, 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
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:
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 -
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
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
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
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'
- 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
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:
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
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
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
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:
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
- 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
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.
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
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:
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:
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:
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
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
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
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
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.
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
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
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
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
[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
Warnes, Gregory R would like to recall the message, Quick running
question.
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
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[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do
[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
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
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
-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
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
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
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
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
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
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
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
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
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
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
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:
-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
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
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,
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)
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
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
)
# 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
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