Duncan Murdoch wrote:
Andrew Piskorski wrote:
I'm currently using R CMD INSTALL to build and install some of my own
custom R packages. Basically, I use a script which first builds a
tarball of my R source code, and then calls R CMD INSTALL, which
builds and installs that source package from
Hi,
Although my question is not directly linked to R functionality, I hope
you can forgive me for posing it here. I have been looking for the
answer for a long time (~ 4 weeks) and have not been able to find it. My
question is:
Suppose I have an m*n matrix, with a random (normally distributed)
batchfiles, available on CRAN at
http://cran.r-project.org/contrib/extra/batchfiles/
consists of a set of Windows XP batch files (they may run on
NT/2000 too but that has not been tested) which facilitate:
1. starting R, automatically locating it in the registry
each time they are run,
Hi Gurus!
I have a job that is to get randomly samples from point-based GIS data (sp
called shape GIS files) under the total sum resctricted.
For example, I would like to take random smaples under the 1000 persons in
each city.
The randomly sampled persons should not be over 1000 any case.
Check out the maptools package.
It allows you to read ESRI shapefiles.
On 7/6/05, Kum-Hoe Hwang [EMAIL PROTECTED] wrote:
Hi Gurus!
I have a job that is to get randomly samples from point-based GIS data (sp
called shape GIS files) under the total sum resctricted.
For example, I would like
Neither lme nor lmer has provision for fitting multivariate models.
On 7/5/05, Constantinos Antoniou [EMAIL PROTECTED] wrote:
Dear all,
is it possible to estimate a multivariate multilevel model in R (I
guess the term in R is mixed-effects model). I can estimate
univariate models using
Mario de Frutos Dieguez escribió:
Im doing an aplication in Java and i have a program made in R what i
want to launch with Java.
I have the following instructions:
Runtime r = Runtime.getRuntime();
try
{
System.out.println (Llamada a R...);
p = r.exec(sRutaR);
GIS-related packages in R:
shapefiles
maptools
sp
spdep
adehabitat
GRASS
PBSmapping
etc.
--Xiaohua
On 7/6/05, Kum-Hoe Hwang [EMAIL PROTECTED] wrote:
Hi Gurus!
I have a job that is to get randomly samples from point-based GIS data (sp
called shape GIS files) under the total sum
Hello,
I've run the sktest command to test for the normality of a variable but I do
not understand the output. How do I interpret the output?
Gideon Osoma
[[alternative HTML version deleted]]
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R-help@stat.math.ethz.ch mailing list
Hi all,
I am trying to call R programs from VB.NET. For this purpose I published a
simple R COM class with proper registry values. After this step, I am not
able to call the COM object from .NET. I cannot find the reference component
name for R in .NET. All the examples provided on R website are
Hello and sorry to disturb.
I'm trying to plot the confidence intervals for the fixed effects of a lme.
I want to obtain graphically, if it is possible, a bar with Estimate, upper
and lower CI for each level of the factors.
I know how to do for a lm model but for a lme one, I tried with
How did you set the TZ system variable?
If you did not use Sys.putenv(), try using it instead.
Otherwise, I think you have to ask the package maintainer.
You may be misleading yourself by using Sys.time() to test whether TZ is set.
What does Sys.getenv() tell you?
I get a timezone code from
Hello. I have written a function (Maxent), based on the improved
iterative scaling algorithm of Della Pietra et al., that calculates the
maximum entropy distribution given moment constraints. That is, it
obtains the probability distribution (p) with maximum entropy given
constraints linear in p.
Hello,
I have a string like O1 O2 O3, O1, O2 and O3 are the names of three
objects. How to split it into a vector or three new objects, and
obtain their content? I try to use strsplit to do that, but seems it
doesn't work like that.
And what is - for? the same as -?
Thank you,
Shengzhe
I am trying to use knn to do a nearest neighbor classification. I tried using
my dataset and got an error message so I used a simple example to try and
understand what I was doing wrong and got the same message. Here is what I
typed into R:
try
[,1] [,2] [,3] [,4]
r A A T G
r A A T
wu sz wrote:
Hello,
I have a string like O1 O2 O3, O1, O2 and O3 are the names of three
objects. How to split it into a vector or three new objects, and
obtain their content? I try to use strsplit to do that, but seems it
doesn't work like that.
Please provide an example of what you
What do you think about the following:
library(nlme)
set.seed(1)
n - 3;m - 4
s.e - 0
(X0 - array(rep(rnorm(n), each=m)+s.e*rnorm(m*n),
dim=c(m, n)))
s.e - 1
(X1 - array(rep(rnorm(n), each=m)+s.e*rnorm(m*n),
dim=c(m, n)))
X. - data.frame(Row=as.vector(row(X)),
Do you or Lumley have a citation for this conclusion? Most people go
forward with the ANOV on the basis that the various tests are independent.
Phillip Good
P.S. Tests based on the method of synchronized permutations are
independent.
-Original Message-
From: Douglas Bates
Consider the following extension of an example in ?lme:
fm2 - lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
int - intervals(fm2)
class(int$fixed)
kf - dim(int$fixed)[1]
plot(int$fixed[,2], kf:1,
xlab=x, ylab=, xlim=range(int$fixed),
axes=FALSE)
axis(1)
axis(2,
On Wed, 6 Jul 2005, Phillip Good wrote:
Do you or Lumley have a citation for this conclusion? Most people go
forward with the ANOV on the basis that the various tests are independent.
I don't have a citation. I would have thought that the claim that they
were independent was more in need of
I'm confused: I understood Doug to be describing a traditional,
normal theory ANOVA with k rows in the table for different effects plus
a (k+1)st for residuals and the mean squares (MS) column are all
indpendent chi-squares scaled by the same unknown sigma^2. The k
statistics in
What is the status of interactive graphics in R?
I am thinking along the lines of what is provided by something like
datadesk:
http://www.datadesk.com/products/data_analysis/datadesk/index.shtml
I have tried RGGobi in the past, but found it clumsy (at least on
Windows XP). RGL and iplots
On 7/6/05, Phillip Good [EMAIL PROTECTED] wrote:
Do you or Lumley have a citation for this conclusion? Most people go
forward with the ANOV on the basis that the various tests are independent.
Phillip Good
P.S. Tests based on the method of synchronized permutations are
independent.
On 7/6/05, Douglas Bates [EMAIL PROTECTED] wrote:
...
Perhaps we could review the sequence of events here. This exchange
began with your sending me a message claiming that there is a bug in
lm or anova in R because the results of your simulation were what you
expected.
I meant to write
spencer graves asks:
How is the method of synchronized permutations relevant to a traditional,
normal theory ANOVA?
One ought now ask as I am doing currently whether traditional, normal
theory ANOVA is applicable to the analysis of experimental designs. If in
fact, the results of the various
On 7/6/2005 1:43 PM, Phillip Good wrote:
spencer graves asks:
How is the method of synchronized permutations relevant to a traditional,
normal theory ANOVA?
One ought now ask as I am doing currently whether traditional, normal
theory ANOVA is applicable to the analysis of experimental
Hi list,
1) How can the MM-estimator method=MM in function rlm be tuned to 85%
efficiency? It seems that there is a default tuning to 95%. I presume, but
am not sure, that the MM-estimator uses phi=phi.bisquare as default and
the tuning constant could be set by adding a parameter c=...
Is this
I'd like to do some plots of historical event data on a reverse log
scale, started, say at the year 2000 and going
backwards in time, with tick marks spaced according to log(2000-year).
For example, see:
http://euclid.psych.yorku.ca/SCS/Gallery/images/log-timeline.gif
As an example, I'd like
On 06-Jul-05 Phillip Good wrote:
Do you or Lumley have a citation for this conclusion? Most people go
forward with the ANOV on the basis that the various tests are
independent.
This hardly needs a citation -- Thomas Lumley's explanation (excerpted
below from Doug Bates's mail) is
On 6 Jul 2005 at 12:30, Douglas Bates wrote:
On 7/6/05, Douglas Bates [EMAIL PROTECTED] wrote:
...
Perhaps we could review the sequence of events here. This exchange
began with your sending me a message claiming that there is a bug in
lm or anova in R because the results of your
As Duncan Murdoch indicated, the primary issue is not that the
different tests are (not) statitically independent but that they are
sensitive to different alternative hypotheses.
spencer graves
JRG wrote:
On 6 Jul 2005 at 12:30, Douglas Bates wrote:
On 7/6/05, Douglas
Do you want to move year 2000 to Inf? How about a cube root
transformation instead:
year - seq(0, 4000, 100)
y2000.3 - (sign(year-2000)*
abs(year-2000)^(1/3))
plot(y2000.3, year, axes=FALSE)
axis(1, y2000.3, year)
axis(2)
Of course, one should package the
On 7/6/2005 3:36 PM, Michael Friendly wrote:
I'd like to do some plots of historical event data on a reverse log
scale, started, say at the year 2000 and going
backwards in time, with tick marks spaced according to log(2000-year).
For example, see:
Dear List:
I am encountering an error that I can't resolve. I'm looping through
rows of a dataframe to generate individual tex files using Sweave. At
random points along the way, I encounter the following error
Error in file() : cannot find unused tempfile name
At which point Sweave halts.
The following code produces 6 plots on a page, but the first is
distorted and different from the others:
par(mfrow=c(3,2), las=2)
for (i in 1:6) {
frame()
par(mar=c(7, 7, 1, 1))
axis(2); box(); abline(h=seq(0,1,.5), col=2:4)
}
The first plot's axes are mis-aligned with the plotting area
Brett Magill wrote:
What is the status of interactive graphics in R?
I am thinking along the lines of what is provided by something like
datadesk:
http://www.datadesk.com/products/data_analysis/datadesk/index.shtml
I have tried RGGobi in the past, but found it clumsy (at least on
Thanks Duncan,
That is almost exactly what I want, except I want time to
go in the normal order, not backwards, so:
# plot on reverse log scale
years1500 - runif(500, 1500, 1990) # some fake data
x - -log(2000-years1500)
from - -log(2000-1990)
to - -log(2000-1500)
plot(density(x, from=from,
Brahm, David wrote:
The following code produces 6 plots on a page, but the first is
distorted and different from the others:
par(mfrow=c(3,2), las=2)
for (i in 1:6) {
frame()
par(mar=c(7, 7, 1, 1))
axis(2); box(); abline(h=seq(0,1,.5), col=2:4)
}
The first plot's axes are
Michael Friendly wrote:
Thanks Duncan,
That is almost exactly what I want, except I want time to
go in the normal order, not backwards, so:
# plot on reverse log scale
years1500 - runif(500, 1500, 1990) # some fake data
x - -log(2000-years1500)
from - -log(2000-1990)
to -
Stupid me, I put my comment in the wrong place. Ignore my last message,
this one should be right:
Michael Friendly wrote:
Thanks Duncan,
That is almost exactly what I want, except I want time to
go in the normal order, not backwards, so:
# plot on reverse log scale
years1500 - runif(500,
pretty() works well for numbers and axTicks() can help for potting log axes,
but has anyone written a pretty for chron objects (or other date or date-time
classes)?
It would have natural units of years, months, .., days, hours, (minutes?), and
it would choose the appropriate unit based on the
Dear R list,
I'm trying to calculate Mahalanobis distances for 'Species' of 'iris' data
as obtained below:
Squared Distance to Species From Species:
Setosa Versicolor Virginica
Setosa 0 89.86419 179.38471
Versicolor 89.86419 0 17.20107
Virginica
Not sure if I am missing something essential here but it would
seem as simple as:
# data
set.seed(1)
x - runif(500, 1500, 1990)
# plot
d - density(x, from = 1500, to = 1990)
plot(d$y ~ d$x, log = x)
rug(x)
axis(1, seq(1500, 1990, 10), FALSE, tcl = -0.3)
On 7/6/05, Michael Friendly [EMAIL
[EMAIL PROTECTED] wrote:
pretty() works well for numbers and axTicks() can help for potting log axes,
but has anyone written a pretty for chron objects (or other date or date-time
classes)?
It would have natural units of years, months, .., days, hours, (minutes?), and
it would choose the
I wrote:
par(mfrow=c(3,2), las=2)
for (i in 1:6) {
frame()
par(mar=c(7, 7, 1, 1))
axis(2); box(); abline(h=seq(0,1,.5), col=2:4)
}
The first plot's axes are mis-aligned with the plotting area...
Uwe Ligges [EMAIL PROTECTED] replied:
Yes expected, at first you generate the plot, then
On Wed, Jul 06, 2005 at 10:06:45AM -0700, Thomas Lumley wrote:
(...)
If X, Y, and Z are
independent and Z takes on more than one value then X/Z and Y/Z can't be
independent.
Not really true. I can produce a counterexample on request (admittedly
quite trivial though).
Göran Broström
Dear All,
I knew how to use glm or lm, but I do not know how to perform LSD or
HSD on treatments with them. If someone can help me out, I greatly
appreciate it.
Have a nice weekend.
Ray
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R-help@stat.math.ethz.ch mailing list
On 06-Jul-05 Göran Broström wrote:
On Wed, Jul 06, 2005 at 10:06:45AM -0700, Thomas Lumley wrote:
(...)
If X, Y, and Z are independent and Z takes on more than one
value then X/Z and Y/Z can't be independent.
Not really true. I can produce a counterexample on request
(admittedly quite
Hi, Göran: I'll bite:
(a) I'd like to see your counterexample.
(b) I'd like to know what is wrong with my the following, apparently
defective, proof that they can't be independent: First consider
indicator functions of independent events A, B, and C.
My thanks to Douglas Bates and others for pointing out ANOV's limitations.
Now the question is how to put my new won knowledge into practice.
Before my eyes were opened
if row effect and interaction were both statistically significant
I would report the row effects separately for each
(Ted Harding) wrote:
On 06-Jul-05 Göran Broström wrote:
On Wed, Jul 06, 2005 at 10:06:45AM -0700, Thomas Lumley wrote:
(...)
If X, Y, and Z are independent and Z takes on more than one
value then X/Z and Y/Z can't be independent.
Not really true. I can produce a counterexample on request
Spencer Graves wrote:
Hi, Göran: I'll bite:
(a) I'd like to see your counterexample.
(b) I'd like to know what is wrong with my the following, apparently
defective, proof that they can't be independent: First consider
indicator functions of independent events A, B, and
Dear all,
I have define a discrete distribution P(y_i=x_i)=p_i, which I want to
plot a CDF plot. However, I can not find a function in R to draw it
for me after searching R and R-archive. I only find the one for the
sample CDF instead my theoretical one.
I find stepfun can do it for me, however,
Hi, Duncan Göran:
Consider the following: X, Y, Z have symmetric distributions with
the following restrictions:
P(X=1)=P(X=-1)=x with P(|X|1)=0 so P(|X|1)=1-2x.
P(Y=1)=P(Y=-1)=y with P(|Y|1)=0 so P(|Y|1)=1-2y.
P(Z=1)=P(Z=-1)=z with P(|Z|1)=0 so
On 7/6/05, huang min [EMAIL PROTECTED] wrote:
Dear all,
I have define a discrete distribution P(y_i=x_i)=p_i, which I want to
plot a CDF plot. However, I can not find a function in R to draw it
for me after searching R and R-archive. I only find the one for the
sample CDF instead my
I thought that I would take a stab at this. I should note however that
my solution is heavily biased by the first log scale plot that Michael
referenced below. To wit, my x axis has major ticks at powers of 10 and
minor ticks at 1/10 of each major tick interval.
Thus, here is my approach:
# Set
TukeyHSD in package base works with aov objects.
simint in package multcomp has many more options.
RSiteSearch(Tukey HSD), and RSiteSearch(LSD) also produced some
interesting reading, including cautions by two of the leading
contributors to R and to this list
Hello,
Is there a way to suppress traceback() from returning the full structure of
a dataframe that is passed internally in a function?
As a simple toy example, suppose we had two functions that pass a dataframe
internally:
data(Formaldehyde)
fn2 - function(formula, data, ...) {
res -
Christian Hennig wrote:
Hi list,
1) How can the MM-estimator method=MM in function rlm be tuned to 85%
efficiency? It seems that there is a default tuning to 95%. I presume, but
am not sure, that the MM-estimator uses phi=phi.bisquare as default and
the tuning constant could be set by adding a
Hi Harold,
I know nothing about Sweave (though it certainly sounds like a great
idea!). Does Sweave hold these files open simultaneously - many
operating systems wouldn't be able to cope with 20,000 simultaneously
open files.
Could you be running out of disk space? or inodes - if you're on a
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