Re: [R] Response to R across the university
Antony Unwin wrote: . The course itself went very well. We encouraged people to bring their laptops and work in groups. Using JGR as the interface to R helped a lot, as it was easier for people to load their own data and use the help. Of course, JGR is compulsory in Augsburg. Giving everyone a Butterbreze (a local delicacy) halfway through may have contributed to the good humour of the course as well! I apologize for my ignorance, but what is JGR? Tom __ 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] Response to R across the university
JGR (speak 'Jaguar') is a universal and unified Graphical User Interface for R (it actually abbreviates Java Gui for R). see http://stats.math.uni-augsburg.de/JGR/ On Sun, Apr 13, 2008 at 2:51 PM, Tom Backer Johnsen [EMAIL PROTECTED] wrote: Antony Unwin wrote: . The course itself went very well. We encouraged people to bring their laptops and work in groups. Using JGR as the interface to R helped a lot, as it was easier for people to load their own data and use the help. Of course, JGR is compulsory in Augsburg. Giving everyone a Butterbreze (a local delicacy) halfway through may have contributed to the good humour of the course as well! I apologize for my ignorance, but what is JGR? Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- HUANG Ronggui, Wincent Bachelor of Social Work, Fudan University, China Master of sociology, Fudan University, China Ph.D. Candidate, CityU of HK, http://www.cityu.edu.hk/sa/psa_web2006/students/rdegree/huangronggui.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting a data.frame from HTML code
On Sun, Apr 13, 2008 at 12:37 AM, Martin Morgan [EMAIL PROTECTED] wrote:
Hi Ethan --
Use the XML library
library(XML)
url -
'http://www.nascar.com/races/cup/2007/1/data/standings_official.html'
xml - htmlTreeParse(url, useInternal=TRUE)
The previous line retrieves the html and stores it in an internal
represnetation. There are warnings, but I think these are about
ill-formed HTML at nascar.com
A little looking suggests that the data you're after are table data
(element 'td') inside table rows ('tr') inside a 'tbody' element. A
little bit more looking shows that there's a blank line in the table,
at unlucky row 13, I guess.
So what we'd like to do is to extract all 'td' elements from all the
rows but unlucky 13. We do this with an 'xpath' query, which specifies
the path, from the root of the document through the relevant nodes, to
the data that we want. Here's the query and data extraction
q - //tbody/tr[position()!=13]/td
dat - unlist(xpathApply(xml, q, xmlValue))
The '//tbody' says 'find any tbody node somewhere below the current
(i.e., root, at this point in the query) node', '/' says 'immediately
below the current', we have some access to basic logic testing to
subset the nodes we're after. xmlValue extracts the 'value' (text
content, roughly) of the nodes that we've described the path to. This
is a nice weekend hack, relying on the overall structure of the table
and assuming, for instance, that there is only one tbody on the
page. We'd have to work harder during the week.
And then some R to make it into a data frame
df - as.data.frame(t(matrix(dat, 11)))
(11 because we've counted how many columns there are in the table; we
could have discovered this from the document, e.g.,
count(//tbody/tr[1]/td) as the xpath). The columns are all
character, whereas you'd like some to be numeric.
The page at http://www.w3.org/TR/xpath is very helpful for xpath,
especially section 2.5.
Hope that helps,
Martin
Ethan Pew [EMAIL PROTECTED] writes:
Dear all,
I'd like to use R to read in data from the web. I need some help finding an
efficient way to strip the HTML tags and reformat the data as a data.frame
to analyze in R.
I'm currently using readLines() to read in the HTML code and then grep() to
isolate the block of HTML code I want from each page, but this may not be
the best approach.
A short example:
x1 - readLines(
http://www.nascar.com/races/cup/2007/1/data/standings_official.html,n=-1)
grep1 - grep(table,x1,value=FALSE)
grep2 - grep(/table,x1,value=FALSE)
block1 - x1[grep1:grep2]
It seems like there should be a straightforward solution to extract a
data.frame from the HTML code (especially since the data is already
formatted as a table) but I haven't had any luck in my searches so far.
Ultimately I'd like to compile several datasets from multiple webpages and
websites, and I'm optimistic that I can use R to automate the process. If
someone could point me in the right direction, that would be fantastic.
Perhaps, the best way would be to copy the table to a spreadsheet and
then save it as a text file. Afterwards, to insert the data in R, use
read.table.
Paul
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[R] Arrays and functions
Hi, I' am doing a stats project using R to work out the size of a t-test and
wilcoxon test depending on the distribution and sample size. I just can't get
it to work - I want to put my results from the function size() into an array.At
the moment I keep getting the error message:Error in res[distribution, test,
samplesize] - results : subscript out of boundsCan anyone tell me where I'm
going wrong,
please?!size.power.test-function(){k-1000distributions-c(Normal,Uniform)tests-c(t,Wilcoxon)samplesizes-c(10,30,40)res-array(0,c(length(distributions),length(tests),length(samplesizes)))dimnames(res)-list(distributions,tests,samplesizes)for(distribution
in distributions){for(test in tests){for(samplesize in samplesizes){for(i in
1:k){results-size()res[distribution,test,samplesize]-results}output-size.power.testreturn(output)size-function(k=1000,H0=0,mu.true=0,sigma.true=1,alpha=0.05,x1=-sqrt(3),y1=sqrt(3)){distributions-c(Normal,Uniform)tests-c(t,Wil!
coxon)samplesizes-c(10,30,40)reject1-numeric(k)for(distribution in
distributions){for(test in tests){for(samplesize in samplesizes){for(i in
1:k){if(distribution==Normal){#randomly generate data from normal
distribution with true
meandat-rnorm(n=samplesize,mean=mu.true,sd=sigma.true)}else{#randomly generate
data from a uniform
distributiondat-runif(samplesize,min=x1,max=y1)}if(test==t){#perform a
t-test on sampleres-t.test(dat,alternative=two.sided,mu=H0)#record if
p-value is less than alphareject1[i]-(res$p.value=alpha)}else{#perform a
wilcoxon-test on
sampleres-wilcox.test(dat,alternative=two.sided,mu=H0)#record if p-value is
less than
alphareject1[i]-(res$p.value=alpha)}}output-list(sum(reject1)/k)return(output)
A prize an hour, 24 hours a day. Try Big Snap now!
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Re: [R] Skipping specified rows in scan or read.table
On Wed, Apr 9, 2008 at 7:37 PM, Ravi Varadhan [EMAIL PROTECTED] wrote: I have a data file, certain lines of which are character fields. I would like to skip these rows, and read the data file as a numeric data frame. I know that I can skip lines at the beginning with read.table and scan, but is there a way to skip a specified sequence of lines (e.g., 1, 2, 10, 11, 19, 20, 28, 29, etc.) ? If I read the entire data file, and then delete the character fields, the values are still kept as factors, with each value denoted by its level. Since, I have continuous variables, there are as many levels as there are values. I am unable to coerce this to numeric mode. Is there a way to do this so that I can then manipulate the numeric data frame? Read the entire data file to the data frame mydata, and then delete the character fields. Afterwards, mydata - edit(mydata) and, inside edit, coerce the columns that you want to numeric. Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Arrays and functions
Hi, I' am doing a stats project using R to work out the size of a t-test and
wilcoxon test depending on the distribution and sample size. I just can't get
it to work - I want to put my results from the function size() into an array.At
the moment I keep getting the error message:Error in res[distribution, test,
samplesize] - results : subscript out of boundsCan anyone tell me where I'm
going wrong,
please?!size.power.test-function(){k-1000distributions-c(Normal,Uniform)tests-c(t,Wilcoxon)samplesizes-c(10,30,40)res-array(0,c(length(distributions),length(tests),length(samplesizes)))dimnames(res)-list(distributions,tests,samplesizes)for(distribution
in distributions){for(test in tests){for(samplesize in samplesizes){for(i in
1:k){results-size()res[distribution,test,samplesize]-results}output-size.power.testreturn(output)size-function(k=1000,H0=0,mu.true=0,sigma.true=1,alpha=0.05,x1=-sqrt(3),y1=sqrt(3)){distributions-c(Normal,Uniform)tests-c(t,Wil!
coxon)samplesizes-c(10,30,40)reject1-numeric(k)for(distribution in
distributions){for(test in tests){for(samplesize in samplesizes){for(i in
1:k){if(distribution==Normal){#randomly generate data from normal
distribution with true
meandat-rnorm(n=samplesize,mean=mu.true,sd=sigma.true)}else{#randomly generate
data from a uniform
distributiondat-runif(samplesize,min=x1,max=y1)}if(test==t){#perform a
t-test on sampleres-t.test(dat,alternative=two.sided,mu=H0)#record if
p-value is less than alphareject1[i]-(res$p.value=alpha)}else{#perform a
wilcoxon-test on
sampleres-wilcox.test(dat,alternative=two.sided,mu=H0)#record if p-value is
less than
alphareject1[i]-(res$p.value=alpha)}}output-list(sum(reject1)/k)return(output)
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Re: [R] Arrays and functions
On 13-Apr-08 08:43:33, Louisa Hay wrote:
Hi,
I' am doing a stats project using R to work out the size
of a t-test and wilcoxon test depending on the distribution
and sample size.
I just can't get it to work - I want to put my results from
the function size() into an array.
At the moment I keep getting the error message:
Error in res[distribution, test, samplesize] - results :
subscript out of bounds
Can anyone tell me where I'm going wrong,please?!
You have created a 3-dimensional array 'res' with
dimensions 2x2x3.
Apart from anything else, when you make the assignment
res[distribution,test,samplesize]-results
the first value of 'samplesize' you use will be 10.
There is no array element with 3rd index equal to 10
(the maximum possible is 3). Hence (I suspect) your
error message.
I would recommend re-writing your code so that you use
the numbers of elements in each of your vectors
'distributions', 'tests' and 'samplesizes' to set the
ranges in your 'for' loops.
For example:
Ndist-length(distributions)
Ntest-length(tests)
Nsamp-length(samplesizes)
and then you can do, for instance,
for(idist in (1:Ndist)){
for(itest in (1:Ntest)){
for(isamp in (1:Nsamp)){
for(i in (1:k)){
results-size()
res[idist,itest,isamp]-results
}
}
}
}
I also suspect that there are a lot of other things in
your code which could do with looking at too, but at
least the above approach should get you past the subscript
out of bounds problem!
Best wishes,
Ted.
size.power.test-function(){
k-1000
distributions-c(Normal,Uniform)
tests-c(t,Wilcoxon)
samplesizes-c(10,30,40)
res-array(0,c(length(distributions),
length(tests),
length(samplesizes))
)
dimnames(res)-list(distributions,tests,samplesizes)
for(distribution in distributions){
for(test in tests){
for(samplesize in samplesizes){
for(i in 1:k){
results-size()
res[distribution,test,samplesize]-results
}
output-size.power.test
return(output)
}
}
}
}
size-function(k=1000,H0=0,mu.true=0,
sigma.true=1,alpha=0.05,
x1=-sqrt(3),y1=sqrt(3)){
distributions-c(Normal,Uniform)
tests-c(t,Wilcoxon)
samplesizes-c(10,30,40)
reject1-numeric(k)
for(distribution in distributions){
for(test in tests){
for(samplesize in samplesizes){
for(i in 1:k){
if(distribution==Normal){
#randomly generate data from normal distribution
#with true mean
dat-rnorm(n=samplesize,mean=mu.true,sd=sigma.true)
}else{
#randomly generate data from a uniform distribution
dat-runif(samplesize,min=x1,max=y1)
}
if(test==t){
#perform a t-test on sample
res-t.test(dat,alternative=two.sided,mu=H0)
#record if p-value is less than alpha
reject1[i]-(res$p.value=alpha)
}else{
#perform a wilcoxon-test on sample
res-wilcox.test(dat,alternative=two.sided,mu=H0)
#record if p-value is less than alpha
reject1[i]-(res$p.value=alpha)
}
}
output-list(sum(reject1)/k)
return(output)
}
}
}
}
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E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 13-Apr-08 Time: 10:23:11
-- XFMail --
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[R] R help for PMML models
Hi List, What would be the syntax for outputting a linear regression model and /or a logistic regression model to PMML . Regards, Ajay www.decisionstats.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] R help for PMML models
What would be the syntax for outputting a linear regression model and /or a logistic regression model to PMML . There is a pmml.lm method in the pmml package (on CRAN). I have improved code for that (and a pmml.glm) based on a student (Ashraf Fouadi) traineeship I supervised. It is planned to contribute this to the pmml package, but if this is urgent I can send it in a private message. Kind regards, Tobias www.decisionstats.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.
Re: [R] lm() of one matrix against another
Thanks for both replies, here is the cleaner version,
n-5
N-10
data.x-matrix(1:(n*N),ncol=n)
data.y-matrix(1:(n*N) + rnorm(n*N,sd=1),ncol=n)
matplot(data.x,data.y,t=p,pch=1:n,bty=n)
mapply(function(x,y){res - lm(y~x) ; lines(x,predict(res)) ; res} ,
as.data.frame(data.x),as.data.frame(data.y),SIMPLIFY=F)
Out of curiosity, I'm not sure if one could get the lines colored
corresponding to their index within mapply (or any function of the
apply family for that matter). Is there a special trick to refer to
the index under evaluation?
Thanks again,
baptiste
On 12 Apr 2008, at 20:08, Henrique Dallazuanna wrote:
Try
mapply(function(x,y)lm(y~x),as.data
.frame(data.x),as.data.frame(data.y),SIMPLIFY=F)
2008/4/12, baptiste Auguié [EMAIL PROTECTED]:
Hello R list,
I have two matrices of identical dimensions, and I want to fit a
straight line for each pair of columns and plot the resulting lines.
I got it to work with a for loop, but there must be a better way,
n-5
N-10
data.x-matrix(1:(n*N),ncol=n)
data.y-matrix(1:(n*N) + rnorm(n*N,sd=1),ncol=n)
matplot(data.x,data.y,t=p,pch=1:n,bty=n)
for (ii in 1:n)
{
test - lm(y~x,data=list(x=data.x[,ii],y=data.y[,ii]) )
lines(data.x[,ii],test$coefficients[1] + test$coefficients[2] *
data.x[,ii],lty=2,col=ii)
}
Thanks,
baptiste
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
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25° 25' 40 S 49° 16' 22 O
_
Baptiste Auguié
Physics Department
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
http://projects.ex.ac.uk/atto
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[R] getGraphicsEvent plotting two graph
Hi the list,
I need to use getGraphicsEvent to plot two graph. On the following toy
example:
- the function b is ploting two graph depending on a parameter
- the function a is calling b according to some user answers. It is
suppose to call b until the user press Return, but it does not.
b - function(x){
dev.off(2);dev.off(3)
windows();windows(3,3,xpos=0)
dev.set(2);plot(1:x)
dev.set(3);plot(1:x^2)
return(NULL)
}
b(2)
a - function(y){
b(y)
getGraphicsEvent(Arrow Up or Return,
onKeybd=function(key){
if(key!=ctrl-J){
if(key==Up){y - y+1}else{}
b(y)
cat(\n*** This function a never gets here... ***\n)
return(NULL)
}else{
return(TRUE)
}
}
)
}
a(3)
Is there something wrong in my code, or something I did not understand
in getGraphicsEvent ?
I try on R 2.2.1, then on R 2.7
Thanks for your help.
Christophe
Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
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Re: [R] Computing time when calling C functions - why does an extra function call induce such an overhead?
I've not seen any reposnse to this, probably because
-- this is not the list for C programming questions (use R-devel)
-- there is no example provided for the times quoted.
-- the code is not compilable.
But I got a compiler warning on
int *ipiv = (int *) R_alloc((int) nrA, sizeof(int));
foo.c:8: warning: cast from pointer to integer of different size
(it should be *nrA) and that's most likely your error. (BTW, using
liberal casts like this is just stopping your tools helping you!)
The overhead of C function call is measured in nanosecs on modern systems,
especially to functions in the same compilation unit.
On Thu, 10 Apr 2008, Søren Højsgaard wrote:
Dear list,
I am a little puzzled by computing time in connection with calling C
functions. With the function mysolve1 given below I solve Ax=B, where
the actual matrix operation takes place in mysolve2. Doing this 5000
times takes 3.51 secs. However, if I move the actual matrix inversion
part into mysolve1 (by uncommenting the two commented lines and skip the
call to mysolve2) then the computations take only 0.03 secs. Can anyone
tell me why there is such a time-overhead in introducing the extra
function call to mysolve2?
I am on windows XP using R 2.6.1
Best regards
Søren
SEXP mysolve1(SEXP Ain, SEXP Bin, SEXP tolin)
{
int *Adims, *Bdims;
double tol = asReal(tolin);
SEXP A, B;
PROTECT(A = duplicate(Ain));
PROTECT(B = duplicate(Bin));
Adims = INTEGER(coerceVector(getAttrib(A, R_DimSymbol), INTSXP));
Bdims = INTEGER(coerceVector(getAttrib(B, R_DimSymbol), INTSXP));
int nrA, ncB;
double *Ap, *Bp;
nrA = Adims[0];
ncB = Bdims[1];
Ap = REAL(A);
Bp = REAL(B);
/* int info, *ipiv = (int *) R_alloc(nrA, sizeof(int)); */
/* F77_CALL(dgesv)(nrA, ncB, Ap, nrA, ipiv, Bp, nrA, info); */
mysolve2(Ap, nrA, Bp, ncB, tol);
UNPROTECT(2);
return B;
}
void mysolve2(double *A, int *nrA, double *B, int *ncB, double *tolin)
{
int info;
int *ipiv = (int *) R_alloc((int) nrA, sizeof(int));
F77_CALL(dgesv)(nrA, ncB, A, nrA, ipiv, B, nrA, info);
}
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Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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[R] .Rprofile, date tagging history, loading packages
Dear R-Helpers,
I'm fiddling with my .Rprofile in Windows XP R 2.7.0 Beta. I prefer to
manually save my workspace but automatically save my command history via
the .Rprofile. That is working fine once I found that utils:: was
required before the loadhistory savehistory functions. What I would
like to do is add a separator line with a date between the histories of
each session. Something like,
=History for Sun Apr 13 09:43:50 2008
Is this possible? I have it print the date at startup, but that doesn't
appear as part of the history.
Also, I'm loading two packages at startup, which is working fine with
this code:
local({
myOriginal - getOption(defaultPackages)
myAutoLoads - c(Hmisc,ggplot2)
myBoth - c(myOriginal,myAutoLoads)
options(defaultPackages = myBoth)
})
But when reading AITR, I noticed it has a .Rprofile example that looks
much simpler. It just loads the one additional package without checking
the defaultPackages. Is this just as good? Does it even need to be in
the .First function definition, or could it simply be a command by
itself in .Rprofile?
.First - function() {
options(prompt=$ , continue=+\t) # $ is the prompt
options(digits=5, length=999) # custom numbers and printout
x11() # for graphics
par(pch = +) # plotting character
source(file.path(Sys.getenv(HOME), R, mystuff.R))
# my personal functions
library(MASS) # attach a package
}
Thanks,
Bob
My whole .Rprofile:
# Startup Settings
# Place any R commands below.
options(width=64, digits=5, show.signif.stars=TRUE)
set.seed(1234)
setwd(/myRfolder)
myPackages - c(car,foreign,hexbin,
ggplot2,gmodels,gplots, Hmisc,
lattice, reshape,ggplot2,Rcmdr)
utils::loadhistory(file = myCumulative.Rhistory)
# Load packages automatically below.
local({
myOriginal - getOption(defaultPackages)
# Edit next line to include your favorites.
myAutoLoads - c(Hmisc,ggplot2)
myBoth - c(myOriginal,myAutoLoads)
options(defaultPackages = myBoth)
})
# Things put here are done first.
.First - function()
{
cat(\n Welcome to R!)
cat(\n , paste(date()), \n\n )
}
# Things put here are done last.
.Last - function()
{
graphics.off()
cat(\n\n myCumulative.Rhistory has been saved on ,paste(date())
)
cat(\n\n Goodbye!\n\n)
utils::savehistory(file=myCumulative.Rhistory)
}
=
Bob Muenchen (pronounced Min'-chen), Manager
Statistical Consulting Center
U of TN Office of Information Technology
200 Stokely Management Center, Knoxville, TN 37996-0520
Voice: (865) 974-5230
FAX: (865) 974-4810
Email: [EMAIL PROTECTED]
Web: http://oit.utk.edu/scc,
News: http://listserv.utk.edu/archives/statnews.html
=
__
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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] .Rprofile, date tagging history, loading packages
Muenchen, Robert A (Bob) wrote:
Dear R-Helpers,
I'm fiddling with my .Rprofile in Windows XP R 2.7.0 Beta. I prefer to
manually save my workspace but automatically save my command history via
the .Rprofile. That is working fine once I found that utils:: was
required before the loadhistory savehistory functions. What I would
like to do is add a separator line with a date between the histories of
each session. Something like,
=History for Sun Apr 13 09:43:50 2008
Is this possible? I have it print the date at startup, but that doesn't
appear as part of the history.
See ?timestamp. I think it does what you want.
I don't know the relative merits of the two methods below; I suspect
they're all pretty much equivalent (but watch out for things like search
order, and which functions are available at which time.)
Duncan Murdoch
Also, I'm loading two packages at startup, which is working fine with
this code:
local({
myOriginal - getOption(defaultPackages)
myAutoLoads - c(Hmisc,ggplot2)
myBoth - c(myOriginal,myAutoLoads)
options(defaultPackages = myBoth)
})
But when reading AITR, I noticed it has a .Rprofile example that looks
much simpler. It just loads the one additional package without checking
the defaultPackages. Is this just as good? Does it even need to be in
the .First function definition, or could it simply be a command by
itself in .Rprofile?
.First - function() {
options(prompt=$ , continue=+\t) # $ is the prompt
options(digits=5, length=999) # custom numbers and printout
x11() # for graphics
par(pch = +) # plotting character
source(file.path(Sys.getenv(HOME), R, mystuff.R))
# my personal functions
library(MASS) # attach a package
}
Thanks,
Bob
My whole .Rprofile:
# Startup Settings
# Place any R commands below.
options(width=64, digits=5, show.signif.stars=TRUE)
set.seed(1234)
setwd(/myRfolder)
myPackages - c(car,foreign,hexbin,
ggplot2,gmodels,gplots, Hmisc,
lattice, reshape,ggplot2,Rcmdr)
utils::loadhistory(file = myCumulative.Rhistory)
# Load packages automatically below.
local({
myOriginal - getOption(defaultPackages)
# Edit next line to include your favorites.
myAutoLoads - c(Hmisc,ggplot2)
myBoth - c(myOriginal,myAutoLoads)
options(defaultPackages = myBoth)
})
# Things put here are done first.
.First - function()
{
cat(\n Welcome to R!)
cat(\n , paste(date()), \n\n )
}
# Things put here are done last.
.Last - function()
{
graphics.off()
cat(\n\n myCumulative.Rhistory has been saved on ,paste(date())
)
cat(\n\n Goodbye!\n\n)
utils::savehistory(file=myCumulative.Rhistory)
}
=
Bob Muenchen (pronounced Min'-chen), Manager
Statistical Consulting Center
U of TN Office of Information Technology
200 Stokely Management Center, Knoxville, TN 37996-0520
Voice: (865) 974-5230
FAX: (865) 974-4810
Email: [EMAIL PROTECTED]
Web: http://oit.utk.edu/scc,
News: http://listserv.utk.edu/archives/statnews.html
=
__
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Response to R across the university
http://stats.math.uni-augsburg.de/JGR/ Obviously a shameless product plug :) --- Tom Backer Johnsen [EMAIL PROTECTED] wrote: Antony Unwin wrote: . The course itself went very well. We encouraged people to bring their laptops and work in groups. Using JGR as the interface to R helped a lot, as it was easier for people to load their own data and use the help. Of course, JGR is compulsory in Augsburg. Giving everyone a Butterbreze (a local delicacy) halfway through may have contributed to the good humour of the course as well! I apologize for my ignorance, but what is JGR? Tom __ 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] R project
Hi,I am currently doing a project in which we are to investigate the size and
power of three different one sample tests over three different distributions
using a number of different sample sizes and values for mu1. I have written a
function and was trying to get my answer for each test into the right position
in an array so the output is the power of each combination of test,
distribution, sample size and mu1, however my code is not working and i keep
getting an error message returned. My code is:
proj1.sim-function(){
tests-c(t,Wilcoxon,bootstrap)
distns-c(Normal,Uniform,Beta)
sample.sizes-c(5,10,25,50,100)
mu1s-c(0,0.5,1,1.5,2)
res-array(0,c(length(tests),length(distns),length(sample.sizes),length(mu1s)))
dimnames(res)-list(tests,distns,sample.sizes,mu1s)
for(test in tests){
for(distn in distns){
for(sample.size in sample.sizes){
for(mu1 in mu1s){
result-hypoth.test(sample.size,distn,test,mu1)
res[test,distn,sample.size,mu1]-result
output(res)
}
hypoth.test-function(sample.size,distn,test,mu1){
#Purpose:
#Samples n values from the chosen distribution
#Inputs:
#n - sample size of data to generate
#distn - the distribution to generate data from
#test - which test to use
#H0 - the null hypothesis
#mu.true - the true value of the mean under the chosen distribution
#sigma.true - the true value of the variance under the chosen distribution
#alpha - trimming level
#K - number of simulations to perform
#Outputs:
#reject.null - the number of times we reject the null hypothesis
H0-0
alpha-0.05
K-1100
sigma-1
#create vectors for the results
reject-numeric(K)
mu1-numeric(5)
sample.size-numeric(5)
#loop through the observations the required number of K simulations
for(i in 1:K){
#determine whether the data comes from a Normal or Uniform distribution
if(distn==Normal){
#Normal distribution
dat-rnorm(n=sample.size,mean=mu1,sd=sigma)
} else if(distn==Uniform){
dat-runif(n=sample.size,min=-sqrt(3)+mu1, max=sqrt(3)+mu1)
} else {
z-rbeta(n=sample.size,shape1=0.8,shape2=7.2)
dat-((z-0.1)*(sigma/0.1))+H0
}
#determine which test is required to sample the observations
if(test==t){
#t-test
res-t.test(dat,alternative=two.sided,mu=H0)
} else if(test==Wilcoxon){
res-wilcox.test(dat,alternative=two.sided,mu=H0)
} else {
nboot-(K-1)
n-length(dat)
bootmean-NULL
for(i in 1:nboot){
rdata-sample(dat,n,replace=T)
bootmean[i]-mean(rdata)
}
nlo-round((nboot+1)*(alpha/2))
nhi-round((nboot+1)*((1-alpha)/2))
bootmean-sort(bootmean)
low-bootmean[nlo]
high-bootmean[nhi]
res-c(low,high)
}
#record whether we reject the null or not i.e. whether the p-value is less
#than or equal to the given alpha level(reject), or not (do not reject)
if(test==bootstrap){
reject[i]-(H0low|H0high)
} else {
reject[i]-(res$p.value=alpha)
}
#sum together the total number of null hypothesis rejected
reject.null-sum(reject)
}
power-(reject.null)/K
return(power)
} Would you be able to tell me where I am going wrong? Thanks,Nicola Smith
_
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Matched pairs with two data frames
Hi, I have a frame treat and want to find matched pairs in the data frame control. In the matched (combined) data frame there should be two variables (0/1),indicating the source of the data (treat or control), so that it is possibe to set a filter (extraxt/select data). #Here are the dataframes (my real data frames have many variables) treat - data.frame(age=c(1,1,2,2,2,4), school=c(10,10,20,20,20,11), out1=c(9.5,2.3,3.3,4.1,5.9,4.6)) control - data.frame(age=c(1,1,1,1,3,2), school=c(10,10,10,10,33,20), out2=c(1.1,2,3.5,4.9,5.2,6.5)) print(treat) print(control) matched.data.frame - ?? #Match treat control by age school #My SPSS syntax would be similar to this: MATCH FILES FILE=treat /IN=fromtreat /FILE=control /IN=fromcontrol /BY age school. SELECT IF fromdad AND fromfam. #select data, set filter The /IN= option creates a 0/1 variable that indicates the source of the data The resultand matched data frame should have the following structure: age schoolout1out2 fromtreat fromcontrol 1 10 9.5 1.1 1 1 1 10 2.3 2.0 1 1 4 11 4.6 NA 1 0 3 33 NA 5.2 0 1 I tried which and match, but I failed and was unlucky looking at the help/archive. Merge doesn´t do the job, because it makes all possible matches. Thank´s for any help! Udo Udo KN G Ö I Clinic for Child an Adolescent Psychiatry Philipps University of Marburg / 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] plotting muliple CI ellipses for EB estimates
Dear Samuel, The radius reflect the desired coverage of the ellipse. You should be able to use radius - sqrt(qchisq(.95, 2)), I think. I hope this helps, John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of Sam Field Sent: April-13-08 11:47 AM To: r-help@r-project.org Subject: [R] plotting muliple CI ellipses for EB estimates I have empirical Bayes estimates for slopes and intercepts for a number of subjects and I would like to plot the slopes and intercepts with confidence ellipses. These ellipses would be based on the confidence intervals for the slope and intercepts (forming the major and minor axis of each ellipse), and the correlation in the slope and intercepts. The ellipse function in the car library looks like the way to go, the add= argument would allow me to over-plot. There are three arguments that generate the ellipse. center shape radius Center would be the posterior means for the intercept and slopes. shape would be the posterior covariance matrices (I think) I don't know what I would use for the radius argument however. My guess would be the upper bound of a confidence interval for either the slope or the intercept, but this does not return sensible results. I guess I need to know more about the geometry of ellipse, but if anybody can provide any assistance, I would really appreciate it. thanks! -- Note the new contact information*** Samuel H. Field, Ph.D. Senior Research Investigator CHERP/Division of Internal Medicine - University of Pennsylvania Philadelphia VA Medical Center 3900 Woodland Ave (9 East) Philadelphia, PA 19104 (215) 823-5800 EXT. 6155 (Office) (215) 823-6330 (Fax) __ 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] question about nlminb
Hi Spencer,
Thanks for your email.
Do you have a reference for generating the variance-covariance matrix
from the restricted variance-covariance? Is this a well known
technique?
Regards,
John
On 10/04/2008, Spencer Graves [EMAIL PROTECTED] wrote:
Hi, John:
I just got the following error right after the attempt to use
'rmvnorm'.
Error: could not find function rmvnorm
I tried 'library(mvtnorm)', but the 'rmvnorm' in that package gave me
the following:
Error in rmvnorm(1, mean = c(3, -20, -10, 3, 2), sd = c(0.1, 15, 4, :
unused argument(s) (sd = c(0.1, 15, 4, 0.15, 0.8), cov = c(1, 0.5, 0.5,
0.5, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 1,
0.5, 0.5, 0.5, 0.5, 0.5, 1))
Then I got 87 hits to RSiteSearch(rmvnorm, 'fun').
Regarding, How would I go about getting the entire variance-covariance
matrix?, this is really easy: Just define a 5 x 4 matrix A so the
5-dimensional 'opt' you want is a constant plus A times the 4-dimensional
restricted 'opt'. [Please don't use the same name for two different things
like 'opt' in your function below. Half a century ago, when Fortran was
young, that was very smart programming. Today, it's primary effect it to
make it difficult for mere mortals to understand your code. Use something
like 'opt5' for one and 'opt4' for the other.]
Then
Sig5 = A %*% vcov.nlminb(opt) %*% t(A).
I believe the A matrix you want is as follows:
A = matrix(NA, dim=c(5, 4))
A[1:4, 1:4] - diag(4)
A[5, ] - (-1)
However, since your example was not self contained, I have not tested
this. Hope this helps. Spencer
John Pitchard wrote:
Hi Spencer,
Sorry for not producing code as a worked example.
Here's an example:
==
# setting the seed number
set.seed(0)
# creating a correlation matrix
corr - diag(5)
corr[lower.tri(corr)] - 0.5
corr[upper.tri(corr)] - 0.5
# Data for the minimisation
mat - rmvnorm(1, mean=c(3, -20, -10, 3, 2), sd=c(0.1, 15, 4,
0.15, 0.8), cov=corr)
obj.fun - function(opt, mat) {
opt - c(opt, 1-sum(opt))
LinearComb - mat%*%opt
obj - -min(LinearComb)
obj
}
opt - nlminb(rep(0,4), lower=rep(-3, 4), upper=rep(3, 4), obj.fun,
mat=mat)
opt.x - opt$parameters
opt.x - c(opt.x, 1-sum(opt.x))
# using vcov.nlminb from the MASS library to obtain the covariance matrix
vcov.nlminb(opt)
I have a variance-covariance matrix for 4 of the elements in the
vector but not the last component. How would I go about getting the
entire variance-covariance matrix?
Thanks in advance for any help.
Regards,
John
On 09/04/2008, Spencer Graves [EMAIL PROTECTED] wrote:
Have you considered optimizing over x1 = x[1:(length(x)-1]? You
could feed a wrapper function 'f2(x1, ...)' that computes xFull = c(x1,
1-sum(x1)) and feeds that to your 'fn'.
If this makes sense, great. Else, if my answer is not useful, be so
kind as to PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide
commented, minimal, self-contained, reproducible code.
Spencer
John Pitchard wrote:
Dear All,
I wanted to post some more details about the query I sent to s-news
last
week.
I have a vector with a constraint. The constraint is that the sum of
the
vector must add up to 1 - but not necessarily positive, i.e.
x[n] - 1 -(x[1] + ...+x[n-1])
I perform the optimisation on the vector x such that
x - c(x, 1-sum(x))
In other words,
fn - function(x){
x - c(x, 1 - sum(x))
# other calculations here
}
then feed this into nlminb()
out - nlminb(x, fn)
out.x - out$parameters
out.x - c(out.x, 1 - sum(out.x))
out.x
I would like to calculate standard errors for each of the components
of x.
Is this possible by outputing the Hessian matrix? Furthermore, how
would I
calculate this for the last component (if this is indeed possible)
which has
the restriction (i.e. 1-sum(out.x))?
Any help would be much appreciated.
Regards,
John
[[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.
__
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
Re: [R] Matched pairs with two data frames
Udo Seems you might want merge() HTH ... Peter Alspach -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Udo Sent: Monday, 14 April 2008 6:41 a.m. To: r-help@r-project.org Subject: [R] Matched pairs with two data frames Hi, I have a frame treat and want to find matched pairs in the data frame control. In the matched (combined) data frame there should be two variables (0/1),indicating the source of the data (treat or control), so that it is possibe to set a filter (extraxt/select data). #Here are the dataframes (my real data frames have many variables) treat - data.frame(age=c(1,1,2,2,2,4), school=c(10,10,20,20,20,11), out1=c(9.5,2.3,3.3,4.1,5.9,4.6)) control - data.frame(age=c(1,1,1,1,3,2), school=c(10,10,10,10,33,20), out2=c(1.1,2,3.5,4.9,5.2,6.5)) print(treat) print(control) matched.data.frame - ?? #Match treat control by age school #My SPSS syntax would be similar to this: MATCH FILES FILE=treat /IN=fromtreat /FILE=control /IN=fromcontrol /BY age school. SELECT IF fromdad AND fromfam. #select data, set filter The /IN= option creates a 0/1 variable that indicates the source of the data The resultand matched data frame should have the following structure: age schoolout1out2 fromtreat fromcontrol 1 10 9.5 1.1 1 1 1 10 2.3 2.0 1 1 4 11 4.6 NA 1 0 3 33 NA 5.2 0 1 I tried which and match, but I failed and was unlucky looking at the help/archive. Merge doesn´t do the job, because it makes all possible matches. Thank´s for any help! Udo Udo KN G Ö I Clinic for Child an Adolescent Psychiatry Philipps University of Marburg / 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. The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. __ 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] question about nlminb
It's very well known that if a random vector X has a finite mean
mu and covariance Sig, and Y = A X, then
(1) EY = A %*% mu
and
(2) cov(Y) = A %*% Sig %*% t(X)
= tcrossprod(A %*% Sig, A)
Expression (1) says that mathematical expectation is a linear
operator. Expression (2) follows by application of (1). See any good
reference that discusses expected values. I didn't find a web site with
a 2 minute search, but I would expect to find it in C. R. Rao (1973)
Linear Statistical Inference and Its Application, 2nd ed. (Wiley) and in
many other places.
Best Wishes,
Spencer
John Pitchard wrote:
Hi Spencer,
Thanks for your email.
Do you have a reference for generating the variance-covariance matrix
from the restricted variance-covariance? Is this a well known
technique?
Regards,
John
On 10/04/2008, Spencer Graves [EMAIL PROTECTED] wrote:
Hi, John:
I just got the following error right after the attempt to use
'rmvnorm'.
Error: could not find function rmvnorm
I tried 'library(mvtnorm)', but the 'rmvnorm' in that package gave me
the following:
Error in rmvnorm(1, mean = c(3, -20, -10, 3, 2), sd = c(0.1, 15, 4, :
unused argument(s) (sd = c(0.1, 15, 4, 0.15, 0.8), cov = c(1, 0.5, 0.5,
0.5, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 0.5, 0.5, 1,
0.5, 0.5, 0.5, 0.5, 0.5, 1))
Then I got 87 hits to RSiteSearch(rmvnorm, 'fun').
Regarding, How would I go about getting the entire variance-covariance
matrix?, this is really easy: Just define a 5 x 4 matrix A so the
5-dimensional 'opt' you want is a constant plus A times the 4-dimensional
restricted 'opt'. [Please don't use the same name for two different things
like 'opt' in your function below. Half a century ago, when Fortran was
young, that was very smart programming. Today, it's primary effect it to
make it difficult for mere mortals to understand your code. Use something
like 'opt5' for one and 'opt4' for the other.]
Then
Sig5 = A %*% vcov.nlminb(opt) %*% t(A).
I believe the A matrix you want is as follows:
A = matrix(NA, dim=c(5, 4))
A[1:4, 1:4] - diag(4)
A[5, ] - (-1)
However, since your example was not self contained, I have not tested
this. Hope this helps. Spencer
John Pitchard wrote:
Hi Spencer,
Sorry for not producing code as a worked example.
Here's an example:
==
# setting the seed number
set.seed(0)
# creating a correlation matrix
corr - diag(5)
corr[lower.tri(corr)] - 0.5
corr[upper.tri(corr)] - 0.5
# Data for the minimisation
mat - rmvnorm(1, mean=c(3, -20, -10, 3, 2), sd=c(0.1, 15, 4,
0.15, 0.8), cov=corr)
obj.fun - function(opt, mat) {
opt - c(opt, 1-sum(opt))
LinearComb - mat%*%opt
obj - -min(LinearComb)
obj
}
opt - nlminb(rep(0,4), lower=rep(-3, 4), upper=rep(3, 4), obj.fun,
mat=mat)
opt.x - opt$parameters
opt.x - c(opt.x, 1-sum(opt.x))
# using vcov.nlminb from the MASS library to obtain the covariance matrix
vcov.nlminb(opt)
I have a variance-covariance matrix for 4 of the elements in the
vector but not the last component. How would I go about getting the
entire variance-covariance matrix?
Thanks in advance for any help.
Regards,
John
On 09/04/2008, Spencer Graves [EMAIL PROTECTED] wrote:
Have you considered optimizing over x1 = x[1:(length(x)-1]? You
could feed a wrapper function 'f2(x1, ...)' that computes xFull = c(x1,
1-sum(x1)) and feeds that to your 'fn'.
If this makes sense, great. Else, if my answer is not useful, be so
kind as to PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide
commented, minimal, self-contained, reproducible code.
Spencer
John Pitchard wrote:
Dear All,
I wanted to post some more details about the query I sent to s-news
last
week.
I have a vector with a constraint. The constraint is that the sum of
the
vector must add up to 1 - but not necessarily positive, i.e.
x[n] - 1 -(x[1] + ...+x[n-1])
I perform the optimisation on the vector x such that
x - c(x, 1-sum(x))
In other words,
fn - function(x){
x - c(x, 1 - sum(x))
# other calculations here
}
then feed this into nlminb()
out - nlminb(x, fn)
out.x - out$parameters
out.x - c(out.x, 1 - sum(out.x))
out.x
I would like to calculate standard errors for each of the components
of x.
Is this possible by outputing the Hessian matrix? Furthermore, how
would I
calculate this for the last component (if this is indeed possible)
which has
the restriction (i.e. 1-sum(out.x))?
Any help would be much appreciated.
Regards,
John
[[alternative HTML version deleted]]
Re: [R] nonlinear curve fitting on a torus
Having seen no reply to this, I will offer a couple of comments
that may or may not be useful. Googling for geodesic equation on a
torus produced interesting hits, but RSiteSearch(geodesic equation on
a torus) found nothing. RSiteSearch(torus) returned 33 hits, some of
which referred to a package geozoo.
If you want a solution of a differential equation, you might
consider lsoda {odesolve}. The 'fda' package may also be useful.
To say more, I'd prefer to hear more specifics from you. PLEASE
do read the posting guide http://www.R-project.org/posting-guide.html;
and provide commented, minimal, self-contained, reproducible code.
Doing so can make it much easier for people to understand what you
want. If you provide code that doesn't quite work, someone who is
interested can copy it from your email into R and try things, possibly
generating a solution to your problem. Without a self-contained
example, you restrict the pool of possible respondents to people who
have actually worked with a geodesic equation on a torus -- or to
fools like me who are willing to expose their ignorance commenting on
something we know essentially nothing about.
Hope this helps.
Spencer Graves
Sungsu wrote:
Dear R users.
I have data observed on the surface of a torus, and
am trying to fit the nonlinear regression using
the geodesic equation on a torus. Could anyone give
me a helpful advise on this problem? I would
definitely appreicate your reply.
Sincerely,
SUNGSU KIM
[[alternative HTML version deleted]]
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[R] Assigning to multiple variables
If we have a function that returns 2 or more values (such as dim as applied to a matrix), can we assign these 2 or more values to an equal number of differently named variables in one line? For example, is there any way to do something like this: [NumberRows NumberColumns] - dim(MatrixA) Thanks in advance! Scott __ 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 equivalent of erfcinv in matlab
I am converting some matlab code into R that use inverse of the complementary error function, erfcinv and did not find an equivalent in R, is there such a function in some contributed modules? Thanks. __ 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] Assigning to multiple variables
Normally in R one returns a list and assigns that to a single variable but if you really want to do it here is how: http://tolstoy.newcastle.edu.au/R/help/04/06/1430.html On Sun, Apr 13, 2008 at 4:56 PM, Scott Romans [EMAIL PROTECTED] wrote: If we have a function that returns 2 or more values (such as dim as applied to a matrix), can we assign these 2 or more values to an equal number of differently named variables in one line? For example, is there any way to do something like this: [NumberRows NumberColumns] - dim(MatrixA) Thanks in advance! Scott __ 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] [Fwd: Re: Assigning to multiple variables]
Scott Romans wrote: If we have a function that returns 2 or more values (such as dim as applied to a matrix), can we assign these 2 or more values to an equal number of differently named variables in one line? For example, is there any way to do something like this: [NumberRows NumberColumns] - dim(MatrixA) In that case R returns an object (a vector) with two values where the first is the number of rows and the second is the number of columns. Almost everything in R are objects. So: d - dim(attitude) rows - d[1] rows [1] 30 Tom __ 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] [Fwd: Re: Response to R across the university]
Well, I downloaded the install JGR package for Windows and that seemed to work fine, after the installation I ended up with a modified R window which looked nice and uncluttered. Which I like. Very much. On the other hand, I cannot see how to launch the thing again once I have closed that window. There is supposed to be a launcher somewhere (JGR.exe?), but I have not been able to find it. It does not seem to be part of the installation, nor have I been able to locate it at the JGR site. However, there might be a possible problem on my side, at the moment I am working with a setup for Windows from the local IT department here in Bergen which behaves very strangely (I am going to pull the plug on on that one very soon), but there might possibly be a problem elsewhere. Would it be possible for someone to check? Tom __ 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 equivalent of erfcinv in matlab
sun wrote: I am converting some matlab code into R that use inverse of the complementary error function, erfcinv and did not find an equivalent in R, is there such a function in some contributed modules? Basically, it is qnorm() with suitable scaling. The help page for Normal has the construction for erfc() from pnorm() so just solve erfc(x) = y for x. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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] Matched pairs with two data frames
Hi Udo, Perhaps merge(treat,control) does what you need. I hope this helps, Jorge On Sun, Apr 13, 2008 at 2:41 PM, Udo [EMAIL PROTECTED] wrote: Hi, I have a frame treat and want to find matched pairs in the data frame control. In the matched (combined) data frame there should be two variables (0/1),indicating the source of the data (treat or control), so that it is possibe to set a filter (extraxt/select data). #Here are the dataframes (my real data frames have many variables) treat - data.frame(age=c(1,1,2,2,2,4), school=c(10,10,20,20,20,11), out1=c(9.5,2.3,3.3,4.1,5.9,4.6)) control - data.frame(age=c(1,1,1,1,3,2), school=c(10,10,10,10,33,20), out2=c(1.1,2,3.5,4.9,5.2,6.5)) print(treat) print(control) matched.data.frame - ?? #Match treat control by age school #My SPSS syntax would be similar to this: MATCH FILES FILE=treat /IN=fromtreat /FILE=control /IN=fromcontrol /BY age school. SELECT IF fromdad AND fromfam. #select data, set filter The /IN= option creates a 0/1 variable that indicates the source of the data The resultand matched data frame should have the following structure: age schoolout1out2 fromtreat fromcontrol 1 10 9.5 1.1 1 1 1 10 2.3 2.0 1 1 4 11 4.6 NA 1 0 3 33 NA 5.2 0 1 I tried which and match, but I failed and was unlucky looking at the help/archive. Merge doesn´t do the job, because it makes all possible matches. Thank´s for any help! Udo Udo KN G Ö I Clinic for Child an Adolescent Psychiatry Philipps University of Marburg / 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. [[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] Calinsky and Harabasz Index for Cluster Determination with Diana in R
Hello all, I have a set of data points, which I have pair distances for. I managed to create dendrogram for this data set using diana() in R, however this only gives me the tree and not the clusters themselves. I am trying to determine clusters using Calinsky and Harabasz Index (CH Index). I, however, cannot find how to accomplish this using R. Is there anyone who could help me with this? I searched R documentation for implementation of CH index and found some things but not the clustering. Thanks a bunch. Sincerely, Arif. __ 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] Mapping file-Legend- from 2 Files/Tables
Hello, Because no one has answered this. I presume that no one knows the soluition. Fortunately, I found the solution: Keyword: merge() -- table1-read.table(Salesman.data) table2-read.table(Employee.data) data-merge(table1, table2, by.x=User_ID, by.y=User_ID) result-data$Name (for example) Thank you. Kind Regards, Edwin Sendjaja Am Samstag, 12. April 2008 19:40:03 schrieb Edwin Sendjaja: Does anyone know how to solve this. I am so desperate. I'd be terribly grateful for any help. Am Samstag, 12. April 2008 05:19:16 schrieb Edwin Sendjaja: Hello, I have got 2 Tables from different files: Table 1 (lets say file: Salesman.data) | ID | User_ID --- 1| 1 | 4 2| 2 | 6 3| 3 | 7 4| 4 | 2 5| 5 | 3 Table2 (file: Employee.data) -- | User_ID | Name -- 1| 1 | Donna 2| 2 | John 3| 3 | Michael 4| 4 | Wolf 5| 5 | Tim 6| 6 | Edward 7| 7 | Shaun What i want do is: I want to map the table 2 into table 1. instead of User_ID I want to use the name of the person which is related to the User_ID. The legend should look like this _ |LEGEND | |-| | -2- John | | -3- Michael | | -4- Wolf | | -6-Edward| | -7- Shaun | -- Does anyone know how I can create such a mapping legend? Is there any good command to do this? I've tried using replace but this is not a good solution. because it replaces only 1 values. Kind Regards, Edwin Sendjaja __ 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-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 equivalent of erfcinv in matlab
Peter Dalgaard wrote: sun wrote: I am converting some matlab code into R that use inverse of the complementary error function, erfcinv and did not find an equivalent in R, is there such a function in some contributed modules? Basically, it is qnorm() with suitable scaling. The help page for Normal has the construction for erfc() from pnorm() so just solve erfc(x) = y for x. Thanks for your quick answer and useful information! But please forgive my ignorance, I do not really know how to solve this inverse function actually. for example, erfc - function(x) 2 * pnorm(x * sqrt(2), lower = FALSE) erfc(0.3) [1] 0.6713732 How do I find 0.3 given 0.6713732? Thanks! __ 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 equivalent of erfcinv in matlab
At a guess ... erfc - function(x) 2 * pnorm(x * sqrt(2), lower = FALSE) erfcinv - function(x) qnorm(x/2, lower = FALSE)/sqrt(2) erfc(0.3) [1] 0.6713732 erfcinv(erfc(0.3)) [1] 0.3 It may not hurt to include these wrappers in R for matlab refugees. They seem to be coming thick and fast these days. Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of sun Sent: Monday, 14 April 2008 8:50 AM To: [EMAIL PROTECTED] Subject: Re: [R] R equivalent of erfcinv in matlab Peter Dalgaard wrote: sun wrote: I am converting some matlab code into R that use inverse of the complementary error function, erfcinv and did not find an equivalent in R, is there such a function in some contributed modules? Basically, it is qnorm() with suitable scaling. The help page for Normal has the construction for erfc() from pnorm() so just solve erfc(x) = y for x. Thanks for your quick answer and useful information! But please forgive my ignorance, I do not really know how to solve this inverse function actually. for example, erfc - function(x) 2 * pnorm(x * sqrt(2), lower = FALSE) erfc(0.3) [1] 0.6713732 How do I find 0.3 given 0.6713732? Thanks! __ 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] [Fwd: Re: Response to R across the university]
On Sun, Apr 13, 2008 at 11:36 PM, Tom Backer Johnsen [EMAIL PROTECTED] wrote: On the other hand, I cannot see how to launch the thing again once I have closed that window. There is supposed to be a launcher somewhere (JGR.exe?), but I have not been able to find it. It does not seem to be part of the installation, nor have I been able to locate it at the JGR site. To the best of my knowledge, there is no JGR.exe. JGR needs loaded like any R library, via library(). You can set R to automatically load JGR at the beginning of a new session. Simply add library(JGR) JGR() to the Rprofile.site. If missing, create the file within your installation ./etc directory. Regards, Liviu __ 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] [Fwd: Re: Response to R across the university]
Tom, Yes, just re-execute JGR-15.exe (I assume your are on windows downloaded the latest version). Window's explorer search should find it. For convenience, I make a shortcut on my desktop pointing to JGR-xxx.exe. BTW, I do most of my development work in JGR. Thanks to all the Augsburg JGR team!!! On Sun, Apr 13, 2008 at 2:36 PM, Tom Backer Johnsen [EMAIL PROTECTED] wrote: Well, I downloaded the install JGR package for Windows and that seemed to work fine, after the installation I ended up with a modified R window which looked nice and uncluttered. Which I like. Very much. On the other hand, I cannot see how to launch the thing again once I have closed that window. There is supposed to be a launcher somewhere (JGR.exe?), but I have not been able to find it. It does not seem to be part of the installation, nor have I been able to locate it at the JGR site. However, there might be a possible problem on my side, at the moment I am working with a setup for Windows from the local IT department here in Bergen which behaves very strangely (I am going to pull the plug on on that one very soon), but there might possibly be a problem elsewhere. Would it be possible for someone to check? Tom __ 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. -- HTH, Jim Porzak Responsys, Inc. San Francisco, CA http://www.linkedin.com/in/jimporzak [[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 equivalent of erfcinv in matlab
[EMAIL PROTECTED] wrote: At a guess ... erfc - function(x) 2 * pnorm(x * sqrt(2), lower = FALSE) erfcinv - function(x) qnorm(x/2, lower = FALSE)/sqrt(2) erfc(0.3) [1] 0.6713732 erfcinv(erfc(0.3)) [1] 0.3 It may not hurt to include these wrappers in R for matlab refugees. They seem to be coming thick and fast these days. Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ Thanks very much indeed. This solved my problem. I think it will be very helpful to have these wrapper functions at least in some extra packages for the ease of people migrating. __ 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 equivalent of erfcinv in matlab
Bill.Venables at csiro.au writes: At a guess ... erfc - function(x) 2 * pnorm(x * sqrt(2), lower = FALSE) erfcinv - function(x) qnorm(x/2, lower = FALSE)/sqrt(2) erfc(0.3) [1] 0.6713732 erfcinv(erfc(0.3)) [1] 0.3 It may not hurt to include these wrappers in R for matlab refugees. They seem to be coming thick and fast these days. There's a page on the wiki about matlab to R (actually I think it's titled Octave to R -- this could go on there whether or not it gets into base R. I would put it on myself, right now, but the wiki appears to be down? ping wiki.r-project.org PING econum.umh.ac.be (193.190.194.5) 56(84) bytes of data. Ben Bolker __ 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] SQL INSERT using RMySQL
Hi All,
I figured out my problem. There was a combination of lack of
understanding on my part, and a bit of missing functionality. I made
a small patch to the rmysqlWriteTable() function passes the field
names to MySQL corresponding to the data columns passed in:
diff -ru RMySQL.orig/R/MySQLSupport.R RMySQL/R/MySQLSupport.R
--- RMySQL.orig/R/MySQLSupport.R2007-05-31 22:36:02.0 -0400
+++ RMySQL/R/MySQLSupport.R 2008-04-11 17:50:29.0 -0400
@@ -616,7 +616,9 @@
on.exit(unlink(fn), add = TRUE)
sql4 - paste(LOAD DATA LOCAL INFILE ', fn, ',
INTO TABLE , name,
- LINES TERMINATED BY '\n' , sep=)
+ LINES TERMINATED BY '\n' ,
+ ( , paste(names(field.types), collapse=, ),
);,
+ sep=)
rs - try(dbSendQuery(new.con, sql4))
if(inherits(rs, ErrorClass)){
warning(could not load data into table)
I also defined a useful function for describing the structure of an
existing table:
setGeneric(
dbDescribeTable,
function(conn, name, ...)
standardGeneric(dbDescribeTable),
valueClass = character
)
setMethod(
dbDescribeTable,
signature(conn=MySQLConnection, name=character),
def = function(conn, name, ...){
rs - dbGetQuery(conn, paste(describe, name))
fields - rs$Type
names(fields) - rs$Field
if(length(fields)==0)
fields - character()
fields
},
valueClass = character
)
And I now have working code:
## Columns in the table
dbDescribeTable(con, past_purchases)
idcustomer_id item_upc
int(10) unsigned int(11) bigint(12)
suggested quantity total
tinyint(1) int(11) int(11)
on_sale actual_price featured
tinyint(1) double tinyint(1)
date
date
## columns in my data (note the absence of the primary key 'id')
head(fulldata)
customer_iditem_upc suggested quantity total on_sale
1 3 632 FALSE1 1 FALSE
2 3 733 FALSE1 1 FALSE
3 3 1116095 FALSE1 1 FALSE
4 3 1117164 FALSE1 1 FALSE
5 3 1117210 FALSE1 1 FALSE
6 3 1119092 FALSE1 1 FALSE
actual_price featured date
110.49FALSE 2008-03-22
2 4.99FALSE 2008-03-22
3 5.49FALSE 2008-03-22
4 9.99FALSE 2008-03-22
5 4.19FALSE 2008-03-22
6 3.99FALSE 2008-03-22
dim(fulldata)
[1] 75 9
## Size of the table before adding my data
dbGetQuery(con, SELECT COUNT(ID) FROM past_purchases)[1,1]
[1] 675
## Insert the data
dbWriteTable(
+ con,
+ past_purchases,
+ value=fulldata,
+ overwrite=FALSE,
+ append=TRUE,
+ row.names=FALSE #,
+ #field.types=field.types
+ )
[1] TRUE
## Size of the table after adding my data
dbGetQuery(con, SELECT COUNT(ID) FROM past_purchases)[1,1]
[1] 750
-Greg
On Apr 11, 2008, at 10:57PM , Chris Stubben wrote:
Greg,
If you have a MySQL table with an auto_increment field, you could just
insert a NULL value into that column and the database will
increment the key
(it may not work in SQL STRICT mode, I'm not sure). I don't think
there's
any way to specify which columns you want to load data into using
dbWriteTable yet, but that would be a nice feature since LOAD data now
allows that (and SET syntax and other options).
Try this code below - I used cbind(NA, x) to insert a null into the
first
column.
Chris
dbSendQuery(con, create table tmp (id int not null auto_increment
primary
key, a char(1), b char(1)))
MySQLResult:(369,1,67)
x-data.frame( a=letters[1:3], b=letters[4:6])
x
a b
1 a d
2 b e
3 c f
dbWriteTable(con, tmp, cbind(NA, x), row.name=FALSE, append=TRUE)
[1] TRUE
dbWriteTable(con, tmp, cbind(NA, x), row.name=FALSE, append=TRUE)
[1] TRUE
dbReadTable(con, tmp)
id a b
1 1 a d
2 2 b e
3 3 c f
4 4 a d
5 5 b e
6 6 c f
Gregory. R. Warnes wrote:
Hi All,
I've finally gotten around to database access using R. I'm happily
extracting rows from a MySQL database using RMySQL, but am having
problems appending rows to an existing table.
What I *want* to do is to append rows to the table, allowing the
database to automatically generate primary key values. I've only
managed to add rows by using
dbWriteTable( con, past_purchases, newRecords, overwrite=FALSE,
append=TRUE, ...)
And this only appears to properly append rows (as opposed to
overwriting them) IFF
Re: [R] prediction intervals from a mixed-effects models?
On Apr 13, 2008, at 1:41PM , Dieter Menne wrote: Spencer Graves spencer.graves at pdf.com writes: How can I get prediction intervals from a mixed-effects model? Consider the following example: library(nlme) fm3 - lme(distance ~ age*Sex, data = Orthodont, random = ~ 1) df3.1 - with(Orthodont, data.frame(age=seq(5, 20, 5), Subject=rep(Subject[1], 4), Sex=rep(Sex[1], 4))) predict(fm3, df3.1, interval='prediction') # M01 M01 M01 M01 # 22.69012 26.61199 30.53387 34.45574 # NOTE: The 'interval' argument to the 'predict' function was ignored. # It works works for an 'lm' object, but not an 'lme' object. In theory, ci from gmodels should work library(gmodels) ci(df3.1) However, I get an error message. I will forward this to Greg to let him check if I did something stupid. gmodels::ci() will give confidence intervals for the fixed effects via ci(fm3) ci() won't generate prediction intervals for individual parameters, and according to ?predict.lme it won't either. -Greg Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R equivalent of erfcinv in matlab
That's not a bad idea. If the wiki comes up again, please do it. They are so short I wonder that they just can't go in to base R though. It's not particularly matlab terminology, it's engineering and physics terminology pretty widely. See, e.g. Abramowitz and Stegun. For specifcity, here are the four I would suggest. erf - function (x) 2 * pnorm(x * sqrt(2)) - 1 erfc - function (x) 2 * pnorm(x * sqrt(2), lower = FALSE) erfinv - function (x) qnorm((1 + x)/2)/sqrt(2) erfcinv - function (x) qnorm(x/2, lower = FALSE)/sqrt(2) But I don't feel strongly enough about it to push it on R-devel myself right now. I always forget the connexion and it seems to come up when you least expect it. I've just added them to my little horde of useful stuff, so I'm OK now! Bill. Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ben Bolker Sent: Monday, 14 April 2008 11:00 AM To: [EMAIL PROTECTED] Subject: Re: [R] R equivalent of erfcinv in matlab Bill.Venables at csiro.au writes: At a guess ... erfc - function(x) 2 * pnorm(x * sqrt(2), lower = FALSE) erfcinv - function(x) qnorm(x/2, lower = FALSE)/sqrt(2) erfc(0.3) [1] 0.6713732 erfcinv(erfc(0.3)) [1] 0.3 It may not hurt to include these wrappers in R for matlab refugees. They seem to be coming thick and fast these days. There's a page on the wiki about matlab to R (actually I think it's titled Octave to R -- this could go on there whether or not it gets into base R. I would put it on myself, right now, but the wiki appears to be down? ping wiki.r-project.org PING econum.umh.ac.be (193.190.194.5) 56(84) bytes of data. Ben Bolker __ 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] Equivalent to a BY command in SAS
Hi, I'm very new to R and absolutely love it. Does anyone know how to use something in R that functions like a BY command in SAS? For example, let's say you have a variable x, and you want to see the mean. Easy... mean(x) But what if you want to see the mean of x conditional on another discrete variable? My best attempts so far are something like... mean(x, y_cat=1) ...which of course doesn't work. I have downloaded plenty of R user guides that are very informative, but am not seeing much on detailed descriptives or data manipulation (for my life, I can't figure out how to sort an attached data frame, but that's another issue). Thanks. -- View this message in context: http://www.nabble.com/Equivalent-to-a-BY-command-in-SAS-tp16670452p16670452.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] Equivalent to a BY command in SAS
On Sun, Apr 13, 2008 at 7:36 PM, zerfetzen [EMAIL PROTECTED] wrote: Hi, I'm very new to R and absolutely love it. Does anyone know how to use something in R that functions like a BY command in SAS? For example, let's say you have a variable x, and you want to see the mean. Easy... mean(x) But what if you want to see the mean of x conditional on another discrete variable? My best attempts so far are something like... Using the built-in dataset 'CO2' : # compute the mean 'conc' for every level of 'Plant' tapply(CO2$conc, CO2$Plant, FUN=mean) Qn1 Qn2 Qn3 Qc1 Qc3 Qc2 Mn3 Mn2 Mn1 Mc2 Mc3 Mc1 435 435 435 435 435 435 435 435 435 435 435 435 ?tapply for details ?by for more details Dylan mean(x, y_cat=1) ...which of course doesn't work. I have downloaded plenty of R user guides that are very informative, but am not seeing much on detailed descriptives or data manipulation (for my life, I can't figure out how to sort an attached data frame, but that's another issue). Thanks. -- View this message in context: http://www.nabble.com/Equivalent-to-a-BY-command-in-SAS-tp16670452p16670452.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Equivalent to a BY command in SAS
Le dim. 13 avr. à 22:36, zerfetzen a écrit : Hi, I'm very new to R and absolutely love it. Does anyone know how to use something in R that functions like a BY command in SAS? For example, let's say you have a variable x, and you want to see the mean. Easy... mean(x) But what if you want to see the mean of x conditional on another discrete variable? My best attempts so far are something like... mean(x, y_cat=1) ...which of course doesn't work. I have downloaded plenty of R user guides that are very informative, but am not seeing much on detailed descriptives or data manipulation (for my life, I can't figure out how to sort an attached data frame, but that's another issue). Thanks. You didn't give much detail about what exactly you want to do (have a look at the Posting Guide), but... perhaps by() will do what you what. See ?by . Bye! --- Vincent Goulet, Associate Professor École d'actuariat Université Laval, Québec [EMAIL PROTECTED] http://vgoulet.act.ulaval.ca __ 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] looping problem
Hi R-users,
I would like to do looping for this process below to estimate alpha beta from
gamma distribution:
Here are my data:
day_data1 -
123456 789 10 11 12 13 14 15
16 17 18 19 20 21 22 23
1943 48.3 18.5 0.0 0.0 18.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.8 2.8
1944 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 6.6 0.0 0.0 0.0 0.0 0.0 0.0
1945 5.3 0.0 0.0 0.0 0.0 2.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 5.3 0.0 0.0 0.0 0.0 0.0 0.0
1946 0.0 0.0 0.0 0.0 0.0 2.3 0.0 0.0 0.0 0.0 4.8 0.3 1.5 0.0 0.8
0.0 0.0 5.8 70.6 12.4 0.5 23.6 0.0
1947 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
2.0 0.0 0.0 0.0 2.8 0.0 0.0 0.0
1948 0.3 20.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5 0.5 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
## To extract all the positive values
x1 - day_data1[,1]
x2 - day_data1[,2]
x3 - day_data1[,3]
x4 - day_data1[,4]
x5 - day_data1[,5]
tol - 1E-6
a1 - x1[x1tol]
a2 - x2[x2tol]
a3 - x3[x3tol]
a4 - x4[x4tol]
a5 - x5[x5tol]
library(MASS)
## Example January Charleville 1943-2007
fitdistr(a1,dgamma, list(shape = 1, rate = 0.1), lower = 0.01)
fitdistr(a2,dgamma, list(shape = 1, rate = 0.1), lower = 0.01)
fitdistr(a3,dgamma, list(shape = 1, rate = 0.1), lower = 0.01)
fitdistr(a4,dgamma, list(shape = 1, rate = 0.1), lower = 0.01)
fitdistr(a5,dgamma, list(shape = 1, rate = 0.1), lower = 0.01)
Here is my code:
alpha.beta - function(data,n)
{ tol - 1E-6
{ for (i in 1:n)
xi - data[,i]
ai - xi [xi tol]
fit - fitdistr(ai,dgamma, list(shape = 1, rate = 0.1), lower = 0.01)
}
fit
}
I’m not sure what went wrong since it gives only one output by right 31 outputs.
Thank you for your attention.
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Re: [R] Equivalent to a BY command in SAS
On 14/04/2008, at 2:36 PM, zerfetzen wrote:
Hi,
I'm very new to R and absolutely love it. Does anyone know how to use
something in R that functions like a BY command in SAS?
For example, let's say you have a variable x, and you want to see
the mean.
Easy...
mean(x)
But what if you want to see the mean of x conditional on another
discrete
variable? My best attempts so far are something like...
mean(x, y_cat=1)
...which of course doesn't work. I have downloaded plenty of R
user guides
that are very informative, but am not seeing much on detailed
descriptives
or data manipulation (for my life, I can't figure out how to sort an
attached data frame, but that's another issue). Thanks.
set.seed(42)
x - rnorm(100)
y - sample(letters[1:3],100,TRUE)
by(x,y,mean)
INDICES: a
[1] 0.1089523
INDICES: b
[1] -0.2253035
INDICES: c
[1] 0.2997985
Or:
tapply(x,y,mean)
a b c
0.1089523 -0.2253035 0.2997985
cheers,
Rolf Turner
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