compiled Linux binary distribution of R, but we don't know, of course.) In that case you don't need to set anything else. Allan (Currently re-compiling BLAS and friends with -march=native.) -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tables without names
On 11/06/2009 5:35 PM, Stavros Macrakis wrote: A table without names displays like a vector: > unname(table(2:3)) [1] 1 1 1 and preserves the table class (as with unname in general): > dput(unname(table(2:3))) structure(c(1L, 1L), .Dim = 2L, class = "table") Does that make sense? R is not consistent in its treatment of such unname'd tables: One of the complaints about the S3 object system is that anything can claim to be of class "foo", even if it doesn't have the right structure so that foo methods work for it. I think that's all you're seeing here: you've got something that is mislabelled as being of class "table". The solution is "don't do that". > In plot, they are considered erroneous input: > plot(unname(table(2:3))) Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ but in melt, they act as though they have names 1:n: > melt(unname(table(2:3))) indicies value 11 1 22 1 (By the way, is the spelling error built into too much code to be corrected?) -s PS What is the standard way of extracting just the underlying vector? c(unname(...)) works -- is that what is recommended? I would use as.numeric(), but I don't claim it's standard. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] replacing zeros by NAs
Other method: a<-matrix(seq(1,20,2), 4,5) a[c(1:2),c(2:4)]<-0 a[a==0]<-NA - Original Message - From: "Robert Kinley" To: Sent: Friday, June 12, 2009 11:59 AM Subject: [R] replacing zeros by NAs something like ... x<-c(1,2,3,0,5,6,0) is.na(x[x==0])<-T x [1] 1 2 3 NA 5 6 NA Robert Kinley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. No virus found in this incoming message. Checked by AVG - www.avg.com 17:59:00 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparing model fits for NLME when models are not nested
Lindsay Banin wrote >Hi there, > >I am looking to compare nonlinear mixed effects models that have different >nonlinear functions (different types of growth curve)embedded. Most of the >literature I can find focuses on comparing nested models with likelihood >ratios and AIC. Is there a way to compare model fits when models are not >nested, i.e. when the nonlinear functions are not the same? > What I like to do in these cases (and, in fact, for comparing model fits in general, even if nested) is graph the results of one vs the other, and of each vs. actual values. If the predicted values from the two models are very similar, then I can choose based on complexity or some other criterion; if they are not similar, then which is closer to the actual values? Is the difference large? Is it "worth it"? It's not a formal test, but I often find it illuminating. HTH Peter Peter L. Flom, PhD Statistical Consultant www DOT peterflomconsulting DOT com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing Rmpi on Fedora Linux [was: Re: help installing Rmpi]
For future reference, I put up the instructions here:
http://www.cybaea.net/Blogs/Data/R-tips-Installing-Rmpi-on-Fedora-Linux.html
Allan
On 12/06/09 10:59, Allan Engelhardt wrote:
On 11/06/09 22:46, ALAN SMITH wrote:
Hello R users and developers,
I would like to install Rmpi so that I may take advantage of all of
the CPUs in my computer
Package "multicore" *may* be easier for this.
, but I cannot get it to install [...]
The configuration file for Rmpi is, unfortunately, completely
brain-damaged with hard-coded assumptions about which subdirectories
should contain header and library files and no way of overriding it.
This is what I did:
[...]
#I have tried two different ways to install openMPI in fedora in the
linux shell
In any recent version of Fedora don't do any of what you suggest;
instead do
# yum install openmpi openmpi-devel openmpi-libs
Then *download* the Rmpi package and unpack it using something like
$ tar xvf Rmpi_0.5-7.tar.gz
(version number may be different).
Then go into the Rmpi directory and change configure.ac. If you are
on a x86_64 platform, the following hack should work (for 32 bit try
s/64/32/g):
+++[cut here]+++
Process this file with autoconf to produce a configure script.
AC_INIT(DESCRIPTION)
AC_PROG_CC
MPI_LIBS=`pkg-config --libs openmpi-1.3.1-gcc-64`
MPI_INCLUDE=`pkg-config --cflags openmpi-1.3.1-gcc-64`
MPITYPE="OPENMPI"
MPI_DEPS="-DMPI2"
AC_CHECK_LIB(util, openpty, [ MPI_LIBS="$MPI_LIBS -lutil" ])
AC_CHECK_LIB(pthread, main, [ MPI_LIBS="$MPI_LIBS -lpthread" ])
PKG_LIBS="${MPI_LIBS} -fPIC"
PKG_CPPFLAGS="${MPI_INCLUDE} ${MPI_DEPS} -D${MPITYPE} -fPIC"
AC_SUBST(PKG_LIBS)
AC_SUBST(PKG_CPPFLAGS)
AC_SUBST(DEFS)
AC_OUTPUT(src/Makevars)
---[cut here]---
The number 1.3.1 may change in future updates to Fedora, I guess
Now (still in Rmpi directory) do
$ autoconf
$ cd ..
$ tar zcvf Rmpi-0.5-7-F1.tar.gz Rmpi
$ R CMD INSTALL Rmpi-0.5-7-F1.tar.gz
Which more-or-less works in R:
> library("Rmpi")
> mpi.spawn.Rslaves(nslaves=2)
2 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 3 is running on: server
slave1 (rank 1, comm 1) of size 3 is running on: server
slave2 (rank 2, comm 1) of size 3 is running on: server
> x=c(10,20)
> mpi.apply(x,runif)
[[1]]
[1] 0.25142616 0.93505554 0.03162852 0.71783194 0.35916139 0.85082154
[7] 0.35404191 0.14221315 0.60063773 0.71805190
[[2]]
[1] 0.84157864 0.63481773 0.38217188 0.67839089 0.27827728 0.35429266
[7] 0.04898744 0.96601584 0.25687905 0.77381186 0.69011927 0.37391028
[13] 0.19017369 0.51196594 0.51970563 0.15791524 0.21358237 0.69642478
[19] 0.12690207 0.44177656
>
Hope this helps!
Allan.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Optimization Question
On Thu, Jun 11, 2009 at 9:56 PM, Brecknock, Peter wrote:
> Apologies if this is not the correct list for this question.
>
> The Rglpk package offers the following example in its documentation
>
> library(Rglpk)
> ## Simple mixed integer linear program.
> ## maximize: 3 x_1 + 1 x_2 + 3 x_3
> ## subject to: -1 x_1 + 2 x_2 + x_3 <= 4
> ## 4 x_2 - 3 x_3 <= 2
> ## x_1 - 3 x_2 + 2 x_3 <= 3
> ## x_1, x_3 are non-negative integers
> ## x_2 is a non-negative real number
> obj <- c(3, 1, 3)
> mat <- matrix(c(-1, 0, 1, 2, 4, -3, 1, -3, 2), nrow = 3)
> dir <- c("<=", "<=", "<=")
> rhs <- c(4, 2, 3)
> types <- c("I", "C", "I")
> max <- TRUE
> Rglpk_solve_LP(obj, mat, dir, rhs, types, max)
>
> ## Same as before but with bounds replaced by
> ## -Inf < x_1 <= 4
> ## 0 <= x_2 <= 100
> ## 2 <= x_3 < Inf
>
> bounds <- list(lower = list(ind = c(1L, 3L), val = c(-Inf, 2)),
> upper = list(ind = c(1L, 2L), val = c(4, 100)))
> Rglpk_solve_LP(obj, mat, dir, rhs, types, max, bounds)
>
> I have 2 questions
>
> 1. What is the purpose of the L in the bounds statement (e.g. 1L, 3L
> etc)?
>
> 2. Is it possible to further constrain a variable such that in the
> optimal solution to the objective function it will be a specific integer
> or an integer multiple of that integer. For example, x_3 must be 2 or
> 4,6,8,10 etc
Regarding your first question, I am not very sure, but it seems that
iL
means the constraint i.
Concerning your second question, the answer is positive. To force x_3
being an even number, just add the following constraints:
x_3 = 2 * y,
y >= 1,
y integer.
Paul
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Re: [R] R 2.9.0 on AIX 5.3: Error: Invalid DESCRIPTION file
loris.benn...@fu-berlin.de (Loris Bennett) writes: > Hi, > > I am trying to install R 2.9.0 on AIX 5.3. During the 'make' run I get > the following error: > >Error: Invalid DESCRIPTION file > >Invalid Priority field. >Packages with priorities 'base' or 'recommended' or 'defunct-base' must >already be known to R. > >See the information on DESCRIPTION files in section 'Creating R >packages' of the 'Writing R Extensions' manual. >Execution halted > > Any ideas? Full output below. > > Thanks > > Loris > > Here is the full output of 'make': > >Target "R" is up to date. >Target "R" is up to date. >Target "R" is up to date. >Target "R" is up to date. >Target "Makedeps" is up to date. >Target "libbz2.a" is up to date. >Target "all" is up to date. >Target "Makedeps" is up to date. >Target "libpcre.a" is up to date. >Target "all" is up to date. >Target "Makedeps" is up to date. >Target "libz.a" is up to date. >Target "all" is up to date. >Target "R" is up to date. >Target "Makedeps" is up to date. >Target "libappl.a" is up to date. >Target "Makedeps" is up to date. >Target "libnmath.a" is up to date. >Target "Makedeps" is up to date. >Target "libunix.a" is up to date. >xlc_r -q64 -I. -I../../src/include -I../../src/include >-I/usr/lpp/X11/include/X11 -DHAVE_CONFIG_H -O -qstrict >-DR_HOME='"/opt/sw/install/R-2.9.0"' -o Rscript ./Rscript.c >Target "Makedeps" is up to date. >/opt/sw/install/R-2.9.0/bin/exec/R is unchanged >Target "Makedeps" is up to date. >Target "internet.so" is up to date. >Target "all" is up to date. >Target "Makedeps" is up to date. >Target "libRlapack.so" is up to date. >/opt/sw/install/R-2.9.0/lib/libRlapack.so is unchanged >Target "lapack.so" is up to date. >Target "all" is up to date. >Target "Makedeps" is up to date. >Target "vfonts.so" is up to date. >Target "all" is up to date. >Target "Makedeps" is up to date. >Target "R_X11.so" is up to date. >building system startup profile >building package 'base' >all.R is unchanged >building package 'tools' >all.R is unchanged >Target "Makedeps" is up to date. >../../../../library/tools/libs/tools.so is unchanged >Error: Invalid DESCRIPTION file > >Invalid Priority field. >Packages with priorities 'base' or 'recommended' or 'defunct-base' must >already be known to R. > >See the information on DESCRIPTION files in section 'Creating R >packages' of the 'Writing R Extensions' manual. >Execution halted >make: 1254-004 The error code from the last command is 1. > > >Stop. >make: 1254-004 The error code from the last command is 1. > > >Stop. >make: 1254-004 The error code from the last command is 1. > > >Stop. >make: 1254-004 The error code from the last command is 1. > > >Stop. I'm still stuck with this problem. Does anyone know how the description files could cause a problem? Cheers Loris -- Dr. Loris Bennett Computer Centre Freie Universität Berlin Berlin, Germany __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Please Help pairwise.t.test!!
Chunhao Tu wrote >Hi R users, >My question is, If I have 3 groups, A, B, C and I know mean of A =20, B=21, >and C=20.5 and I also know the >standard error of A =1.1, B=2.2, C=3.2. Plus, I know A has 30 observations, >B has 78, C has 45. But I do not have the raw data. > >Can I use pairwise.t.test to conduct a Bonferroni test? If yes, Could you >give me a hint? If the data in each group is normally distributed, you could use the mean and sd and N in rnorm and then test the results. But if you don't know that, then I think it's a bit up in the air. A - N = 30, sem = 1.1, mean = 20 sd = 1.1*30^.5 = 6.02 B - N = 78, sem = 2.2, mean = 21 sd = 2.2*78^.5 = 19.43 C - N = 45, sem = 3.2, mean = 20.5, sd = 3.2*45^.5 = 21.46 let's do just A and B, to keep it a bit simpler: if both are normal: A <- rnorm(n = 30, mean = 20, sd = 6.02) B <- rnorm(n = 78, mean = 21, sd = 19.43) t.test(A,B) t = .927 but if A is uniform and B is normal A <- rnorm(n = 30, mean = 20, sd = 6.02) B <- runif(n = 78, mean = 21, sd = 19.43) t.test(A,B) t = 0.42 HTH, and hope I didn't mess up one of the calculations due to insufficient caffeine intake Peter Peter L. Flom, PhD Statistical Consultant www DOT peterflomconsulting DOT com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GRASS raster data processing
Perhaps reading ?readRAST6 would help? It does say:
vname: A vector of GRASS 6.0 raster file names
so you could write:
Kar <- readRAST6(c("Incis_Kar", "DEM_Kar"), plugin=FALSE)
and plot(Incis_Kar ~ DEM_Kar, data=Kar) should get you there - in spearfish:
sp <- readRAST6(c("erosion1", "elevation.dem"), plugin=FALSE)
plot(erosion1 ~ elevation.dem, data=sp)
works for me. (Aside - using @ in S4 classes should be avoided unless you
both know what you are doing and need to be doing it, use the provided
access mechanisms, here treating a Spatial*DataFrame as an ordinary data
frame.)
Roger
Nikos Alexandris wrote:
>
>
> Maayt:
>> I just imported two raster maps into R using the SPGRASS6 package, one
>> containing elevation data and the other containing an erosion index:
>
>> Kar_inc <-readRAST6("Incis_Kar", plugin=FALSE)
>> Kar_dem <- readRAST6("DEM_Kar", plugin=FALSE)
>>
>> I just wanted to make a xy plot of erosion parameter vs elevation. How
>> does
>> this work? I don't get how to handle SpatialGridDataFrames...
>
>
> Maarten,
>
> you can check some web-pages with respect to GRASS & R [1][2]. This is a
> question for grass-stats actually [3].
>
> A quick answer: check the structure of the newly created object and you
> will find that the "numbers" are to be found in (e.g. for "Incis_Kar" )
> kar_...@data$incis_kar.
>
> So use "@data" and the "$" to access a "slot".
> Kind regards, Nikos
> ---
>
> [1] http://grass.osgeo.org/wiki/R
> [2] http://grass.ibiblio.org/statsgrass/index.php#grassR
> [3] http://grass.osgeo.org/statsgrass/index.php
>
>
>
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[R] fix for RMate (TextMate/E-Texteditor bundle)
Arg, I already needed to fix the bundle. If anyone downloaded it yesterday, please update, the help index building was broken (on Macs). Should work now. Repo/Infos: http://github.com/swissr/rmate.tmbundle/tree/master -- Regards, Hans-Peter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] replacing zeros by NAs
Try this also: is.na(x) <- x == 0 On Fri, Jun 12, 2009 at 6:59 AM, Robert Kinley wrote: > something like ... > > > x<-c(1,2,3,0,5,6,0) > > is.na(x[x==0])<-T > > x > [1] 1 2 3 NA 5 6 NA > > > Robert Kinley > > > > >[[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Comparing nonlinear regressions for different subsets of data
I have a dataset with four different treatments and two different values for each sample. I need to compare the subsets(the different treatments) somehow. The data look suspiciously much like some kind of e-function to me, or maybe michaelis-menten so they are not linear. With linear models it's straight forward enough but what about nonlinear regressions? With linear model I do: data<-read.csv(file, header=T) attach(data) mod1<-lm(column1~column2) mod2<-lm(column1~column2+treatment) anova(mod1,mod2) The I can also go on to get the interaction by: mod3<-lm(column1~column2*treatment) But the same kind of methodology does not seem to work for nls functions. How should I do? Can I linearize the data? how to do that in a good way? The best would of course be if I could do it without linearization. Regards Martin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Squaring one column of data
Hi, A fairly basic problem I think, here although searching the inetrnet doesn't seem to reveal a solution. I have a dataset with two columns of real numbers. It is read in via read.table. I simply need to square the data in the second column and then plot it. I have tried extracting the second column (b <- z[2]) and then squaring it and merging it to a variable which is the first column extracted. Firstly thsi seems very convoluted, secondly it gives a seg fault (I'm guessing because memory hasn't been allocated for the second column on the creation of teh first variable). So any ideas about the easy way of doing the matsh so I can then just use plot(z, .) as before? Cheers in advance, Kenny -- View this message in context: http://www.nabble.com/Squaring-one-column-of-data-tp23997104p23997104.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Multinomial logistic regression in an ANOVA-like framework
Dear all, I have a problem for multinomial logistic regression: the response variable is multinomial (score 1-5) and the two predictors are categorical; all that comes from panelists (it's a kind of preference study), which I treat as a block and include in the model (is it correct?). I would like to see the results in the ANOVA-like framework. Fitting the multinom() function from the nnet package works pretty well and using the Anova() from the package car I got the hypothesis testing for the predictors as well as their interaction. However, I would like to go further and (because I am do look at means when interpreting the results) I would like to make some kind of multiple comparisons, if it is at all possible. Any suggestions if I am doing anything wrong and if not, what could I do to get these multiple comparisons? Thank you, Stats Wolf __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Squaring one column of data
Have sorted it, it was simple, for anyone else who needs it: z[2] <- z[2]*z[2] squares the second column of a data table and writes it back to the second column Kenny Kenny Larsen wrote: > > Hi, > > A fairly basic problem I think, here although searching the inetrnet > doesn't seem to reveal a solution. I have a dataset with two columns of > real numbers. It is read in via read.table. I simply need to square the > data in the second column and then plot it. I have tried extracting the > second column (b <- z[2]) and then squaring it and merging it to a > variable which is the first column extracted. Firstly thsi seems very > convoluted, secondly it gives a seg fault (I'm guessing because memory > hasn't been allocated for the second column on the creation of teh first > variable). > > So any ideas about the easy way of doing the matsh so I can then just use > plot(z, .) as before? > > Cheers in advance, > > Kenny > -- View this message in context: http://www.nabble.com/Squaring-one-column-of-data-tp23997104p23997558.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Squaring one column of data
Kenny Larsen wrote:
Hi,
A fairly basic problem I think, here although searching the inetrnet doesn't
seem to reveal a solution. I have a dataset with two columns of real
numbers. It is read in via read.table. I simply need to square the data in
the second column and then plot it. I have tried extracting the second
column (b <- z[2]) and then squaring it and merging it to a variable which
is the first column extracted. Firstly thsi seems very convoluted, secondly
it gives a seg fault (I'm guessing because memory hasn't been allocated for
the second column on the creation of teh first variable).
So any ideas about the easy way of doing the matsh so I can then just use
plot(z, .) as before?
Cheers in advance,
Kenny
Hi,
A few alternatives,
d <- data.frame(x = seq(1, 10), y=seq(1, 10))
d2 <- d # copy
# variants that make a new column
d$z <- d$y^2
d <- within(d, {z1 <- y^2})
# destructive transformation
d3 <- transform(d2, y=y^2)
ize <- # this may be useful if you want to apply a function to several
columns (orig. idea from vQ)
function(d, columns=names(d), izer=`^`, ...)
{
d[columns] = sapply(d[columns], izer, ...)
d
}
d4 <- ize(d2, "y",`^`, 2)
HTH,
baptiste
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[R] Snap axes to origin rather than around it
I'm trying to plot a graph where the axes go through 0,0, rather than around it combined with a box round the graph, so x<-0:10;y<-0:10 plot(x,y) gives me a box but doesn't go through the point 0,0, but stays at a distance. In trying to circumvent this problem, I wrote plot(x,y) axis(1, pos=c(0,0));axis(2,pos=c(0,0)) which gives me axes that go through the origin, but then I can't make a box round a plot (box() goes again at this fixed distance from the origin rather than through it) Any thoughts, ideas gratefully accepted. Perhaps I've been looking at it so long I'm now missing the obvious! :) Paul Any ideas? -- View this message in context: http://www.nabble.com/Snap-axes-to-origin-rather-than-around-it-tp23997802p23997802.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] External signal in ODE written in C (using deSolve and approx1?)
Dear list
The deSolve package allows you to specify the model code in C or Fortran.
Thanks to the excellent vignette this works fine. However I have not yet
managed to use forcing functions in C code.
In pure R code this works very well with approxfun() specified outside the
model:
###
#Model
lvml <- function(t, x, parms) {
with(as.list(c(parms, x)), {
import <- sigimp(t)
dS <- import - b*S*P + g*K #substrate
dP <- c*S*P - d*K*P #producer
dK <- e*P*K - f*K #consumer
res <- c(dS, dP, dK)
list(res)
})
}
## Parameters
parms <- c(b = 0.0, c = 0.1, d = 0.1, e = 0.1, f = 0.1, g = 0.0)
## vector of timesteps
times <- seq(0, 100, length = 101)
## external signal with rectangle impulse
signal <- as.data.frame(list(times = times,
import = rep(0,length(times
signal$import[signal$times >= 10 & signal$times <= 21] <- 0.2
sigimp <- approxfun(signal$times, signal$import, rule = 2)
## Start values for steady state
y <- xstart <- c(S = 1, P = 1, K = 1)
## Solving
out2 <- as.data.frame(lsoda(xstart, times, lvml, parms))
###
I would like to do the same thing in C, and my guess is that the approx1
function has to be used in some way. So far did not figure out how. If
anyone has managed to do so, or know how to approach this problem, please
let me know.
Best wishes
Glenn
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Re: [R] Snap axes to origin rather than around it
On Jun 12, 2009, at 7:18 AM, Paul Chatfield wrote: I'm trying to plot a graph where the axes go through 0,0, rather than around it combined with a box round the graph, so x<-0:10;y<-0:10 plot(x,y) gives me a box but doesn't go through the point 0,0, but stays at a distance. In trying to circumvent this problem, I wrote plot(x,y) axis(1, pos=c(0,0));axis(2,pos=c(0,0)) which gives me axes that go through the origin, but then I can't make a box round a plot (box() goes again at this fixed distance from the origin rather than through it) Any thoughts, ideas gratefully accepted. Perhaps I've been looking at it so long I'm now missing the obvious! :) Paul Any ideas? See ?par and take note of 'xaxs' and 'yaxs': x <- 0:10 y <- 0:10 plot(x, y, xaxs = "i", yaxs = "i") HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tables without names
> "DM" == Duncan Murdoch > on Fri, 12 Jun 2009 06:09:14 -0400 writes: DM> On 11/06/2009 5:35 PM, Stavros Macrakis wrote: >> A table without names displays like a vector: >> >> > unname(table(2:3)) [1] 1 1 1 >> >> and preserves the table class (as with unname in >> general): >> >> > dput(unname(table(2:3))) structure(c(1L, 1L), .Dim = >> 2L, class = "table") >> >> Does that make sense? R is not consistent in its >> treatment of such unname'd tables: DM> One of the complaints about the S3 object system is that DM> anything can claim to be of class "foo", even if it DM> doesn't have the right structure so that foo methods DM> work for it. I think that's all you're seeing here: DM> you've got something that is mislabelled as being of DM> class "table". The solution is "don't do that". indeed! >> In plot, they are considered erroneous input: >> >> > plot(unname(table(2:3))) Error in xy.coords(x, y, >> xlabel, ylabel, log) : 'x' and 'y' lengths differ >> >> but in melt, they act as though they have names 1:n: >> >> > melt(unname(table(2:3))) indicies value 1 1 1 2 2 1 >> >> (By the way, is the spelling error built into too much >> code to be corrected?) >> >> -s >> >> PS What is the standard way of extracting just the >> underlying vector? c(unname(...)) works -- is that what >> is recommended? DM> I would use as.numeric(), but I don't claim it's DM> standard. many months ago in a discussion about the use (and "misuse") of c() for coercing arrays/matrices to (atomic) vectors, Brian Ripley I think advertized the use of as.vector() with which I strongly agree. as.vector() here has the additional advantage of *not* transforming integer into double. Martin Maechler, ETH Zurich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Slicing an array
Hi all,
I've been trying to work out how to slice an array of arbitrary
dimension. I found a message showing how to stick two arrays together,
but so far have been unable to transform that into what I need. Assume
that I have a four dimensional array for example:
array4d
, , 1, 1
[,1] [,2]
[1,]36
[2,]11
, , 2, 1
[,1] [,2]
[1,]47
[2,]87
, , 1, 2
[,1] [,2]
[1,]78
[2,]87
, , 2, 2
[,1] [,2]
[1,]75
[2,]99
I want to slice the array from the rightmost dimension, getting in sequence:
array4d[,,,1]
array4d[,,,2]
then slicing those 3D arrays, and so on. I'm pretty sure that this will
involve a:
do.call('[',...)
construction, but I haven't been able to work out how to specify the
list of arguments, in particular the index vector, to slice up the last
dimension. I have tried constructing index vectors with NULLs which of
course doesn't work because they just disappear. Any suggestions?
Jim
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[R] Programmatically copying a graphic to the clipboard
Hi all, Is there a cross-platform way to do this? On the mac, I cando this by saving an eps file, and then using pbcopy. Is it possible on other platforms? Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Function for AIC or logLIK for nlsList object
Lindsay Banin wrote: > > Dear R users, > > Does anybody have a function to calculate logLik or AIC for nlsList > objects? After receiving error messages, another user helped me ascertain > that this function is not currently written into R. > how about: library(nlme) example(nlsList) sapply(fm1,logLik) sum(sapply(fm1,logLik)) ? -- View this message in context: http://www.nabble.com/Function-for-AIC-or-logLIK-for-nlsList-object-tp23995762p23998109.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Automate a data load and merge
Hi R list,
I would like to automate, or speed up the process from which I take
several separate datasets, stored in .csv formate, import and merge
them by a common variable. So far I have greatly sped up the loading
process but cannot think of a way to automate the merger of all
datasets into a common data.frame.
My apologies if this has been covered, any R search suggestions are
appreciated.
# All scripts function out of the base directory
rm(list=ls())
setwd('/Users/myuser/Documents/workfolder/')
# Check files and list all .csv in directory
files<-list.files()
files<-files[grep('.csv', files)]
# Create labels for each file (ex. June08.csv becomes June08)
labels<-gsub('.csv', '', files)
# Load all .csv datasets and assign name
item<-vector() # preallocate an index of all items in datasets
for(i in 1:length(files)){
X<-read.csv(files[i])
item<-union(item, X$Item_Name)
assign(labels[i], X)
}
# What is loaded
ls()
# [1] "files""i""item" "June01" "June02" "June03"
"labels"
# What does everything look like?
str(June03)
#'data.frame': 992 obs. of 8 variables:
# $ Item_Name: Factor w/ 992 levels "Birds","Fish",..: 1 2 3 4
5 6 7 8 9 10 ...
# $ Occurance : int 30 30 50 450 75 550 100 500 250 75 ...
str(June01)
#'data.frame': 819 obs. of 8 variables:
# $ Item_Name: Factor w/ 819 levels "Birds","Turtles",..: 1 2
3 4 5 6 7 8 9 10 ...
# $ Occurance : int 30 50 450 750 550 100 500 250 275 450 ...
# Here is where I'm stuck...
#I would like to:
# Create a data.frame with an index column composed of the union of
all items
# Create columns in the frame by a merger of the 'Occurance' in each
loaded dataset and are labeled by their name (eg. June01)
# Automate this procedure so that I do not have to manuualy type in
each column addition when I have a new dataset.
# This is my current strategy, but when I have new datasets I have to
mannually setup the preallocation and merger
allData<-data.frame(Item=item, June01 =NA, June02=NA, June03 =NA)
allData[match(June01$Item_Name, allData$Item ),]$June01 <-
June01$Occurance
allData[match(June02$Item_Name, allData$Item ),]$June02 <-
June02$Occurance
allData[match(June03$Item_Name, allData$Item ),]$June03 <-
June03$Occurance
# Any help to automate this process is greatly appreciated!!!
sessionInfo()
#R version 2.9.0 (2009-04-17)
#i386-apple-darwin8.11.1
#
#locale:
#en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
#
#attached base packages:
#[1] stats graphics grDevices utils datasets methods base
Jon Loehrke
Graduate Research Assistant
Department of Fisheries Oceanography
School for Marine Science and Technology
University of Massachusetts
200 Mill Road, Suite 325
Fairhaven, MA 02719
jloeh...@umassd.edu
T 508-910-6393
F 508-910-6396
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Re: [R] how to trigger variable creation?
well,
for sure, one option is to trace the garbage collector gc() by a
function that enumerates the list of known objects and compares this
with its successor. But that's not reliable, as i can't really control
when to call the garbage collector. i also don't like to enumerate
objects and to compare these lists at each time step.
what else could be done?
cheers,
Thomas
Thomas Liebig schrieb:
Hello R users,
i'm wondering how to trigger variable creation.
Whenever a variable is created i want my own function myFun(...) to be
started.
if (exists("x")) {rm(x)} # after removal of x
# any of these calls
x<-10# should call myFun
x=10 # should call myFun
assign(x,10) # should call myFun
etc.
# afterwards, each of the calls
x<-15# should not call myFun
x=15 # should not call myFun
assign(x,15) # should not call myFun
etc.
Has anyone an idea? Unfortunately, this feature is also missing in the
library trackObjs.
regards,
Thomas
--
Thomas Liebig
Fraunhofer-Institut für Intelligente Analyse- und
Informationssysteme (IAIS)
Schloss Birlinghoven, D-53754 Sankt Augustin, Germany
Email: thomas.lie...@iais.fraunhofer.de
Phone: +49 2241 142050
Fax:+49 2241 142072
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Re: [R] Optimization Question
The "1L", etc., forces the number to be integer:
> is.integer(1)
[1] FALSE
> is.integer(1L)
[1] TRUE
Hope this helps.
Spencer
Paul Smith wrote:
On Thu, Jun 11, 2009 at 9:56 PM, Brecknock, Peter wrote:
Apologies if this is not the correct list for this question.
The Rglpk package offers the following example in its documentation
library(Rglpk)
## Simple mixed integer linear program.
## maximize: 3 x_1 + 1 x_2 + 3 x_3
## subject to: -1 x_1 + 2 x_2 + x_3 <= 4
## 4 x_2 - 3 x_3 <= 2
## x_1 - 3 x_2 + 2 x_3 <= 3
## x_1, x_3 are non-negative integers
## x_2 is a non-negative real number
obj <- c(3, 1, 3)
mat <- matrix(c(-1, 0, 1, 2, 4, -3, 1, -3, 2), nrow = 3)
dir <- c("<=", "<=", "<=")
rhs <- c(4, 2, 3)
types <- c("I", "C", "I")
max <- TRUE
Rglpk_solve_LP(obj, mat, dir, rhs, types, max)
## Same as before but with bounds replaced by
## -Inf < x_1 <= 4
## 0 <= x_2 <= 100
## 2 <= x_3 < Inf
bounds <- list(lower = list(ind = c(1L, 3L), val = c(-Inf, 2)),
upper = list(ind = c(1L, 2L), val = c(4, 100)))
Rglpk_solve_LP(obj, mat, dir, rhs, types, max, bounds)
I have 2 questions
1. What is the purpose of the L in the bounds statement (e.g. 1L, 3L
etc)?
2. Is it possible to further constrain a variable such that in the
optimal solution to the objective function it will be a specific integer
or an integer multiple of that integer. For example, x_3 must be 2 or
4,6,8,10 etc
Regarding your first question, I am not very sure, but it seems that
iL
means the constraint i.
Concerning your second question, the answer is positive. To force x_3
being an even number, just add the following constraints:
x_3 = 2 * y,
y >= 1,
y integer.
Paul
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[R] Gtk objects disappears
Dear John,
I have a question.
When I run a RGtk code in my terminal (without using the R GUI)
R --vanilla << "EOF"
source("myRGtkcode.R")
EOF
the GTK objects do not remain on the screen.
Until now, I "bypass" this problem using the following commands:
require(tcltk)
tkmessageBox("Press to exit")
But it is not really satisfactory and the tcltk Box cannot be
minimized (at least in Mac OSX).
Any idea?
Best regards. Olivier
--
Olivier G. Nuñez
Email: onu...@iberstat.es
Tel : +34 663 03 69 09
Web: http://www.iberstat.es
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Re: [R] triangular plot
You may have more luck with the triangle plot functions available in other R libraries. In addition to triangle.plot in ade4, you have other options (this may not be an exhaustive list): plot.acomp in compositions tri in cwhmisc.cwhtool triax in plotrix ternary in StatDA ternaryplot in vcd ternaryplot in Zelig David L. Carlson Anthropology Department Texas A&M University College Station, TX 77843-4352 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sweave recode(car) and Lyx, compiling but not executing on Mac
I am just beginning to use Sweave with Lyx on a Mac (R2.8.1). I have 12 chunks of Sweave code that work fine, but this piece: <<>>= library(car) cabbages$Year<-recode(cabbages$Year,"'X2001'='2001';'X2002'='2002';'X2003'='2003';'X2004'='2004';'X2005'='2005';'X2006'='2006';'X2007'='2007';'X2008'='2008';'X2009'='2009';'X2010'='2010';'X2011'='2011';'X2012'='2012'") @ just prints out verbatim as a single line running off the page (No recoding occurs). It worked in R before pasting into Lyx. Initially I had the double quotes and single quotes the other way round, but this produced this in the complied pdf: > cabbages$Year <- recode(cabbages$Year, > "\"X2001\"=\"2001\";\"X2002\"=\"2002\";\"X2003\"=\"2003\";\ etc The first double quote in the printout shown above was a single quote before compiling. I have asked on the Lyx forum for help, but maybe someone here can suggest what I might be doing wrong. Of course it could be a Mac/Lyx issue rather than an SWeave/R issue, but any help would be appreciated. Thanks, Graham __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] glm binomial logit - removing extra computations
Hi all, I am using glm function with family binomial(logit) to fit logistic regression model. My data is very big and the algorithm is such that it has to run glm function hundreds of times. Now *I need only the **estimates of the coefficients and std. error in my output, *but apparently glm function is computing several other statistics and parameters (mentioned below) which increases the run time. [aic, boundary, call, coefficients, contrasts, control, converged, data, deviance, df.null, df.residual, effects, family, fitted.values, formula, iter, linear.predictors, method, model, null.deviance, offset, prior.weights, qr, R, rank, residuals, terms, weights, xlevels, y] Is there a way (apart from scratching the glm code), which only do the minimal computations to output my requirements. Any hints can be helpful. Regards Utkarsh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Slicing an array
See the abind package.
On Fri, Jun 12, 2009 at 8:36 AM, Jim Lemon wrote:
> Hi all,
> I've been trying to work out how to slice an array of arbitrary dimension. I
> found a message showing how to stick two arrays together, but so far have
> been unable to transform that into what I need. Assume that I have a four
> dimensional array for example:
>
> array4d
> , , 1, 1
>
> [,1] [,2]
> [1,] 3 6
> [2,] 1 1
>
> , , 2, 1
>
> [,1] [,2]
> [1,] 4 7
> [2,] 8 7
>
> , , 1, 2
>
> [,1] [,2]
> [1,] 7 8
> [2,] 8 7
>
> , , 2, 2
>
> [,1] [,2]
> [1,] 7 5
> [2,] 9 9
>
> I want to slice the array from the rightmost dimension, getting in sequence:
>
> array4d[,,,1]
> array4d[,,,2]
>
> then slicing those 3D arrays, and so on. I'm pretty sure that this will
> involve a:
>
> do.call('[',...)
>
> construction, but I haven't been able to work out how to specify the list of
> arguments, in particular the index vector, to slice up the last dimension. I
> have tried constructing index vectors with NULLs which of course doesn't
> work because they just disappear. Any suggestions?
>
> Jim
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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[R] Creating this vector, any suggetions?
Suppose I have the first vector: c(1, 6, 8, 9) I will like to create a second vector of size 10 composed of 0 and 1's. The second vector will be composed of four 1's and six 0's. The position of the 1's will be specificed by the first vector. So essentially, I want a second vector in the form: c(1, 0, 0, 0, 0, 1, 0, 1, 1, 0) Any help is greatly appreciated! -- View this message in context: http://www.nabble.com/Creating-this-vector%2C-any-suggetions--tp24000348p24000348.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] coupled ODE population model
I'm fairly new to R, and I'm trying to write out a population model that satisfies the following; the system consists of s species, i= 1, 2,...,s network of interactions between species is specified by a (s x s) real matrix, C[i,j] x[i] being the relative population of the "ith" species (0 =< x[i] =< 1, sum(x[i]=1) the evolution rule being considered is as follows; xprime[i] = f[i] if x[i] > 0 or f[i] >= 0 xprime[i] = 0 if x[i] = 0 and f[i] < 0 where f[i] = sum(C[i,j]*x[j]) - x[i]*sum(C[k,j]*x[j]) I have a bit of attempted code written out, but are there any tricks or tips that would condense or make this mess look nicer? -Justin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating this vector, any suggetions?
njhuang86 wrote: > > Suppose I have the first vector: c(1, 6, 8, 9) > > I will like to create a second vector of size 10 composed of 0 and 1's. > The second vector will be composed of four 1's and six 0's. The position > of the 1's will be specificed by the first vector. So essentially, I want > a second vector in the form: > > c(1, 0, 0, 0, 0, 1, 0, 1, 1, 0) > > Any help is greatly appreciated! > z <- numeric(10) pos <- c(1,6,8,9) z[pos] <- 1 -- View this message in context: http://www.nabble.com/Creating-this-vector%2C-any-suggetions--tp24000348p24000457.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating this vector, any suggetions?
Try this: x <- c(1, 6, 8, 9) tabulate(x, nbins = max(x) + 1) On Fri, Jun 12, 2009 at 11:45 AM, njhuang86 wrote: > > Suppose I have the first vector: c(1, 6, 8, 9) > > I will like to create a second vector of size 10 composed of 0 and 1's. The > second vector will be composed of four 1's and six 0's. The position of the > 1's will be specificed by the first vector. So essentially, I want a second > vector in the form: > > c(1, 0, 0, 0, 0, 1, 0, 1, 1, 0) > > Any help is greatly appreciated! > -- > View this message in context: > http://www.nabble.com/Creating-this-vector%2C-any-suggetions--tp24000348p24000348.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R: Creating this vector, any suggetions?
try this > a<-c(1, 6, 8, 9) > 1*(1:10 %in% a) [1] 1 0 0 0 0 1 0 1 1 0 Stefano -Messaggio originale- Da: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]per conto di njhuang86 Inviato: Friday, June 12, 2009 4:45 PM A: r-help@r-project.org Oggetto: [R] Creating this vector, any suggetions? Suppose I have the first vector: c(1, 6, 8, 9) I will like to create a second vector of size 10 composed of 0 and 1's. The second vector will be composed of four 1's and six 0's. The position of the 1's will be specificed by the first vector. So essentially, I want a second vector in the form: c(1, 0, 0, 0, 0, 1, 0, 1, 1, 0) Any help is greatly appreciated! -- View this message in context: http://www.nabble.com/Creating-this-vector%2C-any-suggetions--tp24000348p24000348.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Rispetta l'ambiente: Se non ti è necessario, non stampare questa mail. "Le informazioni contenute nel presente messaggio di posta elettronica e in ogni suo allegato sono da considerarsi riservate e il destinatario della email è l'unico autorizzato ad usarle, copiarle e, sotto la propria responsabilità, divulgarle. Chiunque riceva questo messaggio per errore senza esserne il destinatario deve immediatamente rinviarlo al mittente cancellando l'originale. Eventuali dati personali e sensibili contenuti nel presente messaggio e/o suoi allegati vanno trattati nel rispetto della normativa in materia di privacy ( DLGS n.196/'03)". __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tables without names
On Fri, Jun 12, 2009 at 6:09 AM, Duncan Murdoch wrote: > On 11/06/2009 5:35 PM, Stavros Macrakis wrote: > >> A table without names displays like a vector: >> >>> unname(table(2:3)) >>[1] 1 1 1 >> >> and preserves the table class (as with unname in general): >> >>> dput(unname(table(2:3))) >>structure(c(1L, 1L), .Dim = 2L, class = "table") >> >> Does that make sense? R is not consistent in its treatment of such >> unname'd >> tables: >> > > One of the complaints about the S3 object system is that anything can claim > to be of class "foo", even if it doesn't have the right structure so that > foo methods work for it. Yes, that is one of its flaws. More specifically, in this case, operations on S3 objects can change them from being valid to being invalid. > I think that's all you're seeing here: you've got something that is > mislabelled as being of class "table". Yes. > The solution is "don't do that". Agreed! But it's not clear to me how unname can *know* how not to do that in the general case. After all, unname on a vector of POSIXct's leaves a valid POSIXct object. ... >> PS What is the standard way of extracting just the underlying vector? >> c(unname(...)) works -- is that what is recommended? >> > > I would use as.numeric(), but I don't claim it's standard. > Makes sense, as does the suggestion as.vector. So I guess the summary of 'stripping' operations is: c --- strip all attributes (including most but not all classes) except for names unname -- strip name attributes, but no other attributes (including class) unclass -- strip only class attribute as.vector -- strip all attributes including class and name; convert generic vectors to atomic vectors Am I missing others? -s [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Slicing an array
Jim,
Is
do.call( '[', list( array4d,TRUE,TRUE,TRUE,1 ) )
what you want?
HTH,
Chuck
On Fri, 12 Jun 2009, Jim Lemon wrote:
Hi all,
I've been trying to work out how to slice an array of arbitrary dimension. I
found a message showing how to stick two arrays together, but so far have
been unable to transform that into what I need. Assume that I have a four
dimensional array for example:
array4d
, , 1, 1
[,1] [,2]
[1,]36
[2,]11
, , 2, 1
[,1] [,2]
[1,]47
[2,]87
, , 1, 2
[,1] [,2]
[1,]78
[2,]87
, , 2, 2
[,1] [,2]
[1,]75
[2,]99
I want to slice the array from the rightmost dimension, getting in sequence:
array4d[,,,1]
array4d[,,,2]
then slicing those 3D arrays, and so on. I'm pretty sure that this will
involve a:
do.call('[',...)
construction, but I haven't been able to work out how to specify the list of
arguments, in particular the index vector, to slice up the last dimension. I
have tried constructing index vectors with NULLs which of course doesn't work
because they just disappear. Any suggestions?
Jim
__
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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Re: [R] Tables without names
On Fri, Jun 12, 2009 at 10:57 AM, Stavros Macrakis wrote: > On Fri, Jun 12, 2009 at 6:09 AM, Duncan Murdoch wrote: > >> On 11/06/2009 5:35 PM, Stavros Macrakis wrote: >> >>> A table without names displays like a vector: >>> >>> > unname(table(2:3)) >>> [1] 1 1 1 >>> >>> and preserves the table class (as with unname in general): >>> >>> > dput(unname(table(2:3))) >>> structure(c(1L, 1L), .Dim = 2L, class = "table") >>> >>> Does that make sense? R is not consistent in its treatment of such >>> unname'd >>> tables: >>> >> >> One of the complaints about the S3 object system is that anything can claim >> to be of class "foo", even if it doesn't have the right structure so that >> foo methods work for it. > > > Yes, that is one of its flaws. More specifically, in this case, operations > on S3 objects can change them from being valid to being invalid. > > >> I think that's all you're seeing here: you've got something that is >> mislabelled as being of class "table". > > > Yes. > > >> The solution is "don't do that". > > > Agreed! But it's not clear to me how unname can *know* how not to do that > in the general case. After all, unname on a vector of POSIXct's leaves a > valid POSIXct object. > > ... >>> PS What is the standard way of extracting just the underlying vector? >>> c(unname(...)) works -- is that what is recommended? >>> >> >> I would use as.numeric(), but I don't claim it's standard. >> > > Makes sense, as does the suggestion as.vector. So I guess the summary of > 'stripping' operations is: > > c --- strip all attributes (including most but not all classes) except for > names > unname -- strip name attributes, but no other attributes (including class) > unclass -- strip only class attribute > as.vector -- strip all attributes including class and name; convert generic > vectors to atomic vectors > > Am I missing others? There is also unlist. Also c and unlist are generic so their action can depend on the class of their argument. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] triangular plot
On Jun 12, 2009, at 10:13 AM, David Carlson wrote: You may have more luck with the triangle plot functions available in other R libraries. In addition to triangle.plot in ade4, you have other options (this may not be an exhaustive list): plot.acomp in compositions tri in cwhmisc.cwhtool triax in plotrix Your posting was especially helpful because it is not reproducible with the combination of resutls from ??"triangle" amd ??"ternary". But in plotrix the function is triax.plot ternary in StatDA ternaryplot in vcd Very nice looking plot if you add labels with the id= parameter. In the help page example using , id=rownames(tab), was what worked for me. ternaryplot in Zelig David L. Carlson Anthropology Department Texas A&M University College Station, TX 77843-4352 David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R course in Italy
Quantide is pleased to announce the above course in Milan: -- Introduction to the R language 6-7th July 2009 Milano Italy -- * Who Should Attend ? This is a course suitable for beginners and improvers in the R language and is ideal for people wanting an all round introduction to R * Course Goals - To allow attendees to understand the technology behind the R package - Improve attendees programming style and confidence - To enable users to access a wide range of available functionality * Course Outline 1. Introduction to the R language and the R community 2. The R Environment 3. R data objects 4. Functions and Operators 5. Data import and export 7. Standard Graphics 8. Advanced Graphics 9. Introduction to R Statistics The cost of this course is Euro 500+VAT Should your organization have more than 3 possible attendees why not talk to us about hosting a customized and focused course delivered at your premises? Should you want to book a place on this course or have any questions please visit: http://www.quantide.com/formazioneR.php or contact: Daniela Manzato daniela.manz...@quantide.com +39 328 537 51 09 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Studentized intervals
I am trying to find studentized bootstrap intervals for the skewness of a data
set. I have tried the following (nerve.dat is a set of data containing
observations on one variable) (using Windows XP):
x <- scan("e:/Flashbackup2009/Nonparametrics/nerve.dat")
n <- length(x)
library(e1071)
skewness(x)
library(boot)
sampleskew <- function(x,d) {return(skewness(x[d]))}
bb <- boot(x,sampleskew,R=1000)
boot.ci(bb)
This gives four intervals (Normal, Basic, Percentile, BCa)
But gives the following warning message:
Warning message:
In boot.ci(bb, type = "all") :
bootstrap variances needed for studentized intervals
The questions is: Why does the function not provide the bootstrap variances (or
estimates thereof) for computing the studentized intervals?
Another question: How then can I compute the studentized intervals without
physically doing a double bootstrap. Does the function use a "nonparametric
delta mathod"?
Any help is much appreciated. I have probably overlooked something?
Thank you.
Jacob
Jacob L van Wyk, Dept. of Statistics, University of Johannesburg (APK),
Box 524, Auckland Park, 2006.
Office: +27 11 559 3080, Fax: +27 11 559 2499
This email and all contents are subject to the following disclaimer:
http://www.uj.ac.za/UJ_email_legal_disclaimer.htm
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Re: [R] Sweave recode(car) and Lyx, compiling but not executing on Mac
Dear Graham, I just tried a similar recode() command using Sweave on a Windows system (not through LyX) and it worked fine. I hope this helps, John > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Graham Smith > Sent: June-12-09 10:27 AM > To: r-help@r-project.org > Subject: [R] Sweave recode(car) and Lyx, compiling but not executing on Mac > > I am just beginning to use Sweave with Lyx on a Mac (R2.8.1). I have > 12 chunks of Sweave code that work fine, but this piece: > > <<>>= > library(car) > cabbages$Year<- > recode(cabbages$Year,"'X2001'='2001';'X2002'='2002';'X2003'='2003';'X2004'=' 2 > 004';'X2005'='2005';'X2006'='2006';'X2007'='2007';'X2008'='2008';'X2009'='20 0 > 9';'X2010'='2010';'X2011'='2011';'X2012'='2012'") > @ > > just prints out verbatim as a single line running off the page (No > recoding occurs). It worked in R before pasting into Lyx. > > Initially I had the double quotes and single quotes the other way > round, but this produced this in the complied pdf: > > cabbages$Year <- recode(cabbages$Year, > "\"X2001\"=\"2001\";\"X2002\"=\"2002\";\"X2003\"=\"2003\";\ etc > > The first double quote in the printout shown above was a single quote > before compiling. > > I have asked on the Lyx forum for help, but maybe someone here can > suggest what I might be doing wrong. Of course it could be a Mac/Lyx > issue rather than an SWeave/R issue, but any help would be > appreciated. > > Thanks, > > Graham > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Automate a data load and merge
See if this works for you:
# read into a list and then rbind to single data frame
input <- do.call(rbind, lapply(files, function(.file){
X <- read.csv(.file)
X$label <- gsub('.csv$', '', .file) # add name
X
}))
# use the reshape package
require(reshape)
i.melt <- melt(input, id=c("label", "Item_name"), measure="Occurance")
output <- cast(i.melt, Item_name ~ label)
On Fri, Jun 12, 2009 at 9:27 AM, Jon Loehrke wrote:
> Hi R list,
>I would like to automate, or speed up the process from which I take
> several separate datasets, stored in .csv formate, import and merge
> them by a common variable. So far I have greatly sped up the loading
> process but cannot think of a way to automate the merger of all
> datasets into a common data.frame.
>My apologies if this has been covered, any R search suggestions are
> appreciated.
>
> # All scripts function out of the base directory
> rm(list=ls())
> setwd('/Users/myuser/Documents/workfolder/')
>
> # Check files and list all .csv in directory
> files<-list.files()
> files<-files[grep('.csv', files)]
> # Create labels for each file (ex. June08.csv becomes June08)
> labels<-gsub('.csv', '', files)
>
> # Load all .csv datasets and assign name
>
> item<-vector() # preallocate an index of all items in datasets
> for(i in 1:length(files)){
>X<-read.csv(files[i])
>item<-union(item, X$Item_Name)
>assign(labels[i], X)
>}
> # What is loaded
> ls()
> # [1] "files""i""item" "June01" "June02" "June03"
> "labels"
>
> # What does everything look like?
> str(June03)
> #'data.frame': 992 obs. of 8 variables:
> # $ Item_Name: Factor w/ 992 levels "Birds","Fish",..: 1 2 3 4
> 5 6 7 8 9 10 ...
> # $ Occurance : int 30 30 50 450 75 550 100 500 250 75 ...
>
> str(June01)
> #'data.frame': 819 obs. of 8 variables:
> # $ Item_Name: Factor w/ 819 levels "Birds","Turtles",..: 1 2
> 3 4 5 6 7 8 9 10 ...
> # $ Occurance : int 30 50 450 750 550 100 500 250 275 450 ...
>
> # Here is where I'm stuck...
> #I would like to:
> # Create a data.frame with an index column composed of the union of
> all items
> # Create columns in the frame by a merger of the 'Occurance' in each
> loaded dataset and are labeled by their name (eg. June01)
> # Automate this procedure so that I do not have to manuualy type in
> each column addition when I have a new dataset.
>
> # This is my current strategy, but when I have new datasets I have to
> mannually setup the preallocation and merger
>
> allData<-data.frame(Item=item, June01 =NA, June02=NA, June03 =NA)
> allData[match(June01$Item_Name, allData$Item ),]$June01 <-
> June01$Occurance
> allData[match(June02$Item_Name, allData$Item ),]$June02 <-
> June02$Occurance
> allData[match(June03$Item_Name, allData$Item ),]$June03 <-
> June03$Occurance
>
> # Any help to automate this process is greatly appreciated!!!
>
> sessionInfo()
> #R version 2.9.0 (2009-04-17)
> #i386-apple-darwin8.11.1
> #
> #locale:
> #en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> #
> #attached base packages:
> #[1] stats graphics grDevices utils datasets methods base
>
>
> Jon Loehrke
> Graduate Research Assistant
> Department of Fisheries Oceanography
> School for Marine Science and Technology
> University of Massachusetts
> 200 Mill Road, Suite 325
> Fairhaven, MA 02719
> jloeh...@umassd.edu
> T 508-910-6393
> F 508-910-6396
>
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Automate a data load and merge
I think the last should be:
output <- cast(i.melt, Item_name ~ label, sum)
On Fri, Jun 12, 2009 at 9:27 AM, Jon Loehrke wrote:
> Hi R list,
>I would like to automate, or speed up the process from which I take
> several separate datasets, stored in .csv formate, import and merge
> them by a common variable. So far I have greatly sped up the loading
> process but cannot think of a way to automate the merger of all
> datasets into a common data.frame.
>My apologies if this has been covered, any R search suggestions are
> appreciated.
>
> # All scripts function out of the base directory
> rm(list=ls())
> setwd('/Users/myuser/Documents/workfolder/')
>
> # Check files and list all .csv in directory
> files<-list.files()
> files<-files[grep('.csv', files)]
> # Create labels for each file (ex. June08.csv becomes June08)
> labels<-gsub('.csv', '', files)
>
> # Load all .csv datasets and assign name
>
> item<-vector() # preallocate an index of all items in datasets
> for(i in 1:length(files)){
>X<-read.csv(files[i])
>item<-union(item, X$Item_Name)
>assign(labels[i], X)
>}
> # What is loaded
> ls()
> # [1] "files""i""item" "June01" "June02" "June03"
> "labels"
>
> # What does everything look like?
> str(June03)
> #'data.frame': 992 obs. of 8 variables:
> # $ Item_Name: Factor w/ 992 levels "Birds","Fish",..: 1 2 3 4
> 5 6 7 8 9 10 ...
> # $ Occurance : int 30 30 50 450 75 550 100 500 250 75 ...
>
> str(June01)
> #'data.frame': 819 obs. of 8 variables:
> # $ Item_Name: Factor w/ 819 levels "Birds","Turtles",..: 1 2
> 3 4 5 6 7 8 9 10 ...
> # $ Occurance : int 30 50 450 750 550 100 500 250 275 450 ...
>
> # Here is where I'm stuck...
> #I would like to:
> # Create a data.frame with an index column composed of the union of
> all items
> # Create columns in the frame by a merger of the 'Occurance' in each
> loaded dataset and are labeled by their name (eg. June01)
> # Automate this procedure so that I do not have to manuualy type in
> each column addition when I have a new dataset.
>
> # This is my current strategy, but when I have new datasets I have to
> mannually setup the preallocation and merger
>
> allData<-data.frame(Item=item, June01 =NA, June02=NA, June03 =NA)
> allData[match(June01$Item_Name, allData$Item ),]$June01 <-
> June01$Occurance
> allData[match(June02$Item_Name, allData$Item ),]$June02 <-
> June02$Occurance
> allData[match(June03$Item_Name, allData$Item ),]$June03 <-
> June03$Occurance
>
> # Any help to automate this process is greatly appreciated!!!
>
> sessionInfo()
> #R version 2.9.0 (2009-04-17)
> #i386-apple-darwin8.11.1
> #
> #locale:
> #en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> #
> #attached base packages:
> #[1] stats graphics grDevices utils datasets methods base
>
>
> Jon Loehrke
> Graduate Research Assistant
> Department of Fisheries Oceanography
> School for Marine Science and Technology
> University of Massachusetts
> 200 Mill Road, Suite 325
> Fairhaven, MA 02719
> jloeh...@umassd.edu
> T 508-910-6393
> F 508-910-6396
>
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Studentized intervals
The help page ?boot.ci says
Variance estimates are required for studentized intervals.
(and the warning you got repeated the point).
Package 'boot' is support software for a book by Davison & Hinkley
which explains how to used boot.ci() for studentized examples and has
several examples. You will need to study it for further elucidation.
On Fri, 12 Jun 2009, Van Wyk, Jaap wrote:
I am trying to find studentized bootstrap intervals for the skewness of a data
set. I have tried the following (nerve.dat is a set of data containing
observations on one variable) (using Windows XP):
x <- scan("e:/Flashbackup2009/Nonparametrics/nerve.dat")
n <- length(x)
library(e1071)
skewness(x)
library(boot)
sampleskew <- function(x,d) {return(skewness(x[d]))}
bb <- boot(x,sampleskew,R=1000)
boot.ci(bb)
This gives four intervals (Normal, Basic, Percentile, BCa)
But gives the following warning message:
Warning message:
In boot.ci(bb, type = "all") :
bootstrap variances needed for studentized intervals
The questions is: Why does the function not provide the bootstrap
variances (or estimates thereof) for computing the studentized
intervals? Another question: How then can I compute the studentized
intervals without physically doing a double bootstrap. Does the
function use a "nonparametric delta mathod"?
Any help is much appreciated. I have probably overlooked something?
Thank you.
Jacob
Jacob L van Wyk, Dept. of Statistics, University of Johannesburg (APK),
Box 524, Auckland Park, 2006.
Office: +27 11 559 3080, Fax: +27 11 559 2499
This email and all contents are subject to the following disclaimer:
http://www.uj.ac.za/UJ_email_legal_disclaimer.htm
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] Sweave recode(car) and Lyx, compiling but not executing on Mac
John, Thanks, its difficult when you don't know where the problem is. The code works fine directly in R on the Mac, and from whta you say it works with Sweave, so it seems to narrow it down to Lyx/Sweave/Mac interaction. Graham 2009/6/12 John Fox : > Dear Graham, > > I just tried a similar recode() command using Sweave on a Windows system > (not through LyX) and it worked fine. > > I hope this helps, > John > >> -Original Message- >> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On >> Behalf Of Graham Smith >> Sent: June-12-09 10:27 AM >> To: r-help@r-project.org >> Subject: [R] Sweave recode(car) and Lyx, compiling but not executing on > Mac >> >> I am just beginning to use Sweave with Lyx on a Mac (R2.8.1). I have >> 12 chunks of Sweave code that work fine, but this piece: >> >> <<>>= >> library(car) >> cabbages$Year<- >> > recode(cabbages$Year,"'X2001'='2001';'X2002'='2002';'X2003'='2003';'X2004'=' > 2 >> > 004';'X2005'='2005';'X2006'='2006';'X2007'='2007';'X2008'='2008';'X2009'='20 > 0 >> 9';'X2010'='2010';'X2011'='2011';'X2012'='2012'") >> @ >> >> just prints out verbatim as a single line running off the page (No >> recoding occurs). It worked in R before pasting into Lyx. >> >> Initially I had the double quotes and single quotes the other way >> round, but this produced this in the complied pdf: >> > cabbages$Year <- recode(cabbages$Year, >> "\"X2001\"=\"2001\";\"X2002\"=\"2002\";\"X2003\"=\"2003\";\ etc >> >> The first double quote in the printout shown above was a single quote >> before compiling. >> >> I have asked on the Lyx forum for help, but maybe someone here can >> suggest what I might be doing wrong. Of course it could be a Mac/Lyx >> issue rather than an SWeave/R issue, but any help would be >> appreciated. >> >> Thanks, >> >> Graham >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparing model fits for NLME when models are not nested
At 05:42 AM 6/12/2009, Lindsay Banin wrote: Hi there, I am looking to compare nonlinear mixed effects models that have different nonlinear functions (different types of growth curve)embedded. Most of the literature I can find focuses on comparing nested models with likelihood ratios and AIC. Is there a way to compare model fits when models are not nested, i.e. when the nonlinear functions are not the same? Transform back into original units, if necessary, and compare distributions of and statistics of residuals from fitted values in original units. This is not a significance-test, but instead a measure of the better approximation to the observed model. Types of measures: 1) rms residual, 2) max absolute residual, 3) mean absolute residual. In my opinion, models should be chosen based on the principles of causality (theory), degree of approximation and parsimony. None of these involve significance testing. Choosing models based upon significance testing (which merely identifies whether or not the experiment is large enough to distinguish an effect clearly) amounts to admitting intellectually that you have no subject matter expertise, and you must therefore fall back on the crumbs of significance testing to get glimmers of understanding of what's going on. (Much like stepwise regression techniques.) As an example, suppose you have two models, one with 5 parameters and one with only 1. The rms residual error for the two models are 0.50 and 0.53 respectively. You have a very large study, and all 4 additional parameters are significant at p = 0.01 or less. What should you do? What I would do is select the 1 parameter study as my baseline model. It will be easy to interpret physically, will generalize to other studies much better (stable), and is almost identical in degree of approximation as the 5 parameter model. I would be excited that a one parameter model could do this. The fact that the other 4 parameters have detectable effects at a very low level is not important for modeling the study, but may conceivably have some special significance on their own for future investigations. So not being able to do significance testing on non-nested models is not that big a loss, in my opinion. Such tests encourage wrong thinking, in my opinion. What I've expressed as an opinion here (which I am sure some will disagree with) is similar to the philosophy of choosing the number of principal components to use, or number of latent factors in factor analysis. What investigation do people ever do on the small eigenvalue principal components, even if their contributions are "statistically significant"? Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 "Vere scire est per causas scire" __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] package Rgraphviz or similar
Hello R users
I am looking for a package to visualize "relatively
planar" directed graphs, with say 100 nodes and
specified using an adjacency list.
'Rgraphviz', currently listed on the R-FAQ, seemed
suitable (FAQ version 2.9.2009-06-05)
But when I looked for the package, I found it had been
recently "removed" and was instead directed to archive
copies (http://cran.r-project.org/web/packages/Rgraphviz)
Can anybody suggest an alternative R package ('igraph'
perhaps)? Or would I be better it generate my own .gv
GraphViz files and then pass these directly to
GraphViz. Or will 'Rgraphviz' return soon?
Any suggestions much appreciated, Robbie
---
Robbie Morrison
PhD student -- policy-oriented energy system simulation
Technical University of Berlin (TU-Berlin), Germany
University email (redirected) : morri...@iet.tu-berlin.de
Webmail (preferred) : rob...@actrix.co.nz
[from IMAP client]
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Re: [R] package Rgraphviz or similar
Robbie Morrison wrote:
> Hello R users
>
> I am looking for a package to visualize "relatively
> planar" directed graphs, with say 100 nodes and
> specified using an adjacency list.
>
> 'Rgraphviz', currently listed on the R-FAQ, seemed
> suitable (FAQ version 2.9.2009-06-05)
>
> But when I looked for the package, I found it had been
> recently "removed" and was instead directed to archive
> copies (http://cran.r-project.org/web/packages/Rgraphviz)
Rgraphviz is available in Bioconductor
http://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html
Martin
>
> Can anybody suggest an alternative R package ('igraph'
> perhaps)? Or would I be better it generate my own .gv
> GraphViz files and then pass these directly to
> GraphViz. Or will 'Rgraphviz' return soon?
>
> Any suggestions much appreciated, Robbie
> ---
> Robbie Morrison
> PhD student -- policy-oriented energy system simulation
> Technical University of Berlin (TU-Berlin), Germany
> University email (redirected) : morri...@iet.tu-berlin.de
> Webmail (preferred) : rob...@actrix.co.nz
> [from IMAP client]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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[R] FBI Homicide data?
Dear all, do you know if it's available and where the "FBI Homicide" dataset? It has at least the following columns: "victim age", "homicide age". A scatterplot of this data is visible here: http://www.uml.edu/gallery/main.php?g2_itemId=6016 Thanks for your help! mario -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using lattice dotplot with two equal data points
I'm wondering if I am dealing with a limitation in lattice. It's probably due to my own limitations though. I'm working with a lattice dotplot. The x-axis is set at "free". In one panel, there are only two data points that have equal x-axis values. Since no range exists, lattice isn't plotting those points. It reports: "Error Packet using 6 'x' and 'units' must have length>0" Is there a way that I can get it to plot anyway? Do I have to manipulate that one panel? Any suggestions on how to do that? I'd rather have some sort of automatic backup range set instead. David Chosid Massachusetts Division of Marine Fisheries 1213 Purchase St., 3rd Floor New Bedford, MA 02740 508-990-2860 x140 email: david.cho...@state.ma.us __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave recode(car) and Lyx, compiling but not executing on Mac
Just to follow this up. Changing the document encoding in Lyx from the default (whatever that was) to utf8 (with some help from Jay) allowed some sample"recode" code to run (it wouldn't run initially), but my original code still won't run. Strangely looking at the Latex code window in Lyx shows some strange syntax highlighting in my code cabbages$Year<-recode(cabbages$Year,"'X2001'... The code is higlighted between the $ signs and I wonder if this suggests there are still some sort of encoding problem. Graham 2009/6/12 John Fox : > Dear Graham, > > I just tried a similar recode() command using Sweave on a Windows system > (not through LyX) and it worked fine. > > I hope this helps, > John > >> -Original Message- >> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On >> Behalf Of Graham Smith >> Sent: June-12-09 10:27 AM >> To: r-help@r-project.org >> Subject: [R] Sweave recode(car) and Lyx, compiling but not executing on > Mac >> >> I am just beginning to use Sweave with Lyx on a Mac (R2.8.1). I have >> 12 chunks of Sweave code that work fine, but this piece: >> >> <<>>= >> library(car) >> cabbages$Year<- >> > recode(cabbages$Year,"'X2001'='2001';'X2002'='2002';'X2003'='2003';'X2004'=' > 2 >> > 004';'X2005'='2005';'X2006'='2006';'X2007'='2007';'X2008'='2008';'X2009'='20 > 0 >> 9';'X2010'='2010';'X2011'='2011';'X2012'='2012'") >> @ >> >> just prints out verbatim as a single line running off the page (No >> recoding occurs). It worked in R before pasting into Lyx. >> >> Initially I had the double quotes and single quotes the other way >> round, but this produced this in the complied pdf: >> > cabbages$Year <- recode(cabbages$Year, >> "\"X2001\"=\"2001\";\"X2002\"=\"2002\";\"X2003\"=\"2003\";\ etc >> >> The first double quote in the printout shown above was a single quote >> before compiling. >> >> I have asked on the Lyx forum for help, but maybe someone here can >> suggest what I might be doing wrong. Of course it could be a Mac/Lyx >> issue rather than an SWeave/R issue, but any help would be >> appreciated. >> >> Thanks, >> >> Graham >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mixture of normals
Can anyone send me the R code for fitting a mixture of normal distributions. Or in fact any'combination' of mixtures of distributions. I looke dta mix but it is still not clear to me. Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mixture of normals
The package mixtools appears a more appropriate place to look. On Jun 12, 2009, at 2:57 PM, Jim Silverton wrote: Can anyone send me the R code for fitting a mixture of normal distributions. Or in fact any'combination' of mixtures of distributions. I looke dta mix but it is still not clear to me. Jim [[alternative HTML version deleted]] -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave recode(car) and Lyx, compiling but not executing on Mac
While this is a bit embarrassing , it seems I had two problems, one was that the recode command seems to need utf8 coding rather than the Lyx default (which is fine), plus I had typing error in the data set, which is not fine :-(. I rewrote my code using the with command which allowed it to run, but it then became obvious that the recoded resuts were not what I had expected. The typing error then being obvious. The first entry in my rcode was 'X2001'='2001' but the first level in the data set was "X20001" and this was enough to cause recode to fail in my original code, but run using the with command. Its now working. Thanks to everyone for there help. Graham 2009/6/12 Graham Smith : > I am just beginning to use Sweave with Lyx on a Mac (R2.8.1). I have > 12 chunks of Sweave code that work fine, but this piece: > > <<>>= > library(car) > cabbages$Year<-recode(cabbages$Year,"'X2001'='2001';'X2002'='2002';'X2003'='2003';'X2004'='2004';'X2005'='2005';'X2006'='2006';'X2007'='2007';'X2008'='2008';'X2009'='2009';'X2010'='2010';'X2011'='2011';'X2012'='2012'") > @ > > just prints out verbatim as a single line running off the page (No > recoding occurs). It worked in R before pasting into Lyx. > > Initially I had the double quotes and single quotes the other way > round, but this produced this in the complied pdf: >> cabbages$Year <- recode(cabbages$Year, >> "\"X2001\"=\"2001\";\"X2002\"=\"2002\";\"X2003\"=\"2003\";\ etc > > The first double quote in the printout shown above was a single quote > before compiling. > > I have asked on the Lyx forum for help, but maybe someone here can > suggest what I might be doing wrong. Of course it could be a Mac/Lyx > issue rather than an SWeave/R issue, but any help would be > appreciated. > > Thanks, > > Graham > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mixture of normals
On Jun 12, 2009, at 3:13 PM, David Winsemius wrote: The package mixtools appears a more appropriate place to look. ... as well as: http://cran.r-project.org/web/views/Cluster.html On Jun 12, 2009, at 2:57 PM, Jim Silverton wrote: Can anyone send me the R code for fitting a mixture of normal distributions. Or in fact any'combination' of mixtures of distributions. I looke dta mix but it is still not clear to me. Jim [[alternative HTML version deleted]] -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] xtable for plm objects
Hello,
I am trying to use Sweave to write up a report, and I have used the
plm package to do some panel models. I am trying to use xtable to make
a nice table for my regression objects (returned by the plm command),
but I am getting the error:
Error in UseMethod("xtable") : no applicable method for "xtable"
It seems like I would want to have xtable treat plm objects exactly as
lm objects. Is there a way I can force this behavior?
Thanks,
-stephen
==
Stephen J. Barr
University of Washington
WEB: www.econsteve.com
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[R] funnel plots
for the function funnelplot(), how do I include 95% confidence intervals for the effect estimate ( ie. / \ )? -- View this message in context: http://www.nabble.com/funnel-plots-tp24003106p24003106.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Order data frame
Hi listers, I have a data frame with 5 variables... And I want reorder the data frame according a specific variable X... I checked the sort and order functions... In my case I think that the ORDER function is applicable... But I did not understand at all... The idea is simple... Data order by X... I know that this is very simple... Anyways... How I would do that... Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Order-data-frame-tp24004394p24004394.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Market Basket Analysis / Link Analysis
The concept behind http://themarketinganalysts.com/en/pages/market-basket-analysis/ Market Basket Analysis is relatively simple but it requires a huge server and lots of processing power. If you run into problems and need to run your data on larger machine, please keep us in mind. We would be happy to provide you with a free quote. We are located in the Dallas/Fort Worth area if that helps too. Please feel free to visit our site at www.themarketinganalysts.com. eugene dalt wrote: > > > Hi folks, > > I am looking for Market Basket Analysis / Link Analysis tools in R, > packages or functions. > > Tx - Eugene > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/Market-Basket-AnalysisLink-Analysis-tp23992852p24004518.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mixture of normals
.. and package mixdist. Google on "R mixture models" or similar. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: Friday, June 12, 2009 12:14 PM To: Jim Silverton Cc: r-help@r-project.org Subject: Re: [R] Mixture of normals The package mixtools appears a more appropriate place to look. On Jun 12, 2009, at 2:57 PM, Jim Silverton wrote: > Can anyone send me the R code for fitting a mixture of normal > distributions. > Or in fact any'combination' of mixtures of distributions. I looke > dta mix > but it is still not clear to me. > > > Jim > > [[alternative HTML version deleted]] -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] xtable for plm objects
On Fri, 12 Jun 2009, Stephen J. Barr wrote:
Hello,
I am trying to use Sweave to write up a report, and I have used the
plm package to do some panel models. I am trying to use xtable to make
a nice table for my regression objects (returned by the plm command),
but I am getting the error:
Error in UseMethod("xtable") : no applicable method for "xtable"
It seems like I would want to have xtable treat plm objects exactly as
lm objects. Is there a way I can force this behavior?
I quickly checked and it seems that the xtable() method for "lm" objects
just relies on the fact that
summary(object)$coef
is the matrix with coef/std.error/t-stat/p-value. As this is the case for
"plm" objects, I think you can do
xtable.plm <- xtable:::xtable.lm
and then
xtable(plm_object)
should give the desired result.
hth,
Z
Thanks,
-stephen
==
Stephen J. Barr
University of Washington
WEB: www.econsteve.com
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Re: [R] Order data frame
Try this: DF <- data.frame(ID = sample(5), v = rnorm(5)) DF[order(DF$ID),] On Fri, Jun 12, 2009 at 3:54 PM, MarcioRibeiro wrote: > > Hi listers, > I have a data frame with 5 variables... And I want reorder the data frame > according a specific variable X... > I checked the sort and order functions... In my case I think that the ORDER > function is applicable... But I did not understand at all... The idea is > simple... Data order by X... > I know that this is very simple... Anyways... How I would do that... > Thanks in advance, > Marcio > > -- > View this message in context: > http://www.nabble.com/Order-data-frame-tp24004394p24004394.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Competing risks Kalbfleisch & Prentice method
Dear Terry, Eleni & Heinz, Please forgive me for imposing on your time, but since we have had similar discussions before on this topic, I thought that it would be nice to get your feedback on this problem. I have written a function to compute the cumulative incidence, for a given covariate vector Z, based on Cox PH models for each competing event type. It is based on Cheng, Fine, and Wei (Biometrics 1998), but is fairly straightforward. Fine calls it "indirect regression" approach, since it models each cause-specific hazard and then puts it all together using the basic definition of CIF. I applied it to the Green & Byar data on DES trial for prostate cancer (this data set was also discussed in Kay 1986 and Cheng et al. 1998). The data set is attached as STATA file, which can be read into R using "foreign" package. My function for CIF seems to do ok. However, I am not sure about this. I computed the CIFs of prostate cancer for two sets of covariates (see the code). I compared the indirect CIFs to the "direct regression " CIFs predicted by Fine & Gray's method. There appears to be some significant differences, especially for CVD deaths. The CIF plots for the 3 competing events can be easily generated by runnng the code. Why would there be a big difference between FG direct approach and the indirect CIF computed by my code? Is this because of the modeling assumptions in the direct regression approach of FG? Or is there some problem with my approach? I would appreciate any comments. Thank you, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h tml -Original Message- From: Eleni Rapsomaniki [mailto:er...@medschl.cam.ac.uk] Sent: Friday, March 27, 2009 10:44 AM To: Terry Therneau; tuech...@gmx.at; Ravi Varadhan Cc: r-help@r-project.org Subject: RE: RE: Competing risks Kalbfleisch & Prentice method Dear Prof. Therneau, Thank you for your views on this subject. I think all R users who play with survival analysis are most grateful for the functions you have already supplied us with. I'm guessing Ravi is wondering why you have not implemented the smoothing of the baseline hazard from the Cox model. I actually tried to do this originally, inspired from this thread (i.e use sm.spline to smooth the hazard): https://stat.ethz.ch/pipermail/r-help/2004-July/053843.html but it overestimated the CI (perhaps I implemented it wrong). I was then advised to treat CI as a step function, rather than continuous, which means that F(t+1, cause k)-F(t, cause k) will be 0 unless an event of cause k has occurred in that interval (see also "Competing Risks, by Melanie Pintilie, page 62). This is obviously problematic if one wants to estimate the CI at times that are not close to observed events for either cause (perhaps a parametric model could be used in this case). But then again, this was not an issue wtih my data. Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge -Original Message- From: Terry Therneau [mailto:thern...@mayo.edu] Sent: 27 March 2009 13:53 To: Eleni Rapsomaniki; tuech...@gmx.at; Ravi Varadhan Cc: r-help@r-project.org Subject: RE: Competing risks Kalbfleisch & Prentice method Ravi's last note finished with > I am wondering why Terry Therneau's "survival" package doesn't have > this option. The short answer is that there are only so many hours in a day. I've recently moved the code base from an internal Mayo repository to R-forge, one long term goal with this is to broaden the developer base to n>2 (me and Thomas Lumley). A longer statistical answer: I'm not sure if the "this" of Ravi's question is a. smoothed hazards, b. the K&P cumulative incidence or c. the Fine & Gray model. b. I like the CI model and am using it more. We also have local code. The latest version of survival (on rforge, likely in the next default R release) has added simple CI curves to the survfit function. Adding code for survfit on Cox models is on the todo list. But -- this release also fixes up survfit.coxph to handle weighted Cox models and that was on my list for approx 10 years, i.e., don't hold your breath. I don't release something until it also has a set of worked out test cases to add to the 'tests' directory. a. smoothed hazards. For the case at hand I don't see any particular advantage of this. On the other hand, I often would like to display hazard functions instead of CI functions for Cox models; with time dependent covariates I don
[R] R and Sound
Hello, I recently have started to learn about R, and am interested in using it to generate data that would then get used to produce audio. Basically, I am "envisioning" using R to create the data, based on probability functions (and fractal data), which then gets output as a text data file, and then processed by CSound to produce the finished audio. My interests are based on some of the work by Iannis Xenakis of using probability functions to generate various synthesis parameter data. Just curious if anyone has used this method of working with R. Thanks, -- Mae West - "I like restraint, if it doesn't go too far." - http://www.brainyquote.com/quotes/authors/m/mae_west.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Referencing data frames
Hi, How do I use the string content of a string variable to reference a data frame of the same name? I want to do the typical tasks of 1) building a name with a string variable and using the string variable to create a data frame (or any object) whose name is the string value of the variable and 2) pass on a string to a function as a parameter, and then use that string to refer to an existing data frame. Thanks in advance. Payam -- Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 USA +1 805 388 9911 +1 805 388 5948 fax payam.minoo...@meissner.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Referencing data frames
On 12/06/2009 6:00 PM, Payam Minoofar wrote: Hi, How do I use the string content of a string variable to reference a data frame of the same name? I want to do the typical tasks of 1) building a name with a string variable and using the string variable to create a data frame (or any object) whose name is the string value of the variable and 2) pass on a string to a function as a parameter, and then use that string to refer to an existing data frame. Thanks in advance. assign() and get() do the basic bits. They aren't specific to dataframes. Duncan Murdoch Payam -- Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 USA +1 805 388 9911 +1 805 388 5948 fax payam.minoo...@meissner.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fast JSON <-> R converter?
Is there a *fast* converter between JSON and R? I'm aware of the rjson package, but it is implemented in R, and it is too slow for my purposes. TIA! kynn [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fast JSON <-> R converter?
It is not so much that rjson is implemented in R that makes it slow, just that it does not use vectorized operations. The package RJSONIO http://www.omegahat.org/RJSONIO can be used as a drop-in replacement for rjson and was written to be faster (by using vectorized operations) and extensible via S4 methods. (We use R to JSON in the SVGAnnotation, FlashMXML and RGraphicsDevice packages.) D. Kynn Jones wrote: Is there a *fast* converter between JSON and R? I'm aware of the rjson package, but it is implemented in R, and it is too slow for my purposes. TIA! kynn [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Extracting the name of an object
With apologies if I missed the answer in the response given to my previous question. How do I extract the name of an object and assign it to a string variable? For example, I have a dataframe named comnoglyc How do I assign this name to a variable dfname such that print(dfname) returns "comnoglyc"? Thank you very much. Payam [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] formatting numbers along axes as percents for perspective plot
Hello, I'm producing a 3D plot using the persp function. All my values for X, Y, and Z are decimals ranging from 0 to 1. I'd like to be able format the three axes so that the tick values are 0% 20% 40%, etc... instead of just being 0 .2 .4. Does anyone know how to do this? Many thanks, Steve [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting the name of an object
On 12/06/2009 7:53 PM, Payam Minoofar wrote: With apologies if I missed the answer in the response given to my previous question. How do I extract the name of an object and assign it to a string variable? For example, I have a dataframe named comnoglyc How do I assign this name to a variable dfname such that print(dfname) returns "comnoglyc"? Objects don't know their own names, so this isn't possible in general. However, arguments know what expression was passed as their value, which is somewhat similar. For example, the function > f <- function(x) deparse(substitute(x)) uses substitute() to get the expression passed as x and then converts it to a string using deparse: > f(comnoglyc) [1] "comnoglyc" Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] formatting numbers along axes as percents for perspective plot
Have you considered multiplying all values by 100? On Jun 12, 2009, at 7:56 PM, Stephen Samaha wrote: Hello, I'm producing a 3D plot using the persp function. All my values for X, Y, and Z are decimals ranging from 0 to 1. I'd like to be able format the three axes so that the tick values are 0% 20% 40%, etc... instead of just being 0 .2 .4. Does anyone know how to do this? Many thanks, Steve David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Referencing data frames
Hi Payam,
Here's a basic example using pointless
data frames and an otherwise useless
function to illustrate the issues you
want
> ## Fresh R session with nothing yet defined
> foo <- data.frame(matrix(1:12, ncol = 3))
> bar <- data.frame(matrix(101:112, ncol = 3))
>
> objects()
[1] "bar" "foo"
>
> myrbind <- function(names) {
+ df1 <- get(names[1])
+ df2 <- get(names[2])
+ dfrbind <- rbind(df1, df2)
+ dfrbind.name <- paste(names, collapse = ".")
+ assign(dfrbind.name, dfrbind, pos = 1)
+ invisible()
+ }
>
> dfnames <- c("foo", "bar", "baz")
> myrbind(dfnames)
> objects()
[1] "bar" "dfnames" "foo" "foo.bar.baz" "myrbind"
> foo.bar.baz
X1 X2 X3
1 1 5 9
2 2 6 10
3 3 7 11
4 4 8 12
5 101 105 109
6 102 106 110
7 103 107 111
8 104 108 112
>
HTH
Steven McKinney, Ph.D.
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
-Original Message-
From: r-help-boun...@r-project.org on behalf of Payam Minoofar
Sent: Fri 6/12/2009 3:00 PM
To: r-help@r-project.org
Subject: [R] Referencing data frames
Hi,
How do I use the string content of a string variable to reference a data frame
of the same name? I want to do the typical tasks of 1) building a name with a
string variable and using the string variable to create a data frame (or any
object) whose name is the string value of the variable and 2) pass on a string
to a function as a parameter, and then use that string to refer to an existing
data frame.
Thanks in advance.
Payam
--
Payam Minoofar, Ph.D.
Scientist
Meissner Filtration Products
4181 Calle Tesoro
Camarillo, CA 93012
USA
+1 805 388 9911
+1 805 388 5948 fax
payam.minoo...@meissner.com
[[alternative HTML version deleted]]
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[R] Insignificant variable improves AIC (multinom)?
Hi, I am trying to specify a multinomial logit model using the multinom function from the nnet package. Now I add another independent variable and it halves the AIC as given by summary(multinom()). But when I call Anova(multinom()) from the car package, it tells me that this added variable is insignificant (Pr(>Chisq)=0.39). Thus, the improved AIC suggests to keep the variable but the Anova suggests to drop it. I am sure this is due to my lack of understanding of these models but could someone help me out with a pointer what my mistake is? Thanks so much, Werner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sending a function as an argument to C code.
Christophe Genolini wrote: > > > In order to optimize the code, I would like to write myFunc in C. Is it > possible, in the C code, to call a function define in R (dist1 or dist2) > that will be send to myFunc as an argument ? > > Christophe > > You want to read section 5.11: "Evaluating R expressions from C" in the Writing R Extensions manual. Especially look at the lapply2 example. Ian -- View this message in context: http://www.nabble.com/Sending-a-function-as-an-argument-to-C-code.-tp23994631p24008711.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] standard error beta glm
Ricardo Arias Brito wrote: > > Dear All, > > Is posible calculate Std. Error for glm as lm, using > cov(hat beta) = phi * solve(t(X) %*% hat W %*% X)^-1 > on R? Who is hat W and phi output glm? > > y=rpois(20,4) > fit.glm <- glm(y ~ x, family=poisson > summary(fit.glm) > > Fitted to a model glm using constrast contr.sum and need compute > the error standard for last level of the factor. > > best wishes for all, > > Ricardo. > Does sqrt(diag(vcov(fit.glm))) not give you what you need? Ian -- View this message in context: http://www.nabble.com/standard-error-beta-glm-tp23987737p24008764.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-help] how to install own R withour root?
Hi, i had intstalled R in my home directory and i can run the new install R from /path_of_my_home/R/bin/R but when i type R, it runs the system installed older R 2.4 can i just type an R command and it runs my new installed R? Thanks! On Tue, Jun 9, 2009 at 4:00 PM, Paul Hiemstra wrote: > Hi, > > In addition. You can also install everything just in your home drive. Using > the configure script you can change the installation path of all R related > stuff: > > ./configure --prefix=/home/bla/progsandlibs > > The binaries end up in ~/progsandlibs/bin, and the libraries in > ~/progsandlibs/bin. If you use this consistently with all the programs you > install using ./configure and add progsandlibs to you $PATH, you can install > all the software in your home drive with no difference in functionality. > > cheers, > Paul > > > Patrick Connolly wrote: > >> On Tue, 09-Jun-2009 at 11:50AM +0800, Daofeng Li wrote: >> >> |> Dear list members, >> |> |> i am currently want to install Rpy2 in a linux box which has R 2.4.0 >> |> installed >> |> RPy requries R 2.7.0 or above >> |> but i have no root previlleges >> |> so my question is how to install R 2.7.0 on my own directory? >> >> You might as well install R-2.9.0 while you're at it. >> >> |> and replace the system installed R 2.4.0 when i input R command from >> the >> |> bash Shell? >> >> You can download the R-2.9.0.tar.gz to a directory you have access to. >> I'll call it ~/Rhome/ >> >> uncompress the file with tar xvzf R-2.9.0.tar.gz >> and then move to the R-2.9.0 subdirectory that will be created. >> >> In that directory, you'll find a file called INSTALL which will give >> you very simple clear directions. Don't try to make a site-wide >> installation which isn't appropriate in your case. >> >> The executable will be at ~/Rhome/R-2.9.0/bin/R >> >> Assuming you have a ~/bin directory, I find the simplest thing is to >> make a link in that directory to the executable. >> >> Now the part that might be slightly tricky. If you can't get someone >> with root access to remove the R-2.4.0 installation, it's simple >> enough to prevent it clashing with your newer version. Make the name >> of the link in ~/bin/ something slightly different from R, such as RR >> or whatever you fancy. You then start R with that name. >> >> HTH >> >> >> >> >> > > > -- > Drs. Paul Hiemstra > Department of Physical Geography > Faculty of Geosciences > University of Utrecht > Heidelberglaan 2 > P.O. Box 80.115 > 3508 TC Utrecht > Phone: +3130 274 3113 Mon-Tue > Phone: +3130 253 5773 Wed-Fri > http://intamap.geo.uu.nl/~paul > > -- Daofeng Li,PhD Candidate China Agricultural University [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-help] how to install own R withour root?
You need to adjust your PATH environment variable so that the /path_of_my_home/R/bin comes ahead of the system R/bin directory. (Or you can simply remove the system R/bin and substitute your own R/bin. W. From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Daofeng Li [lid...@gmail.com] Sent: 13 June 2009 15:28 To: Paul Hiemstra Cc: r-help@r-project.org Subject: Re: [R] [R-help] how to install own R withour root? Hi, i had intstalled R in my home directory and i can run the new install R from /path_of_my_home/R/bin/R but when i type R, it runs the system installed older R 2.4 can i just type an R command and it runs my new installed R? Thanks! On Tue, Jun 9, 2009 at 4:00 PM, Paul Hiemstra wrote: > Hi, > > In addition. You can also install everything just in your home drive. Using > the configure script you can change the installation path of all R related > stuff: > > ./configure --prefix=/home/bla/progsandlibs > > The binaries end up in ~/progsandlibs/bin, and the libraries in > ~/progsandlibs/bin. If you use this consistently with all the programs you > install using ./configure and add progsandlibs to you $PATH, you can install > all the software in your home drive with no difference in functionality. > > cheers, > Paul > > > Patrick Connolly wrote: > >> On Tue, 09-Jun-2009 at 11:50AM +0800, Daofeng Li wrote: >> >> |> Dear list members, >> |> |> i am currently want to install Rpy2 in a linux box which has R 2.4.0 >> |> installed >> |> RPy requries R 2.7.0 or above >> |> but i have no root previlleges >> |> so my question is how to install R 2.7.0 on my own directory? >> >> You might as well install R-2.9.0 while you're at it. >> >> |> and replace the system installed R 2.4.0 when i input R command from >> the >> |> bash Shell? >> >> You can download the R-2.9.0.tar.gz to a directory you have access to. >> I'll call it ~/Rhome/ >> >> uncompress the file with tar xvzf R-2.9.0.tar.gz >> and then move to the R-2.9.0 subdirectory that will be created. >> >> In that directory, you'll find a file called INSTALL which will give >> you very simple clear directions. Don't try to make a site-wide >> installation which isn't appropriate in your case. >> >> The executable will be at ~/Rhome/R-2.9.0/bin/R >> >> Assuming you have a ~/bin directory, I find the simplest thing is to >> make a link in that directory to the executable. >> >> Now the part that might be slightly tricky. If you can't get someone >> with root access to remove the R-2.4.0 installation, it's simple >> enough to prevent it clashing with your newer version. Make the name >> of the link in ~/bin/ something slightly different from R, such as RR >> or whatever you fancy. You then start R with that name. >> >> HTH >> >> >> >> >> > > > -- > Drs. Paul Hiemstra > Department of Physical Geography > Faculty of Geosciences > University of Utrecht > Heidelberglaan 2 > P.O. Box 80.115 > 3508 TC Utrecht > Phone: +3130 274 3113 Mon-Tue > Phone: +3130 253 5773 Wed-Fri > http://intamap.geo.uu.nl/~paul > > -- Daofeng Li,PhD Candidate China Agricultural University [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
