Re: [R] Problems with heatmap.2 in the gregmisc package
We're just about to relase a version of gregmisc that improves the code and
documentation so that Rowv=FALSE and/or Colv=FALSE leaves the rows/columns in
the original order.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Sean Davis
Sent: Monday, March 06, 2006 9:25 AM
To: michael watson (IAH-C); r-help
Cc: Warnes, Gregory R
Subject: Re: [R] Problems with heatmap.2 in the gregmisc package
On 3/6/06 9:19 AM, michael watson (IAH-C)
[EMAIL PROTECTED]
wrote:
Hi
Sorry to revisit an old problem, I seemed to solve this in
2004, only
for it to resurface :-S
I am trying to plot a heatmap, and I don't want the columns
of my matrix
re-ordered. The function doesn't seem to behave as the
help would have
you believe:
a - matrix(rnorm(100),nr=20)
a.d - dist(a)
a.hc - hclust(a.d)
a.de - as.dendrogram(a.hc)
# columns are re-ordered
heatmap.2(a, Rowv=a.de, Colv=FALSE)
# columns are re-ordered
heatmap.2(a, Rowv=a.de, Colv=1:5)
# columns are re-ordered
heatmap.2(a, Rowv=a.de, dendrogram=row)
# error
heatmap.2(a, Rowv=a.de, Colv=FALSE, dendrogram=row)
How about:
heatmap.2(a,Rowv=a.de,Colv=1:5,dendrogram=row)
I thought Greg knew about this, but I'm not sure. Have you
updated gregmisc
recently?
Sean
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Re: [R] heatmap.2 in gplots package
Hello Akkineni,
This bug has already been reported and we have a tentative solution that we are
testing. I'll send you a copy of the modified code once we finish testing.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of
Akkineni,Vasundhara
Sent: Wednesday, February 22, 2006 12:09 PM
To: r-help@stat.math.ethz.ch
Subject: [R] heatmap.2 in gplots package
Hello all,
I am using the heatmap.2 function in the gplots package. I
want to supress the reordering of the columns of the data
matrix i pass to the function. I used the statement,
heatmap.2(z,Colv=FALSE,dendrogram=row,col=redgreen(75))
where z, is the matrix of data. The output i want should have
the rows reordered along with the dendrogram and the columns
should be in the original order without any dendrogram. For
the above statement i am getting an error:
Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc),
ylim = 0.5 + :
dimensions of z are not length(x)(+1) times length(y)(+1)
I also tried using ,
heatmap.2(z,Colv=NULL,dendrogram=row,col=redgreen(75))
for which i am getting the output, but the columns are
reordered. How can this be done for the way in which i want
the map to appear?
Thanks,
svakki.
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Re: [R] several plots in one
If you want two series of plotted confidence intervals, first plot one series
using plotCI with the standard arguments, then call plotCI a second time with
add=TRUE. For example:
data(state)
tmp - split(state.area, state.region)
means - sapply(tmp, mean)
stdev - sqrt(sapply(tmp, var))
n - sapply(tmp,length)
ciw - qt(0.975, n) * stdev / sqrt(n)
# First series
plotCI(x=means, uiw=ciw)
# Second series
plotCI(x=means+1e5, uiw=ciw, add=T)
Note that you may need to manually specify xlim and ylim to ensure that the
second series fits on the plot.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of JeeBee
Sent: Wednesday, February 01, 2006 6:02 AM
To: r-help@stat.math.ethz.ch
Subject: [R] several plots in one
Can anyone tell me how I can supply more than one graph to plotCI
(gplots) at once?
Below is what I tried, also with rbind instead of cbind.
What is the way to do this (in general, I think)?
Problem is that lines of 1-st and 2-nd series are mixed,
while they have
nothing to do with each other.
I also tried calling plotCI with argument add=TRUE, which
didn't seem to
work (that is actually what I wanted I think).
(It should look the same as if I called plotCI twice with same
labels/xlim/ylim/etc.)
plotCI(x = cbind(x1,x2),
y = cbind(means1,means2), # means1 == ci1[Estimate,]
xlim = c(0,100), #ylim = c(0.2,0.5),
ylab = System welfare,
pch = 7, col = c(red,blue), type = b,
uiw = cbind(uiw1,uiw2))
Thanks in advance,
JeeBee.
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Re: [R] beginner Q: hashtable or dictionary?
Standard R vectors and list elements can given names, and can be accessed by
them. This allows them to be used like the dictionaries or hashes of other
languages.
For example
x = c(a=1, b=2, c=3)
x[a]
a
1
x[foo] = bar
x[foo]
foo
bar
x
a b c foo
1 2 3 bar
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of context grey
Sent: Sunday, January 29, 2006 8:35 PM
To: r-help@stat.math.ethz.ch
Subject: [R] beginner Q: hashtable or dictionary?
Hi,
Is there something like a hashtable or (python)
dictionary in R/Splus?
(If not, is there a reason why it's not needed /
typical way to accomplish the same thing?)
Thank you
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Re: [R] gplots
The plotmeans() function uses the order of the factor levels. To change the
order in the plot, change the order of the factor levels.
For example:
data(state)
plotmeans(state.area ~ state.region)
Plots the groups in the order
levels(state.region)
levels(state.region)
[1] Northeast South North Central West
You can change the order of the levels using the gdata:::reorder.factor
function:
state.region - reorder.factor(state.region, c(Northeast, North Central,
South West)),
Now, doing
plotmeans(state.area ~ state.region)
will show the plot with the new order.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Stephen
Sent: Monday, January 16, 2006 11:26 AM
To: r-help@stat.math.ethz.ch
Subject: [R] gplots
Hi
I am sure that this question has been asked before ... appologies in
advance
This - which comes out very nicely - better than the commercial stuff.
plotmeans (cdpy~Dodefordpy, Data = Dataset, connect = False,
minbar = 1,
mean.labels = FALSE, col = blue, barwidth = 1.5, barcol = red,
ci.label = FALSE, xlab=Onset, pch = 15, par(las =2)).
Only one snag I want to order the X axis by the way it is
sorted in the
data not by the n size group categories.
The data are sorted by the Dodefordpy categories - not mumeric -
confering to the way I'd like the x axis.
Hence how do I order the x axis not by n but by the way the file is
ordered.
Thanks
S
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major2
minor2.1
year 2005
month12
day 20
svn rev 36812
language R
Nana Mail http://mail.nana.co.il - Get Your Free Personal
Outlook 2003
Now
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Re: [R] Can anyone please tell me how to strip the white spaces f rom a character vector?
If you are interested in trimming leading and trailing whitespace (and not
interior whitespace), you can use the 'trim' function from the 'gdata'
package.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of roger bos
Sent: Tuesday, October 25, 2005 8:52 AM
To: ([EMAIL PROTECTED])
Subject: [R] Can anyone please tell me how to strip the white spaces
from a character vector?
for example:
a$tic[1:10]
[1] AIR ABCB ABXA ACMR ADCT ADEX
[7] ABM AFCE AG ATG
Can anyone please tell me how to strip the white spaces from a$tic?
Thanks,
Roger
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Re: [R] glm contrasts (was: no subject)
estimable in bundle gregmisc (package gmodels) should do this.
(Kiebitzers: Hope I got the bundle/package/library definition correct)
FWIW, we tried gregmisc as a bundle, but it proved to be too much of a pain,
so all of the component packages are now separately provided.
The 'gremgisc' package now simply depends on the individual components.
Thus,
install.package('gregmisc',depend=TRUE)
will get all of the packages.
-Greg
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Re: [R] Problem building/checking library that requires input fro m user
What file are you putting these into?
I believe this is the correct syntax for the \example{} section of an .Rd
file.
If you want to do this in a plain R file, (e.g. package/tests/somename.R),
you can use
if(interactive)
{
num_reps - readline(How many reps do you have... )
num_reps - as.integer(num_reps)
}
else
num_reps - 10
instead.
-G
-Original Message-
From: Ken Termiso [mailto:[EMAIL PROTECTED]
Sent: Monday, October 03, 2005 11:42 AM
To: Warnes, Gregory R; [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Subject: RE: [R] Problem building/checking library that requires input
from user
Thanks, Dr Warnes Prof Ripley...
However, upon following the instructions below, I'm getting
syntax errors on
the line that has \dontshow...below is my code...I get the
same error if i
omit the first block and just try \dontrun...
\dontshow{
num_reps - 10
}
\dontrun{
num_reps - readline(How many reps do you have... )
num_reps - as.integer(num_reps)
}
could this have anything to do with it running on OS X 10.3 ?? (long
shot...but i'm thoroughly lost)..
thanks again,
ken
From: Warnes, Gregory R [EMAIL PROTECTED]
To: 'Ken Termiso' [EMAIL PROTECTED]
Subject: RE: [R] Problem building/checking library that
requires input from
user
Date: Mon, 3 Oct 2005 10:11:15 -0400
Try changing the example code to:
\dontshow{
num_reps - 10
}
\dontrun{
num_reps - readline(How many reps do you have... )
num_reps - as.integer(num_reps)
}
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Ken Termiso
Sent: Monday, October 03, 2005 9:41 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Problem building/checking library that requires
input from
user
Hi all,
I've got a package i've written that i am trying to
check, build, and
install. This is my 1st time doing this, so apologies in
advance... ;)
The package that I've written requires input from the user.
It needs to know
sample sizes and then runs some calcs, (sample sizes are just
integers), and
it gets this info from the user as
num_reps - readline(How many reps do you have... )
num_reps - as.integer(num_reps)
and then loops
for(i in 1:num_reps)
{
#code
}
HOWEVER, I get this error msg when trying to check/build/install:
Error in 1:num_con_biol_reps : NA/NaN argument
Presumably this is because R thinks the variable is never
initialized before
i try to use it as a loop limit...
Anyway around this?? I tried initializing the num_reps
variable in the code
before the readline, but get the same error...
Thanks very much in advance,
Ken
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Re: [R] Advice about system for installing updating all R packa ge in a Linux Lab?
If you have several different versions of R installed, you might want to use
a script like this one, which should work on (at least) 1.9.1 and newer.
script
#!/bin/sh
echo ##
echo ## This script will attempt to install all available R packages
echo ## from the package repositories:
echo ##
echo ## - CRAN: http://cran.r-project.org/;
echo ## - BioCondictor: http://www.bioconductor.org;
echo ##
echo ## As well as Pfizer custom packages
echo ##
echo ## - Rlsf: ~warneg/src/R/Rlsf
echo ## - AffyTool: nlvfs016:rstat-data/
echo ## ExpressionAnalysis/StandardAffyAnalysis/AffyTool
echo ##
echo ##
echo ##
if [ -z '$1' ]; then
RCMD=R
echo ## Parameter 1 : R Command Name = $RCMD (Default)
else
RCMD=$1
echo ## Parameter 1 : R Command Name = $RCMD
fi
export RCMD
echo $RCMD
echo ##
echo ##
echo ##
echo ## Starting R ...
echo ##
$RCMD --vanilla EOF
##
## Update installed packages
##
update.packages (repos =http://cran.r-project.org,ask = FALSE,
installWithVers=TRUE )
##
## Install New Packages from CRAN
##
#
if (exists(new.packages,mode=function))
{
options(repos=http://cran.r-project.org;)
new.list - new.packages(ask=FALSE)
} else
{
CRAN.list - CRAN.packages()[,1]
here.list - installed.packages()[,1]
new.list - CRAN.list[ ! CRAN.list %in% here.list ]
}
install.packages(pkgs=new.list, dependencies=TRUE, installWithVers=TRUE )
##
## Install (New) Bioconductor Packages
##
source(http://www.bioconductor.org/getBioC.R;)
getBioC(groupName=all)
y
EOF
echo ##
echo ## All Done!
echo ##
echo ## *Check the log for failed package installs*
echo ##
echo ##
/script
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Prof
Brian Ripley
Sent: Saturday, August 20, 2005 1:28 AM
To: Paul Johnson
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Advice about system for installing updating all R
package in a Linux Lab?
This is based on the pre-2.1.0 ideas. Try
update.packages(ask=FALSE)
install.packages(new.packages(), dependencies=TRUE)
However, I would suggest that you set up each student with a
library, say
~/R/library, and point R_LIBS at it (set in Renviron.site).
That's what
we do for Windows, and it seems successful. (We have other
reasons to
want very complete central Linux setups, one being that we
run more than
one archtecture where personal libraries are a little harder
to manage.)
On Fri, 19 Aug 2005, Paul Johnson wrote:
Good day:
I'm administering 6 linux systems (FC4) in a student lab
and worry that
users may want packages that are not installed. I get
tired of adding
them one by one. Then I happened upon this page
http://support.stat.ucla.edu/view.php?supportid=30
Many of the commands there are now or about to be deprecated. See my
article in the current R-News.
about installing all R packages from CRAN. That did not
run as it was,
but after some fiddling I arrived at the following script,
which does
run and it builds many packages and reports failures on the rest:
#R_installAll.R
options(repos = http://lib.stat.cmu.edu/R/CRAN/;)
update.packages(ask=F)
x -
packageStatus(repositories=http://cran.r-project.org/src/contrib;)
st - x$avai[Status]
install.packages(rownames(st)[which(st$Status==not installed)],
dependencies=T)
If I run that in batch mode (as root, of course)
R CMD BATCH R_installAll.R
It produces some informative output. Some packages don't
build because
they are for Windows. As Prof Ripley mentioned recently,
some packages
don't build because of gcc-4.0.1. Some fail because I don't
have some
requisite libraries installed. I try to deduce which FC
packages may be
used to fix that and iterate the process now and then.
But, for the most part, the packages to be OK (as far as I
can tell).
The output of a recent update is posted on the net here, in
case you are
interested to see (this lists the ones that don't build plus the
successful updates):
http://lark.cc.ku.edu/~pauljohn/software/R/R_installAll.Rout
I can't see how this does any damage, since the packages that don't
build are very graceful about erasing themselves, and the
ones that do
build are automatically available for the users.
Can you see any downside to scheduling this process to run as a cron
job, say once per week, to keep packages up to date?
None at all. We do something similar (but based on
new.packages and with
a stoplist of packages that we know will not install).
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
[R] Unbundling gregmisc (was: loading gap package)
Let me redirect the topic a bit. I've been considering unbundling gregmisc.
The pro would be that people would find the component packages (i.e. gdata)
more easily. The con is that the packages have a number of
interdependencies, so you pretty much will need to get most of them anyway.
As the latest gregmisc bundle contains a gregmisc package that is just a
stub that depends on and loads the individual packages, there would still be
a gregmisc object.
Comments?
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Constantinos
Antoniou
Sent: Wednesday, May 04, 2005 6:36 AM
To: Prof Brian Ripley
Cc: R-help@stat.math.ethz.ch; Uwe Ligges
Subject: Re: [R] loading gap package
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
=-=-=-=-=
!!! IMPORTANT NOTICE !!!
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If this is legitimate business email, please inform the
sender to address all future correspondence to your
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The original text of this email appears below this notice.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
=-=-=-=-=
On 4 2005, at 12:06 , Prof Brian Ripley wrote:
On Wed, 4 May 2005, Constantinos Antoniou wrote:
On 4 2005, at 11:35 , Uwe Ligges wrote:
Eduwin Pakpahan wrote:
Dear R users, I did install R. 2.0.1, and try to load gap
package. However, below is the message shown when I did load it.
Can anybody
please let me know my mistakes?
library()
library(gap)
Loading required package: MASS Loading required package: genetics
Loading required package: combinat Loading required
package: gdata
Error: package 'gdata' could not be loaded
In addition: Warning message: There is no package called 'gdata'
in: library(pkg, character.only =
TRUE, logical = TRUE, lib.loc = lib.loc)
Let me read the error message for you:
There is no package 'gdata' simply means the package is not
there...
So what about installing it?
Hint: it is part of the package bundle gregmisc.
I have a similar problem with R 2.1.0 on Mac OSX 10.3.9.
library(gregmisc)
Loading required package: gdata
Error: package 'gdata' could not be loaded
In addition: Warning message:
there is no package called 'gdata' in: library(pkg,
character.only =
TRUE, logical = TRUE, lib.loc = lib.loc)
At first I tried getting this gdata from somewhere else,
but I could
not find it (evidence indicated that it is part of the
gregmisc, as I
suspected originally... You email confirms this...)
(For the record, my goal is to get read.xls, which is part (?) of
gdata)
The current version of gregmisc is 2.0.6. That does contain gdata.
It looks to me as if the MacOS X binary is broken (2kb) so you will
need to install from the sources.
Thank you. I had the current version (binary). Reinstalling from
source fixed the issue
Costas
I think we have been here before: it seems the MacOS X binary
packaging does not work for bundles.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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RE: [R] How could I catch the R data-output stream and presented by other software func
There are quite a few packages which allow R to be accessed from other
software systems. Examples include RDCOM (included with Windows R), RSOAP
(http://rsoap.sf.net), Rpy (Python, http://rpy.sf.net), RSPerl
(http://www.omegahat.org/RSPerl/). Duncan Temple Lang, the developer of
RSPerl, has a whole pile of these tools, see http://www.omegahat.org for a
full list.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Michael shen
Sent: Thursday, March 10, 2005 1:37 AM
To: r-help@stat.math.ethz.ch
Subject: [R] How could I catch the R data-output stream and
presented by
other software func
Dear All R-helper,
I wonder to know that could I do the computation staff in R
environment and
get the R data output stream ,then presented by other
software functions in
their GUI.(for example: get the R data output streamand
present the data
using SPSS function in SPSS output GUI). Is there some R
-packages in CRAN
already do this kind of function? and what kind of document
should I read?
Thanks in advance
Michael
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RE: [R] 'combinations' in gtools and stack overflow
The documentation for 'combinations' explicitly describes this problem:
Details:
Caution: The number of combinations and permutations increases
rapidly with 'n' and 'r'!.
To use values of 'n' above about 45, you will need to increase R's
recursion limit. See the 'expression' argument to the 'options'
command for details on how to do this.
and gives an example of the solution:
# To use large 'n', you need to change the default recusion limit
options(expressions=1e5)
cmat - combinations(300,2)
dim(cmat) # 44850 by 2
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Prof
Brian Ripley
Sent: Monday, February 14, 2005 10:23 AM
To: Ho-Joon Lee
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] 'combinations' in gtools and stack overflow
On Mon, 14 Feb 2005, Ho-Joon Lee wrote:
Dear R-users,
Let me ask about the 'stack overflow' error which I got
when I used the
function 'combinations' in gtools.
The following is what I did:
-
library(gtools)
options(expressions=1e5)
combinations(500, 3, 1:500)
# or combinations(400, 2, 1:400)
Error: protect(): stack overflow
-
How can I overcome this error? Is there perhaps any other
function to do this
more efficiently?
R --help lists a flag that you can use to increase the size
of the protect
stack. It is also described in `An Introduction to R'.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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RE: [R] parameter couldn't be set in high-level plot() function
Thanks for your patch, I've modified the code of bandplot appropriately.
This change will be in the next release of the gregmisc bundle.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of R user
Sent: Tuesday, January 25, 2005 1:02 PM
To: r-help@stat.math.ethz.ch
Subject: Re: [R] parameter couldn't be set in high-level
plot() function
Think the problem I had with the bandplot (gplots) function
is solved by
changing the expand.dots = FALSE to expand.dots = TRUE.
Don't understand actually why it says FALSE here, because
that means it
does *not* pass extra arguments to plot.
If I change it to TRUE, my main/xlab/ylab arguments are
passed just like
I wanted.
fragment of bandplot[gplots]
if (!add) {
m - match.call(expand.dots = FALSE)
m$width - m$add - m$sd - m$sd.col - NULL
m$method - m$n - NULL
m[[1]] - as.name(plot)
mf - eval(m, parent.frame())
}
Jonne.
On Mon, 2005-01-24 at 15:50 +0100, R user wrote:
Dear R users,
I am using function bandplot from the gplots package.
To my understanding (viewing the source of bandplot) it calls
function plot (add = FALSE) with the same parameters
(except for a few
removed).
I would like to give extra parameters 'xlab' and 'ylab' to function
bandplot, but, as can be seen below, that raises warnings (and the
labels do not show up at the end).
It does work to call title(... xlab=blah, ylab=foo)
after bandplot
(), but then I have two labels on top of each other, which
is even more
ugly.
Can anyone explain me why this goes wrong?
Thanks in advance,
Jonne.
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--
R user [EMAIL PROTECTED]
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RE: [R] how to call R in delphi?
You can also use SOAP to communicate with R via RSOAP (http://rsoap.sf.net).
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Duncan Murdoch
Sent: Wednesday, January 19, 2005 4:10 AM
To: YiYao_Jiang
Cc: r-help@stat.math.ethz.ch; Jack_Kang; Ivy_Li
Subject: Re: [R] how to call R in delphi?
On Wed, 19 Jan 2005 10:12:07 +0800, YiYao_Jiang
[EMAIL PROTECTED] wrote :
Dear All:
Now I am writing program in delphi , found it is very
convenience to do anova, T-test, F-Test, etc in R , how to
call R in delphi? Thsnks.
Tom referred you to a post about the COM interface.
You can also do some of what you want with direct calls to R.dll. See
the R API: entry points for C code section of the Writing R
Extensions manual. If you're unfamiliar with calling C entries from
Delphi, my web page
http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/
might help, though it is aimed at writing DLLs, rather than using
R.dll.
But that's another option: let R be in charge, and just add some
functions in a DLL written in Delphi.
Duncan Murdoch
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RE: [R] SAS or R software
- Output delivery system (ODS): *Every* piece of SAS output is an
output object that can be captured as
a dataset, rendered in RTF, LaTeX, HTML, PDF, etc. with a relatively
simple mechanism (including graphs)
ods pdf file='mystuff.pdf'';
any sas stuff
ods pdf close;
R now has this ability as well via the sinkplot and textplot commands
provided by the gplots package.
-G
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RE: [R] How to save a complete image of the current state of R ?
Date: Mon, 25 Oct 2004 14:10:15 -0400
MIME-Version: 1.0
X-Mailer: Internet Mail Service (5.5.2654.89)
Content-Type: text/plain; charset=iso-8859-1
It is possible to save all of these items using the save.session and
restore.session functions provided by the 'session' package available from
CRAN.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Andreas Buness
Sent: Friday, October 22, 2004 1:05 PM
To: [EMAIL PROTECTED]
Subject: [R] How to save a complete image of the current state of R ?
Hello,
I like to save the complete state of R, i.e. including
all environments, objects/workspaces, loaded packages etc..
This wish has arisen since I am not able to reproduce
an error which occurs when running R CMD check.
Many thanks for your advice in advance.
Best Regards
Andreas
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RE: [R] Problem with R version 2.0.0 (and patched)
Yes, please provide an example of the data that can lead to the crash.
FWIW, the heatmap.2 function uses only standrd R calls and doesn't use any
external C code. (There isn't any C code in the entire library). So, the
bug is likely to stem from something in base R.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Duncan Murdoch
Sent: Thursday, October 14, 2004 5:01 PM
To: Jean Vidal
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Problem with R version 2.0.0 (and patched)
On Thu, 14 Oct 2004 22:38:34 +0200, Jean Vidal
[EMAIL PROTECTED] wrote :
What I am doing : create a simple correlation matrix on 41
variables, then
plot an heatmap with this program :
library(gplots)
gplots is a package in the gregmisc bundle.
mat-cor(temp.alln,use=pairwise.complete.obs)
I've got no idea what temp.alln is.
... deletions ...
Hope this can help you to track the problem.
Can't track it if I can't reproduce it. Please try to simplify it to
the point where you can post a self-contained example that only uses
base packages. If you can't do that, then send a self-contained
example to the package maintainer of the package containing the code
that crashes. In this case that looks like Greg Warnes
[EMAIL PROTECTED]. It might be an R bug or it
might be a bug in his package; he's in the best position to determine
that.
Duncan Murdoch
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RE: [R] displaying sample size in boxplots
Also note that boxplot.n in the gplots library (part of the gregmisc bundle)
automatically adds the number of observations.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Patrick
Drechsler
Sent: Wednesday, September 29, 2004 1:47 PM
To: [EMAIL PROTECTED]
Subject: Re: [R] displaying sample size in boxplots
Martin Maechler wrote on 29 Sep 2004 17:11:13 MET:
Roger == Roger Bivand [EMAIL PROTECTED]
on Wed, 29 Sep 2004 15:09:17 +0200 (CEST) writes:
[snip]
Roger Perhaps use the names= argument (width can help too):
^^
Indeed!
And that's why -- in the good ol' times when the box plot
was invented
and enhanced, the inventors thought about it.
For that reason there's the 'varwidth = TRUE/FALSE' argument
in boxplot()
Note from help(boxplot) however that the inventors thought
it wiser to make the width proportional to the SQRT of the
sample size rather than the sample.size itself, i.e.,
'varwidth = TRUE' and your proposal are not equivalent.
boxplot(expend~stature, width=sample.size/length(expend),
+ names=paste(levels(stature), , N=,
sample.size, sep=))
Here are the current proposals [for cut paste]:
library(ISwR)
data(energy)
attach(energy)
## 1
boxplot(expend~stature)
sample.size - tapply(expend, stature, length)
ss.ch - paste(N=, sample.size, sep=)
mtext(ss.ch, at=1:length(unique(stature)), line=2, side=1)
## 2 (Roger)
boxplot(expend~stature, width=sample.size/length(expend),
names=paste(levels(stature), , N=, sample.size, sep=))
## 3 (Roger + Martin):
boxplot(expend ~ stature, varwidth= TRUE,
names=paste(levels(stature), , N=, sample.size, sep=))
Thanks for the explanation and the nice summary Martin! I can see
the point you're making about varwidth. I've read that part in
the documentation before but I have to admit that up to now I
didn't see the purpose of this parameter. Although there are
situations were I prefer to see the number in print somewhere on
the plot which I can now easily accomplish with `names'.
Also thanks to Stephano for the pointer to the r-newsletter
article and to Don for showing me how one implements user
defined functions!
Cheers
Patrick
--
For animals, the entire universe has been neatly divided into things
to (a) mate with, (b) eat, (c) run away from, and (d) rocks.
-- (Terry Pratchett, Equal Rites)
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RE: [R] Contrast matrices for nested factors
You should be able to get the behavior you want using the fit.glh() (short
for fit general linear hypothesis) function from the gregmisc/gmodels
package.
-G
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of
Fernando Henrique
Ferraz P. da Rosa
Sent: Monday, September 06, 2004 11:02 PM
To: r-help
Subject: [R] Contrast matrices for nested factors
Hi, I'd like to know if it's possible to specify different
contrast matrices in lm() for a factor that is nested within
another one. This
is useful when we have a model where the nested factor has a different
number of levels, depending on the main factor.
Let me illustrate with an example to make it clearer. Consider
the following data set:
set.seed(1)
y - rnorm(14)
a - factor(c(rep(1,7),rep(2,3),rep(3,4)))
b - factor(c(1,1,1,2,2,3,3,1,1,2,1,1,2,2))
k - factor(c(1,2,3,1,2,1,2,1,2,1,1,2,1,2))
internal - data.frame(y,a,b,k)
Where y is an arbitrary response, a is a main factor, b is a
factor nested within a, and k is the replicate number. It is
easy to see
that depending on the level of a, b has different numbers of
levels. For
instance, when a = 1, we have that b might assume values 1, 2 or 3,
while a = 2 or 3, b might assume only 1 or 2.
I'd like then to use contrasts summing to 0, so I issue:
z - lm(y ~ a + a/b,data=internal,contrasts=list(a=contr.sum,
b=contr.sum))
The problem is, the design matrix is not quite what I
expected.
What happens is, instead of using a different contrast matrix for each
level of a where b is nested, it's using the same contrast matrix for
every b, namely:
contr.sum(3)
[,1] [,2]
110
201
3 -1 -1
So, when a=1, the columns of the design matrix are as
expected.
It sums to 0, because there are levels of b 1, 2 and 3, when a=1. But,
when a=2 or a=3, the same contrast matrix is being used, and then, the
factor effects do not sum to 0. That's obviously because there are no
values for b equal 3, when a != 1, and then the coding that
gets done is
'0' or '1'.
The design matrix lm() is creating is:
model.matrix(z)
(Intercept) a1 a2 a1:b1 a2:b1 a3:b1 a1:b2 a2:b2 a3:b2
11 1 0 1 0 0 0 0 0
21 1 0 1 0 0 0 0 0
31 1 0 1 0 0 0 0 0
41 1 0 0 0 0 1 0 0
51 1 0 0 0 0 1 0 0
61 1 0-1 0 0-1 0 0
71 1 0-1 0 0-1 0 0
81 0 1 0 1 0 0 0 0
91 0 1 0 1 0 0 0 0
10 1 0 1 0 0 0 0 1 0
11 1 -1 -1 0 0 1 0 0 0
12 1 -1 -1 0 0 1 0 0 0
13 1 -1 -1 0 0 0 0 0 1
14 1 -1 -1 0 0 0 0 0 1
What I would like to use is:
(Intercept) a1 a2 a1:b1 a2:b1 a3:b1 a1:b2
11 1 0 1 0 0 0 0 0
21 1 0 1 0 0 0 0 0
31 1 0 1 0 0 0 0 0
41 1 0 0 0 0 1 0 0
51 1 0 0 0 0 1 0 0
61 1 0-1 0 0-1 0 0
71 1 0-1 0 0-1 0 0
81 0 1 0 1 0 0 0 0
91 0 1 0 1 0 0 0 0
10 1 0 1 0-1 0 0 0 0
11 1 -1 -1 0 0 1 0 0 0
12 1 -1 -1 0 0 1 0 0 0
13 1 -1 -1 0 0-1 0 0 0
14 1 -1 -1 0 0-1 0 0 0
(notice that in the second matrix all collumns sum to
0, in the
first they don't).
Thank you,
--
Fernando Henrique Ferraz P. da Rosa
http://www.ime.usp.br/~feferraz
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RE: [R] confidence intervals
You should be able to make small modifications to the ci.lme function
provided in the gregmisc/gmodels package.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Spencer Graves
Sent: Friday, September 03, 2004 11:58 AM
To: [EMAIL PROTECTED]
Cc: Robert Waters; [EMAIL PROTECTED]
Subject: Re: [R] confidence intervals
Hi, Robert:
While it may be difficult to program this in general
(as suggested
by it's position on Doug's To Do list), all the pieces should be
available to support a special script for your specific application.
What fixed and random model(s) interest you most?
hope this helps. spencer graves
Douglas Bates wrote:
Robert Waters wrote:
Dear R users;
Im working with lme and Id like to have an idea of how
can I get CI for the predictions made with the model.
Im not a stats guy but, if Im not wrong, the CIs
should be different if Im predicting a new data point
or a new group. Ive been searching through the web and
in help-lists with no luck. I know this topic had been
asked before but without replies. Can anyone give an
idea of where can I found information about this or
how can I get it from R?
Thanks for any hint
That's not currently implemented in lme. It's on the To
Do list but
it is not very close to the top.
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--
Spencer Graves, PhD, Senior Development Engineer
O: (408)938-4420; mobile: (408)655-4567
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RE: [R] how to add error bar to the data in R?
Alternatively, use the plotCI() function from the gregmisc package.
-G
-Original Message-
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Sent: 9/7/04 5:08 AM
Subject: Re: [R] how to add error bar to the data in R?
Hello,
Use the function xYplot from hmisc package
cheers,
Marta
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[R] [R-pkgs] gregmisc 1.11.2 including read.xls()
Release 1.11.2 of the gregmisc() package of functions is now available on
CRAN at http://cran.r-project.org/src/contrib/Descriptions/gregmisc.html for
both Unix and Windows systems.
The most notable enhancement provided by this release is:
- read.xls(), a function to read Microsoft Excel files by
translating them to csv files via the xls2csv.pl script has
been added. I've also provided Unix and MS-Windows scripts
in R_LIBRARY_DIR/gregmisc/bin which allow you to call
xls2csv directly. The code uses perl libraries which are
included in the package, so perl must be in the execution path.
Other enhancements include:
- Improvements to CrossTable() by Marc Schwartz [EMAIL PROTECTED]
- Improvements to ooplot() by Lodewijk Bonebakker [EMAIL PROTECTED]
- plotCI() and plotmeans() now have improved argument handling.
- The running() function now has an additional parameter `simplify'
which controls whether the returned values are simplified into a
vector/matrix or left as a list.
- A makefile that will download and attempt to install all available
packages from CRAN and Bioconductor is now provided in
$PACKAGE$/gregmisc/tools/
- space() can now space points along the 'y' dimension.
- Fix an error in the permutations code for repeats.allow=T and r2.
Both the bug report and fix are from Elizabeth Purdom
[EMAIL PROTECTED].
- Various fixes for compatibility with R 1.9.X.
See the NEWS and ChangeLog files in the .tar.gz file for additional details.
-Greg
Gregory R. Warnes
Manager, Non-Clinical Statistics
Pfizer Global Research and Development
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RE: [R] Contrasts
Try the fit.contrast() and estimable() functions from my gregmisc package,
or the contrasts() function in Frank Harrell's Design package.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Kimberly Ann
Fernandes
Sent: Monday, May 31, 2004 1:10 PM
To: [EMAIL PROTECTED]
Subject: [R] Contrasts
Hello,
I am trying to figure out how to conduct a t-test on a
specific contrast
for my data. I have four factors in my data and would like
to conduct a
t-test on the average of the data from the first two factors
against the
average of the data on the second two factor (i.e. is the
average of the
first two different from the average of the second two). Is there a
quick way to do this? I found the contrast function, but wasn't sure
how to apply it.
Thank you,
Kim
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[R] [JOB] Toxicogenomics Statistician
Toxicogenomics Statistician
The successful candidate will provide statistical support to nonclinical
areas of RD, especially in the areas of investigative toxicology, safety
biomarkers, and toxicogenomics. The candidate will collaborate with
scientists to plan meaningful experimental studies, statistically analyze
the results of those and other studies, and communicate results. Further,
the candidate will work with programmers to create tools that facilitate
use of advanced statistical methodology by Pfizer scientists.
A minimum of an M.S. - Statistics is required. A PhD - Statistics is
desired. Two years statistical consulting experience, preferably in
pharmaceutical environment using gene expression microarrays, is
required. Experience with other -omics technologies, such as RTPCR,
Protein Mass-Spec, etc, is a strong plus. A Strong science background,
with good working knowledge of biology, chemistry or pharmacology is also
desired. Further, good computational skills in SAS, S-plus or R and good
communication skills (written, oral presentation) are necessary.
Other desirable attributes include:
Several years statistical experience in a scientific environment, with
some pharmaceutical experience
Outstanding communication skills
Ability to balance many projects and clients simultaneously
Works independently, with minimal supervision
Learns new skills quickly
Good team player
Strong statistical knowledge in general linear models, experimental
design, probability, categorical data analysis
Ability to identify and understand relevant scientific literature and
apply knowledge gained from these sources
Ability to identify/develop and apply new quantitative methods as needed
to solve problems in pharmaceutical research
Level will be determined by candidate's background and qualifications.
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[R] [R-pkgs] New package: mcgibbsit, an MCMC run length diagnostic
Package: mcgibbsit
Title: Warnes and Raftery's MCGibbsit MCMC diagnostic
Version: 1.0
Author: Gregory R. Warnes [EMAIL PROTECTED]
Description:
mcgibbsit provides an implementation of Warnes Raftery's MCGibbsit
run-length diagnostic for a set of (not-necessarily independent) MCMC
sampers. It combines the estimate error-bounding approach of Raftery
and Lewis with evaulate between verses within chain approach
of Gelman and Rubin.
Maintainer: Gregory R. Warnes [EMAIL PROTECTED]
License: GPL
Depends: coda
References:
Warnes GR. The Normal Kernel Coupler: An adaptive Markov Chain Monte Carlo
method for efficiently sampling from multi-modal distributions
http://www.analytics.washington.edu/statcomp/projects/mcmc/nkc/, Ph.D.
thesis, Department of Biostatistics, University of Washington,
http://www.biostat.washington.edu/ October 2000. (See Chapter 3, Using
the Normal Kernel Coupler)
Gregory R. Warnes
Manager, Non-Clinical Statistics
Pfizer Global Research and Development
Tel: 860-715-3536
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RE: [R] R apache and PHP
We need to know what kind of error message you are getting before we can be
much help.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Marcello Verona
Sent: Tuesday, April 13, 2004 12:37 PM
To: [EMAIL PROTECTED]
Subject: [R] R apache and PHP
I've developed a web application in PHP and R
my script is
?php
...
exec(R CMD BATCH --silent /home/marcello/R_in/myfile.bat
/home/marcello/R_out/myfile.out);
...
?
This script execute in R batch mode and write the myfile.out.
On Win2000 the similar script is ok, but on linux I've a problem.
I suppose is a permession problem because the same script on
shell run fine
and on Zend debugger (my IDE for php) is also ok.
In this case the owner is marcello , if I run the script by browser
the owner is apache.
I've overwritted all the ownerships of R directory and bin to apache
user but not work.
If a run
exec(ls mydir.txt); is ok (is not a PHP general problem!)
Someone can help me?
Thanks
(and excuse my for my poor english)
Marcello Verona
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[R] Makefile for installing all available packages
Below is a makefile I wrote to download and install all available R packages
from the CRAN and BioConductor package repositories.
The primary advantage of using this makefile instead of R's built-in
install.package() and update.packages() is the creation of a separate
installation log for every package. Further, if make is invoked with '-k',
failure to install a single package will not derail the installation of
other packages.
I hope that this script may be useful to other folks.
-Greg
# Download and install all available R packages from the CRAN and
Bioconductor
# package repositories
#
RCMD ?= R-1.9.0
WGET ?= wget -N -nd -r -A gz -r -l 1 -nv
PACKAGE_FILES = $(wildcard *.gz )
PACKAGE_LOGS = $(addsuffix .log, $(basename $(basename $(PACKAGE_FILES
default: cran bioconductor install
cran:
$(WGET) http://cran.r-project.org/src/contrib/PACKAGES.html;
bioconductor: bioCmain bioCcontrib bioCdata
bioCmain:
$(WGET)
http://www.bioconductor.org/repository/release1.3/package/html/index.html;
bioCcontrib:
$(WGET) http://www.bioconductor.org/contrib/index.html;
bioCdata:
$(WGET) http://www.bioconductor.org/data/metaData.html;
install: $(PACKAGE_LOGS)
%.log: %.tar.gz
$(RCMD) INSTALL $ [EMAIL PROTECTED] 21
mv [EMAIL PROTECTED] $@
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[R] [JOB ADV] Computational Statistician
We've just opened a position for a computational statistician in the
Non-Clinical Statistics group here at Pfizer.
We're looking for someone with strong computational skills in R and SAS,
who is interested in creating real applications. The focus will be on
statistical genetics, but we handle almost every kind of statistics
outside of Phase II and later clinical trials, so there will be plenty of
opportunity to do other things as well.
For further information or to submit an application, please visit
http://pfizer.softshoe.com/cgi-bin/job-show?J_PINDEX=J974700KW.
Thanks,
-Greg
Gregory R. Warnes
Manager, Non-Clinical Statistics
Pfizer Global Research and Development
Tel: 860-715-3536
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[R] [R-pkgs] new version of gregmisc package
gregmisc 0.10.1
---
gregmisc 0.10.1 is now available at ftp://cran.r-project.org/incoming/ and
will move to the regular contributed packages location
(http://cran.r-project.org/src/contrib/PACKAGES.html#gregmisc) as soon as
the CRAN administrators get caught up.
Recent Changes
---
Version 0.10.1
- Fixed bug in textplot() reported by Kevin Wright kevin.d.wright at
pioneer
dot com.
Version 0.10.0
- Now works with and requires R 1.9.0
- Added ooplot() function that mimics Open-Office style plots.
Contributed by Lodewijk Bonebakker [EMAIL PROTECTED]
- Fixed bug in running() that arose when the called function
really needed a minimum number of elements to work on.
- Added several new features to running(), it can now allow sequences
shorter than the requested width to be present at the front, the back,
or on both sides of the full lenth sequences. This allows one to
align the data so that the window is before, after, or around the
indexed point.
- Add enhancements to estimable() provided by Søren Højsgaard
[EMAIL PROTECTED]:
The estimable function now
1) also works on geese and gee objects and
2) can test hypotheses af the forb L * beta = beta0 both as a
single Wald test and row-wise for each row in L.
- Add colorpanel function, which generates a smoothly varying band of
colors over a three color range (lo, mid, high).
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FW: [R] Gregmisc 'running' question
[The new version of gregmisc will be showing up on CRAN shortly.]
-Original Message-
From: Warnes, Gregory R
Sent: Friday, March 26, 2004 6:07 PM
To: 'Sean Davis'
Subject: RE: Quick running question
Hi Sean,
Congratulations, you found a bug!
My running function took an improper shortcut. When allow.fewer=FALSE it
was still passing shorter lists of elements to the called function, and then
overwriting the results for the shorter lists with NAs. I've now corrected
the code to skip evaluation of the function on lists shorter than the
specified length when allow.fewer=FALSE.
I'm attaching the latest version of the gregmisc package with the corrected
code. I've also added a couple of other features while I was mucking
about...
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Don MacQueen
Sent: Friday, March 26, 2004 10:58 AM
To: Sean Davis; r-help
Subject: Re: [R] Gregmisc 'running' question
It says not enough x observations. That's pretty clear.
So ask yourself, what is the minimum number of observations one needs
to do a t test?
Try this to see how many observations t.test was given each time.
running(dat,width=50,fun=function(x) length(x),allow=T)
or this
running(dat,width=50,fun=function(x) cat('x:',x,'\n\n'),allow=T)
-Don
At 9:31 AM -0500 3/26/04, Sean Davis wrote:
Just a quick and probably simple question:
dat - rnorm(500,sd=1+(1:500)/500)
fun - function(x) t.test(x)$p.value
running(dat,width=50,fun=fun,allow=T)
Error in t.test.default(x) : not enough x observations
running(dat,width=50,fun=fun,allow=F)
Error in t.test.default(x) : not enough x observations
fun2 - function(x) mean(x)
running(dat,width=50,fun=fun2,allow=T)
1:1 1:2 1:3 1:4 1:5
1:6
-0.334134613 -0.626595581 -0.368967457 -0.113737178 -0.057448771
0.228643936
1:7 1:8 1:9 1:10 1:11
1:12
-0.058807689 0.021762463 -0.063805657 0.031931121 0.080465708
0.087062800
However, this works fine.
t.test(dat[1:50])$p.value
[1] 0.1661845
Why doesn't t.test work with running here?
Thanks,
Sean
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--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
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[R] Recall: Quick running question
Warnes, Gregory R would like to recall the message, Quick running
question.
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[R] RE: Quick running question
[The new version of gregmisc will be showing up on CRAN shortly.]
-Original Message-
From: Warnes, Gregory R
Sent: Friday, March 26, 2004 6:07 PM
To: 'Sean Davis'
Subject: RE: Quick running question
Hi Sean,
Congratulations, you found a bug!
My running function took an improper shortcut. When
allow.fewer=FALSE it was still passing shorter lists of
elements to the called function, and then overwriting the
results for the shorter lists with NAs. I've now corrected
the code to skip evaluation of the function on lists shorter
than the specified length when allow.fewer=FALSE.
I'm attaching the latest version of the gregmisc package with
the corrected code. I've also added a couple of other
features while I was mucking about...
-Greg
-Original Message-
From: Sean Davis [mailto:[EMAIL PROTECTED]
Sent: Thursday, March 25, 2004 5:25 PM
To: Warnes, Gregory R
Subject: Quick running question
Greg,
I am starting to use running and do the following:
running(1:10,function(h) {t.test(h)},width=5)
Error in t.test.default(h) : not enough x observations
running(1:10,function(h) {t.test(h)},width=5,allow.fewer=T)
Error in t.test.default(h) : not enough x observations
It works fine for mean, median, etc. What am I missing?
Thanks,
Sean
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RE: [R] writing text on graphics' window
Another approach is to use the textplot() function and friends from the
gregmisc library. From ?textplot:
textplot package:gregmisc R Documentation
Display text information in a graphics plot.
Description:
This function displays text output in a graphics window. It is
the equivalent of 'print' except that the output is displayed as a
plot.
-Greg
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Paul Murrell
Sent: Monday, March 22, 2004 7:46 PM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]; Ray Brownrigg
Subject: Re: [R] writing text on graphics' window
Hi
Ray Brownrigg wrote:
From: Duncan Murdoch [EMAIL PROTECTED]
Date: Sun, 21 Mar 2004 06:58:03 -0500
On Sun, 21 Mar 2004 11:07:01 +, you
[EMAIL PROTECTED] wrote:
Does anyone know of a method for writing text to the
graphics window,
where there is *no* plot? Basically, I have developed a
'significance
test' and I would like the output on the graphics window to say
something about the input parameters and the stats of the
significance test.
You need to make sure a graphics device is active and establish a
coordinate system there. The easiest way to do that is to
make a call
to plot() with everything turned off:
plot(0:100,0:100,type='n',axes=FALSE,xlab=,ylab=)
You may also want to reduce the margins if you want your output to
take up the full frame, e.g.
oldmargins - par(mar=c(0,0,0,0))
plot(0:100,0:100,type='n',axes=FALSE,xlab=,ylab=)
An easier way to activate a graphics device and establish a
coordinate
system is to call plot.new().
Try:
plot.new()
text(0, 0, ABC)
par(usr)
[1] -0.04 1.04 -0.04 1.04
The grid package gives you the whole page to play with by default and
gives you more flexibility in how you place the text. Try ...
library(grid)
grid.text(Here's some\ntext, x=unit(1, cm),
y=unit(1, npc) - unit(1, cm),
just=c(left, top))
Paul
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
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[R] xls2csv.pl: Script to translate Excel files into CSV
I've created a Perl script that translates Microsoft Excel (.xls) files into
comma-delimited text files (.csv) using the Perl Spreadsheet::ParseExcel
module.
Usage
-
perl xls2csv.pl excel file [output file] [worksheet number]
Translate the Microsoft Excel spreadsheet file contained in
excel file into comma separated value format (CSV) and store
in output file.
If output file is not specified, the output file will have the
same name as the input file with '.xls' or '.XLS' (if any)
removed and '.csv' appended.
If no worksheet number is given, each worksheet will be written to
a separate file with the name 'output file_worksheet name.csv'.
Dependencies
xls2csv.pl depends on the OLE::Storage-Lite and Spreadsheet::ParseExcel
packages which are available below or from the author's CPAN
http://search.cpan.org/author/KWITKNR/ site.
Where to get it
http://www.analytics.washington.edu/Zope/projects/xls2csv.pl
Contacting the Author
-
The xls2csv.pl script is maintained by Gregory R. Warnes
[EMAIL PROTECTED]
mailto:[EMAIL PROTECTED]. Questions, comments, patches,
etc. are welcome.
-Greg
Gregory R. Warnes
Manager, Non-Clinical Statistics
Pfizer Global Research and Development
Tel: 860-715-3536
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[R] [R-pkgs] FW: Announce: RPy version 0.3.3
-Original Message-
From: Warnes, Gregory R
Sent: Friday, January 16, 2004 3:52 AM
To: 'r-packages'; 'python-announce '; 'rsoap-talk'; 'Dan Nathan'; 'RPy
List'
Subject: Announce: RPy version 0.3.3
RPy Version 0.3.3 is now available from the RPy home page at
http://rpy.sf.net.
What is RPy?
RPy is a very simple, yet robust, Python (http://www.python.org) interface
to the R environment for statistical data analysis and graphics
(http://www.r-project.org). RPy can manages translation between python
and R formats for all kinds of R objects and can execute arbitrary R
functions (including the graphic functions). All errors from the R
language are converted to proper Python exceptions. All module installed
on the R system are available from Python.
Consequently, RPy allows Python programmers to easily add advanced
statistical functionality to Python programs. It allows R programmers the
ability to use Python to control R computations and to interface them with
other systems. Examples include RSOAP
(http://www.analytics.washington.edu/Zope/projects/RSOAP), RSessionDA
(http://www.analytics.washington.edu/Zope/projects/RSOAP), and RStatServer
(http://www.analytics.washington.edu/Zope/projects/RStatServer). These
products, which make heavy use of RPy have been used in a production
environments for two years.
New features in 0.3.3
---
o Now works with R 1.8.X
o Windows version merged into the Unix source tree
o Added lcall() method for calling R functions using a list of (name,
value) pairs for the parameters. This is works around the python
(mis-)feature of using unordered python dictionaries for named
parameters, resulting in the loss of order for named parameters.
o All reported bugs have been fixed.
o New maintainer: Gregory R. Warnes [EMAIL PROTECTED]
For more information visit the RPy home page at http://rpy.sf.net, or the
RPy SourceForge project page at http://www.sf.net/projects/rpy.
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RE: [R] generic/method consistency
Add '...' to the argument list of your methods.
-G
-Original Message-
From: Matt Pocernich [mailto:[EMAIL PROTECTED]
Sent: Friday, December 19, 2003 12:18 PM
To: [EMAIL PROTECTED]
Subject: generic/method consistency
Hi,
I realize the answer is very likely in the section Generic
functions and
methods (or Adding new generics), but I'm not clear what to
do with the
following. Running R CMD check, I get the following warnings for my
generic functions. Does this mean I need the argument
* checking generic/method consistency ... WARNING
leps:
function(x, ...)
leps.default:
function(x, pred, titl, plot)
reliability.plot:
function(x, ...)
reliability.plot.default:
function(x, obar.i, prob.y, titl, mod.names)
summary:
function(object, ...)
summary.prob.bin:
function(object)
Matt Pocernich
NCAR - Research Applications Program
303-497-8312
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RE: [R] Persistent state of R
Starting up R and loading libraries can be very time consuming. For my
RSOAP system (http://www.analytics.washington.edu/Zope/projects/RSOAP/) I
took the step of pre-starting the R process, including the loading of some
libraries, and then handing work of to the pre-started process. You should
be able to use RSOAP from perl, and it would be a simple change to have it
add the bioconductor packages to the pre-loaded set.
Alternatively, I suppose that one could force R to dump core and then start
it from the core image...
-G
-Original Message-
From: michael watson (IAH-C)
To: '[EMAIL PROTECTED]'
Sent: 11/25/03 8:54 AM
Subject: [R] Persistent state of R
Hi
I am using R as a back-end to some CGI scripts, written in Perl. My
platform is Suse Linux 8.2, Apache 1.3.7. So the CGI script takes some
form parameters, opens a pipe to an R process, loads up some
Bioconductor libraries, executes some R commands and takes the ouput and
creates a web page. It is all very neat and works well.
I am trying to make my cgi scripts quicker and it turns out that the
bottle-neck is the loading of the libraries into R - for example loading
up marrayPlots into R takes 10-20 seconds, which although not long, is
long enough for users to imagine it is not working and start clicking
reload
So I just wondered if anyone had a neat solution whereby I could somehow
have the required libraries permanently loaded into R - perhaps I need a
persistent R process with the libraries in memory that I can pipe
commands to? Is this possible?
Thanks
Mick
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RE: [R] Contrast
Or ?contrast in the Design library.
-G
-Original Message-
From: Simon Blomberg [mailto:[EMAIL PROTECTED]
Sent: Tuesday, November 04, 2003 8:32 PM
To: Igor Roytberg; [EMAIL PROTECTED]
Subject: RE: [R] Contrast
see ?fit.contrast in library gregmisc.
Cheers,
Simon.
Simon Blomberg, PhD
Depression Anxiety Consumer Research Unit
Centre for Mental Health Research
Australian National University
http://www.anu.edu.au/cmhr/
[EMAIL PROTECTED] +61 (2) 6125 3379
-Original Message-
From: Igor Roytberg [mailto:[EMAIL PROTECTED]
Sent: Wednesday, 5 November 2003 12:04 PM
To: [EMAIL PROTECTED]
Subject: [R] Contrast
Could anyone please explain how to set up contrasts between
means in R. I want to know if before I conduct an experiment
and believe the mean for 1 and 2 will be different from means
3 and 4, Is this true? That is what I have to prove or
disprove, I thought that contrasts would be the way to go.
Thanks for the help.
Igor
[[alternative HTML version deleted]]
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[R] Off Topic: Good reference for sample size calculations
Hi All,
This is off topic, but we're drawing a blank here..
In a presentation I'll be giving next week, I want to include a reference
to a good general text on computing sample sizes for standard experiments.
Can anyone recommend a good book to use for this purpose?
Thanks,
-Greg
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RE: [R] beginner's question: Graphical presentation of t test
Take a look at the 'plotmeans' function in the gregmisc library. It will
draw the means and error bars for you, allowing you to connect the means for
the paired control and treated groups with something like this:
R code
# sample source data 10 replicates for each enzyme for treated and control
x - rnorm(60)
enzyme - rep(c(ABC123, ABD124, CCF342), length=60)
treat - rep(c(CONTROL,TREATED), length=60)
# create a enzyme by treatment label
group - interaction(enzyme, treat)
# plot the means and confidence intervals
library(gregmisc)
plotmeans( x ~ group, connect=list(1:2,3:4,5:6))
# add p-values
data - data.frame(x, enzyme, treat)
p.vals - by( data, enzyme, function(data) t.test( x ~ treat,
data=data)$p.value )
text(x=c(1.5, 3.5, 5.5), y=rep(0,3), paste(P-value:\n,
format.pval(p.vals)) )
/R code
-Greg
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Sent: Saturday, June 07, 2003 1:43 PM
To: [EMAIL PROTECTED]
Subject: [R] beginner's question: Graphical presentation of t test
Hi,
Is there any way to use R to present t test results for three
groups of
experiments, each of which involves several parallel
experiment series with
groups of control vs treated. I would like to present the
average fold change
of the experimental parameter (concentration of enzymes) as bars with
standard error and the p value above the bar. So, there
should be two groups
(control vs treated) of three bars for the three enzymes.
Thanks
Peter
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RE: [R] round() seems inconsistent when rounding 5s
Actually, under the default IEEE rounding mode, decimal values ending in 5 are always rounded to the nearest even value. This intended to ensure that rounding does not systematically bias computations in one direction, as would happen if 5's were always rounded either up or down. A very useful review of the issues in floating point computations on computer and under IEEE standard arithmetic is the paper What Every Computer Scientist Should Know About Floating-Point Arithmetic, by David Goldberg, published in the March, 1991 issue of Computing Surveys. This paper is reprinted on the Sun website at http://docs.sun.com/source/806-3568/ncg_goldberg.html. -Greg -Original Message- From: Marc R. Feldesman [mailto:[EMAIL PROTECTED] Sent: Saturday, March 15, 2003 5:49 PM To: Rashid Nassar; r-help Subject: Re: [R] round() seems inconsistent when rounding 5s At 01:53 PM 3/15/2003, Rashid Nassar wrote: It may be my lack of unerstanding, but round() seems to me to give inconsistent results when rounding 5s as in the following examples? Not really. Floating point numbers can't be precisely represented in binary and so the internal representation of 1.5 might be very different from what you think it is. If you've done any programming at all, this is one of the first lessons you learn about real numbers and computers. Dr. Marc R. Feldesman Professor and Chairman Emeritus Anthropology Department - Portland State University email: [EMAIL PROTECTED] email: [EMAIL PROTECTED] fax:503-725-3905 Sometimes the lights are all shining on me, other times I can barely see, lately it's occurred to me, what a long strange trip it's been... Jerry the boys __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is... [[dropped]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] RSessionDA 1.0-rc1 released.
Release 1.0-rc1 of RSessionDA is now available. This version provides significantly improved security and should now be usable on public internet sites. Description: RSessionDA provides an interface to R from the open-source web application development system Zope http://www.zope.org. This interface permits evaluation of functions in the R language using information in Zope. R data objects, graphics files, printed output, script transcripts, and data files can be returned to Zope for display making it easy to create web applications that include advanced statistical functionality. See http://software.biostat.washington.edu/statsoft/snake/RSessionDA for details. -Greg LEGAL NOTICE\ Unless expressly stated otherwise, this message is... [[dropped]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] RE: Text Rotation (was: Take care with codes()!)
I've just uploaded gregmisc_0.8.2.tar.gz to CRAN. It should show up in the package repository in a day or two. This version of the gregmisc package provides an enhanced 'balloonplot' function with 'rowsrt', 'colsrt' arguments to control rotation of the labels, and 'rowmar', 'colmar' to control the amount of space reserved for the labels. Here's an example: # Create an Example Data Frame Containing Car x Color data, with long car names carnames - c(BMW: High End, German, Renault: Medium End, French, Mercedes: High End, German, Seat: Imaginary, Unknown Producer) carcolors - c(red,white,silver,green) datavals - round(rnorm(16, mean=100, sd=60),1) data - data.frame(Car=rep(carnames,4), Color=rep(carcolors, c(4,4,4,4) ), Value=datavals ) # generate balloon plot with default scaling, the column labels will overlap balloonplot( data$Color, data$Car, data$Value) # try again, with column labels rodated 90 degrees, and given more space balloonplot( data$Car, data$Color, data$Value, colmar=3, colsrt=90) -Greg -Original Message- From: Warnes, Gregory R Sent: Saturday, March 08, 2003 10:12 AM To: 'Ramon Alonso-Allende'; Warnes, Gregory R Cc: '[EMAIL PROTECTED]'; '[EMAIL PROTECTED]' Subject: RE: Text Rotation (was: Take care with codes()!) You can use the graphics parameter srt to rotate displayed text by a specified number of degrees, e.g. srt=45 to put it on an angle, srt=90 to put it vertical. If you do this, may need to modify the call to text to increase ylim and change the plot location to give you more room. I'm working to update the 'balloonplot' function in the gregmisc package now to handle this case gracefully. -Greg -Original Message- From: Ramon Alonso-Allende [mailto:[EMAIL PROTECTED] Sent: Saturday, March 08, 2003 6:41 AM To: Warnes, Gregory R Cc: '[EMAIL PROTECTED]'; '[EMAIL PROTECTED]' Subject: Re: Take care with codes()! (was [R] type of representation) Hi I have been ussing this code displayed while a go to do balloons plots. My problem is that the labels of the data i'm working on now are to big and they overlap in the X axis. Is there any way i can plot the text vertically or with some inclination? Thanks Ramon Warnes, Gregory R wrote: Ahh yes, sorry about that. Here's the corrected snippet: # Create an Example Data Frame Containing Car x Color data carnames - c(bmw,renault,mercedes,seat) carcolors - c(red,white,silver,green) datavals - round(rnorm(16, mean=10, sd=4),1) data - data.frame(Car=rep(carnames,4), Color=rep(carcolors, c(4,4,4,4) ), Value=datavals ) # show the data data # plot the Car x Color combinations, using 'cex' to specify the dot size plot(x=as.numeric(data$Car), # as.numeric give numeric values y=as.numeric(data$Color), cex=data$Value/max(data$Value)*12, # standardize size to (0,12) pch=19, # filled circle col=skyblue, # dot color xlab=Car, # x axis label ylab=Color, # y axis label xaxt=n, # no x axis lables yaxt=n, # no y axis lables bty=n, # no box around the plot xlim=c(0,nlevels(data$Car )+0.5), # extra space on either end of plot ylim=c(0.5,nlevels(data$Color)+1.5) # so dots don't cross into margins ) # add text labels text(x=1:nlevels(data$Car), y=nlevels(data$Car)+1, labels=levels(data$Car)) text(x=0, y=1:nlevels(data$Color), labels=levels(data$Color) ) # add borders between cells abline(v=(0:nlevels(data$Car)+0.5)) abline(h=(0:nlevels(data$Color)+0.5)) # annotate with actual values text(x=as.numeric(data$Car), # as.numeric give numeric values y=as.numeric(data$Color), labels=format(data$Value), # label value col=black, # textt color ) # put a nice title title(main=Car by Color Popularity\n(Dot size proportional to popularity)) -Greg -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Friday, January 03, 2003 1:53 PM To: Warnes, Gregory R Cc: '[EMAIL PROTECTED]'; '[EMAIL PROTECTED]' Subject: RE: Take care with codes()! (was [R] type of representation) From the help page of codes(): Normally `codes' is not the appropriate function to use with an unordered factor. Use `unclass' or `as.numeric' to extract the codes used in the internal representation of the factor, as these do not assume that the codes are sorted. and this is one of the `normally' cases. Your code will only work correctly if the levels are in alphabetical order (in the locale in use). On Fri, 3 Jan 2003, Warnes, Gregory R wrote: How about this snippet: # Create
RE: [R] Moving average
Or look at the 'running' function in the gregmisc package. -Greg -Original Message- From: Huntsinger, Reid [mailto:[EMAIL PROTECTED] Sent: Friday, March 07, 2003 10:13 AM To: 'Wayne Jones'; [EMAIL PROTECTED] Subject: RE: [R] Moving average Try filter in package ts. Reid Huntsinger -Original Message- From: Wayne Jones [mailto:[EMAIL PROTECTED] Sent: Friday, March 07, 2003 9:37 AM To: [EMAIL PROTECTED] Subject: [R] Moving average Hi, Does anyone know if R has the functionality to calculate a simple moving average. I cant seem to find it in the help menu. thanks, Wayne Dr Wayne R. Jones Statistician / Research Analyst KSS Group plc St James's Buildings 79 Oxford Street Manchester M1 6SS Tel: +44(0)161 609 4084 Mob: +44(0)7810 523 713 KSS Ltd A division of Knowledge Support Systems Group plc Seventh Floor St James's Buildings 79 Oxford Street Manchester M1 6SS England Company Registration Number 2800886 (Limited) 3449594 (plc) Tel: +44 (0) 161 228 0040 Fax: +44 (0) 161 236 6305 mailto:[EMAIL PROTECTED] http://www.kssg.com The information in this Internet email is confidential and may b... [[dropped]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is... [[dropped]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Initial release of RSessionDA
Announcing the initial release of RSessionDA. RSessionDA provides objects for interacting with R from Zope www.zope.org, a full-featured web application development system. These objects permit evaluation of functions in the R language using information in Zope. R data objects, graphics files, printed output, script transcripts, and data files can be returned to Zope for display. These tools make it easy to create web applications that include advanced statistical functionality. RSessionDA is built on RSOAP package, which provides access to R via the SOAP http://www.w3.org/TR/SOAP/; communications protocol. This allows Zope to access multiple independent R sessions running (if desired) on a separate compute server. For more information on or to download RSessionDA see: http://software.biostat.washington.edu/statsoft/snake/RSessionDA or http://www.zope.org/Members/warnes/RSessionDA/ For more information on or to download RSOAP see: http://software.biostat.washington.edu/statsoft/snake/RSOAP or For more information on Zope see: http://www.zope.org -Greg LEGAL NOTICE\ Unless expressly stated otherwise, this message is... [[dropped]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] help
Alternatively, use the 'plotCI' function (or for standard errors, 'plotmeans' function) in the gregmisc package. -Greg -Original Message- From: Marc Schwartz [mailto:[EMAIL PROTECTED]] Sent: Friday, February 21, 2003 8:38 AM To: 'Thanjavur Bragadeesh'; [EMAIL PROTECTED] Subject: RE: [R] help -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] On Behalf Of Thanjavur Bragadeesh Sent: Monday, February 10, 2003 4:08 PM To: [EMAIL PROTECTED] Subject: [R] help Hi, help.I would like to plot the mean and standard deviation against a factor in the xaxis- in other words I want an errorplot. I also want to put the standard deviation like a T on top of a barplot. How can do this in R Bragadeesh Look at the barplot2() function in the gregmisc package on CRAN. A quick example using barplot2() and faked numbers: library(gregmisc) barplot2(c(5, 8, 4, 6, 9), plot.ci = TRUE, ci.l = c(5, 8, 4, 6, 9), ci.u = c(5.5, 8.3, 4.25, 6.7, 10.5)) This will give you 5 vertical bars, with the upper bounds of the confidence intervals plotted on top of the bars. Note that I have specified that the lower bounds are the same as the bar values, which results in no lower intervals being plotted. If you want both upper and lower bounds plotted, use appropriate values for the 'ci.l' argument. There are other options for axis configuration, grid lines and so forth in barplot2() if you should need them. Hope that helps, Marc Schwartz __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] pairlists (was: data manipulation function descriptions)
-Original Message- From: Luke Tierney [mailto:[EMAIL PROTECTED]] R does not provide a pairlist data structure. This creates a dilemma when translating some list-based xlispstat code, or, more importantly, when implementing an algorithm for which parilists are the natural data structure to use. ... Pairlists were and still are used internally for many things. ... Wouldn't it, therefore, make sense to provide a 'pairlist' package which exposes the internal pairlist structure and provides appropriate functions (car, cdr, ...), instead of expecting people to keep re-implementing these features? -Greg LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] search contrasts tutorial
You might also find the help pages for 'fit.contrasts', 'estimable', and 'glh.test' functions in the gregmisc library useful. -Greg -Original Message- From: Tito de Morais Luis [mailto:[EMAIL PROTECTED]] Sent: Thursday, February 13, 2003 8:52 AM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Subject: Re: [R] search contrasts tutorial Hi, Did you look at : http://pbil.univ-lyon1.fr/R/enseignement.html There is a huge list of statistical courses based on R. You may find what you look for. It's in French but this should not be a problem for you ;-) HTH L. Tito Le jeu 13/02/2003 à 17:30, Robert Espesser a écrit : I'm looking for a tutorial or notes on the use of contrasts factor in linear model in R, I've found some mails and infos about in various documents about R, but I've probably missed a good review on this subject. -- L. Tito de Morais UR RAP IRD de Dakar BP1386 Dakar Sénégal Tél: +221 849 33 31 Fax: +221 832 16 75 Courriel: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] testing slope
For testing the hypothesis Beta[X] + Beta[Vn3] + Beta[X:Vn3] = 0 you can use the estimable function from the gregmisc package: estimable(m2, c(Intercept=0, X=1, Vn2=0, Vn3=1, X:Vn2=0, X:Vn3=1) ) See the estimable help page for details. -Greg -Original Message- From: Ronaldo Reis Jr. [mailto:[EMAIL PROTECTED]] Sent: Tuesday, February 04, 2003 2:51 PM To: R-Help Subject: [R] testing slope Hi all, I try to test a linear slope using offset. I have: m2 - glm(Y~X*V) summary(m2) Call: glm(formula = Y ~ X * V) Deviance Residuals: Min1QMedian3Q Max -2.01688 -0.56028 0.05224 0.53213 3.60216 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 1.3673 0.8476 1.613 0.119788 X 4.0235 0.1366 29.453 2e-16 *** Vn2 0.9683 1.1987 0.808 0.427131 Vn3 4.6043 1.1987 3.841 0.000787 *** X:Vn2 4.1108 0.1932 21.279 2e-16 *** X:Vn3-4.0069 0.1932 -20.740 2e-16 *** --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 (Dispersion parameter for gaussian family taken to be 1.53955) Null deviance: 15303.977 on 29 degrees of freedom Residual deviance:36.949 on 24 degrees of freedom AIC: 105.39 Number of Fisher Scoring iterations: 2 It is clear that X slope is diferent of Zero. X 4.0235 0.1366 29.453 2e-16 *** It is too clear that X:Vn2's slope is diferent of X's slope and diferent of Zero, because is greater than X'slope. X:Vn2 4.1108 0.1932 21.279 2e-16 *** But, the X:Vn3' slope is different of X'slope, but not necessarily different of Zero. How I make to introduce this parameter in a new model for test? An offset only with Vn3 slope??? I try: m2 - glm(Y~V*offset(0*X)) m2 - glm(Y~X*V+V*offset(0*X)) m2 - glm(Y~V:X+V*offset(0*X)) but neither work :(( Thanks for all. Ronaldo -- If you live in a country run by committee, be on the committee. -- Graham Summer -- | //|\\ [*][***] || ( õ õ ) [Ronaldo Reis Júnior ][PentiumIII-600 ] | V [ESALQ/USP-Entomologia, CP-09 ][HD: 30 + 10 Gb ] || / l \ [13418-900 Piracicaba - SP][RAM: 128 Mb] | /(lin)\ [Fone: 19-429-4199 r.229 ][Video: SiS620-8Mb ] ||/(linux)\ [[EMAIL PROTECTED] ][Modem: Pctel-onboar] |/ (linux) \[ICQ#: 5692561][Kernel: 2.4.18 ] || ( x ) [*][***] ||| _/ \_Powered by Gnu/Debian Woody D+:) | Lxuser#: 205366 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Decreasing my personal entropy ...
Lattice plots and trellice plots are actually displayed by thier 'print' methods. So, to get ta plot to be displayed in a non-interactive context, such as a script, explicitly call print on the results of the plot command. -Greg -Original Message- From: Gunter, Bert To: R-Help (E-mail) Sent: 1/31/03 8:45 AM Subject: [R] Decreasing my personal entropy ... R-Listers: A very minor -- and maybe silly -- question just for personal enlightenment. In S (either R or S-Plus, AFAIK) when one types or pastes a trellis graphics command into the commands/console window, the graph is automatically produced: e.g., trellis.device(...) xyplot(y~x) If one puts these in a function and calls the function, the same occurs. However, if one sources in these command from a file (i.e., using source()), automatic printing does not occur; one must explicitly call print(xyplot(y~x)) . Why do things work this way? Many thanks. Bert Gunter Biometrics Research RY 84-16 Merck Company P.O. Box 2000 Rahway, NJ 07065-0900 Phone: (732) 594-7765 mailto: [EMAIL PROTECTED] The business of the statistician is to catalyze the scientific learning process. -- George E.P. Box -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Version 0.8.0 of the gregmisc package is now available
Version 0.8.0 of the gregmisc package is now (or will shortly be) available on CRAN. New in this release: - Enhanced and bug-fixed 'CrossTable' function (contributed by Marc Schwartz) - Augmented the 'barplot2' function with an 'add' argument to allow for the addition of a barplot to an existing graphic. (contributed by Marc Schwartz) - Added the 'baloonplot' function which creates a visual 2-way table containing circles whose area corresponds to the size of the corresponding measurement. - Renamed 'contrast.lm' to 'fit.contrast'. This new name is more descriptive and makes it easier to create and use methods for other classes, eg lme. - New contrast.lm function which generates a 'depreciated' warning and calls fit.contrast. - Enabled fit.contrast for lme object now that Doug Bates has provided the necessary support for contrasts in the nlme package. (Thanks Doug!) Requires the newly released nlme 3.1-37. - 'make.contrasts' has been augmented to check for too many submitted contrast rows - Updated wapply.R to allow specification of evaluation points when method is 'width' or 'range' using the 'pts' argument. - Updated wapply.Rd to add 'pts' argument - Fixed typos, spelling errors, grammatical errors and lack of clarity in various help pages. Description of the package: Package: gregmisc Description: Misc Functions written/maintained by Gregory R. Warnes Title: Greg's Miscellaneous Functions Version: 0.8.0 Date: 2003/01/30 Maintainer: Gregory R. Warnes [EMAIL PROTECTED] Author: Gregory R. Warnes. Includes code provided by Ben Bolker, Bendix Carstensen, Don MacQueen, William Venables, Marc Schwartz, Ben Bolker, Ian Wilson, and Kjetil Halvorsen License: GPL (version 2 or later) Depends: R (= 1.6.0), MASS, nlme (= 3.1-37) Built: R 1.6.1; sparc-sun-solaris2.8; Thu Jan 30 17:13:52 EST 2003 Index: CrossTable Cross Tabulation with Tests for Factor Independence aggregate.table Create 2-Way Table of Summary Statistics balloonplot Plot a graphical matrix where each cell contains a dot whose size reflects the relative magnitude of the corresponding component. bandplotPlot x-y Points with Locally Smoothed Mean and Standard Deviation barplot2Enhanced Bar Plots boxplot.n Produce a Boxplot Annotated with the Number of Observations ci Compute Confidence Intervals combinationsEnumerate the Combinations or Permutations of the Elements of a Vector combine Combine R Objects With a Column Labeling the Source contrast.lm Compute and test arbitrary contrasts for regression objects (Depreciated, use 'fit.contrasts' instead.) rdirichlet Functions for the Dirichlet Distribution estimable Compute and test estimable linear functions of the fitted coefficients (including contrasts) of regression objects factorial Compute factorial function fast.prcomp Efficient computation of principal components and singular value decompositions. fit.contrastCompute and test arbitrary contrasts for regression objects glh.testTest a General Linear Hypothesis for a Regression Model hist2d Compute and Plot a 2-Dimensional Histogram interleave Interleave Rows of Data Frames or Matrices lowess Scatter Plot Smoothing make.contrasts Construct a User-Specified Contrast Matrix nobsCompute the Number of Non-missing Observations permute Randomly Permute the Elements of a Vector plotCI Plot Error Bars plotmeans Plot Group Means and Confidence Intervals qqnorm.aov Makes a half or full normal plot for the effects from an aov model quantcutCreate a Factor Variable Using the Quantiles of a Continuous Variable rename.vars Rename variables in a dataframe reorder Reorder the Levels of a Factor running Apply a Function Over Adjacent Subsets of a Vector space Space points in an x-y plot so they don't overlap. undocumentedUndocumented functions wapply Compute the Value of a Function Over a Local Region Of An X-Y Plot LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list
RE: [R] Downloading Package
If your system is set up appropriately, you should be able to use the menu Packages - Install Packages from Cran to get a list of packages, then select the desired package and press OK. -Greg -Original Message- From: Peter von Rohr [mailto:[EMAIL PROTECTED]] Sent: Thursday, January 30, 2003 6:57 AM To: Vincent Stoliaroff Cc: [EMAIL PROTECTED] Subject: Re: [R] Downloading Package Hello Vincent, I am a beginner in using R so my question could seem very simple. I would like to download the package multiv to do multivariate data analysis. The package I download seems to be a file meant for UNIX and I am using a Window OS. How could I download and install correctly this file? although i am not using R for windows, but there are binaries for windows available for multiv at: http://www.stat.math.ethz.ch/CRAN/bin/windows/contrib/multiv.zip you may want to read the documentation about how to install pakages from http://stat.ethz.ch/CRAN/doc/manuals/R-admin.pdf (chapter 5). depending on where you are physically, you may want to select another cran mirror for a list of mirrors see: http://cran.r-project.org/mirrors.html hth, peter -- Peter von Rohr http://www.inf.ethz.ch/~vonrohr Institute of Scientific Computing[EMAIL PROTECTED] ETH-Zentrum, HRS H23 phone: +41 1 632 7473 CH - 8092 Zurich fax: +41 1 632 1374 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: Take care with codes()! (was [R] type of representation)
Ahh yes, sorry about that. Here's the corrected snippet: # Create an Example Data Frame Containing Car x Color data carnames - c(bmw,renault,mercedes,seat) carcolors - c(red,white,silver,green) datavals - round(rnorm(16, mean=10, sd=4),1) data - data.frame(Car=rep(carnames,4), Color=rep(carcolors, c(4,4,4,4) ), Value=datavals ) # show the data data # plot the Car x Color combinations, using 'cex' to specify the dot size plot(x=as.numeric(data$Car), # as.numeric give numeric values y=as.numeric(data$Color), cex=data$Value/max(data$Value)*12, # standardize size to (0,12) pch=19, # filled circle col=skyblue, # dot color xlab=Car, # x axis label ylab=Color, # y axis label xaxt=n, # no x axis lables yaxt=n, # no y axis lables bty=n, # no box around the plot xlim=c(0,nlevels(data$Car )+0.5), # extra space on either end of plot ylim=c(0.5,nlevels(data$Color)+1.5) # so dots don't cross into margins ) # add text labels text(x=1:nlevels(data$Car), y=nlevels(data$Car)+1, labels=levels(data$Car)) text(x=0, y=1:nlevels(data$Color), labels=levels(data$Color) ) # add borders between cells abline(v=(0:nlevels(data$Car)+0.5)) abline(h=(0:nlevels(data$Color)+0.5)) # annotate with actual values text(x=as.numeric(data$Car), # as.numeric give numeric values y=as.numeric(data$Color), labels=format(data$Value), # label value col=black, # textt color ) # put a nice title title(main=Car by Color Popularity\n(Dot size proportional to popularity)) -Greg -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] Sent: Friday, January 03, 2003 1:53 PM To: Warnes, Gregory R Cc: '[EMAIL PROTECTED]'; '[EMAIL PROTECTED]' Subject: RE: Take care with codes()! (was [R] type of representation) From the help page of codes(): Normally `codes' is not the appropriate function to use with an unordered factor. Use `unclass' or `as.numeric' to extract the codes used in the internal representation of the factor, as these do not assume that the codes are sorted. and this is one of the `normally' cases. Your code will only work correctly if the levels are in alphabetical order (in the locale in use). On Fri, 3 Jan 2003, Warnes, Gregory R wrote: How about this snippet: # Create an Example Data Frame Containing Car x Color data carnames - c(bmw,renault,mercedes,seat) carcolors - c(red,white,silver,green) datavals - round(rnorm(16, mean=10, sd=4),1) data - data.frame(Car=rep(carnames,4), Color=rep(carcolors, c(4,4,4,4) ), Value=datavals ) # show the data data # plot the Car x Color combinations, using 'cex' to specify the dot size plot(x=codes(data$Car), # codes give numeric values y=codes(data$Color), cex=data$Value/max(data$Value)*12, # standardize size to (0,12) pch=19, # filled circle col=skyblue, # dot color xlab=Car, # x axis label ylab=Color, # y axis label xaxt=n, # no x axis lables yaxt=n, # no y axis lables bty=n, # no box around the plot xlim=c(0,nlevels(data$Car )+0.5), # extra space on either end of plot ylim=c(0.5,nlevels(data$Color)+1.5) # so dots don't cross into margins ) # add text labels text(x=1:nlevels(data$Car), y=nlevels(data$Car)+1, labels=levels(data$Car)) text(x=0, y=1:nlevels(data$Color), labels=levels(data$Color) ) # add borders between cells abline(v=(0:nlevels(data$Car)+0.5)) abline(h=(0:nlevels(data$Color)+0.5)) # annotate with actual values text(x=codes(data$Car), # codes give numeric values y=codes(data$Color), labels=format(data$Value), # label value col=black, # textt color ) # put a nice title title(main=Car by Color Popularity\n(Dot size proportional to popularity)) -Greg -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] Sent: Friday, January 03, 2003 4:46 AM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Subject: [R] type of representation Hi I have some data that i want to plot but i don't find how to do it. I have car types (bmw,renault,mercedes,seat ...), colors and a number for each car type-color relation.I want to come up with a matrix representation of cars vs colors where in each intersection i could set a dot proportional in size to my third variable. Can anybody give me a clue of hoe to come up with such representation. Thanks Ramon __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help LEGAL NOTICE\ Unless expressly stated otherwise, this message is ... [[dropped]] __ [EMAIL PROTECTED] mailing list
