On Fri, 2004-05-14 at 00:08, Peter Nelson wrote:
I've been unable to find a R package that provides the means of
performing Clarke Ainsworth's BIO-ENV procedure or something
comparable. Briefly, they describe a method for comparing two separate
sample ordinations, one from species data and
Dear list,
I would like to export the summary statistics of a regression to latex code.
Is there an easy way of doing that?
Ulrich
--
__
Ulrich Leopold MSc.
Computational Bio- and Physical Geography (CBPG)
Institute for Biodiversity and Ecosystem
On Fri, 2004-05-14 at 00:08, Peter Nelson wrote:
I've been unable to find a R package that provides the means of
performing Clarke Ainsworth's BIO-ENV procedure or something
comparable. Briefly, they describe a method for comparing two separate
sample ordinations, one from species data and
Try: Search in Google for r code latex
And look for eg. the second entry.
You kann also use Sweave (library(tools))
Matthias
-Ursprüngliche Nachricht-
Von: Ulrich Leopold [mailto:[EMAIL PROTECTED]
Gesendet: Freitag, 14. Mai 2004 10:14
An: [EMAIL PROTECTED]
Betreff: [R] Export
Murray Jorgensen [EMAIL PROTECTED] writes:
Greetings all!
This problem occurs using R 1.8.1 on Windows XP. I downloaded the
binaries for R and all packages, including the VR bundle, in December
2003.
The data consists of NZ$ prices and attributes for 643 cars.
summary(price)
On 14 May 2004, Peter Dalgaard wrote:
Murray Jorgensen [EMAIL PROTECTED] writes:
Greetings all!
This problem occurs using R 1.8.1 on Windows XP. I downloaded the
binaries for R and all packages, including the VR bundle, in December
2003.
The data consists of NZ$ prices and
Dear R-helpers
I have a problem related to the use of NLME
I think is simply a matter of getting the nlme coding correct, but i cannot
get my brain around it
I am analysing some 24 growth curves of some cells , and i wanted to say
that there are significant differences between the curves in
Hi all,
Can we solve Quadratic Program with Quadratic Constraint in R ?
Regards,
TEMANNI Ramzi
DEA Student
LimBio
http://www.limbio-paris13.org
UFR de Santé, Médecine et Biologie Humaine (SMBH)
Léonard de Vinci 74, rue Marcel Cachin
93017 Bobigny Cedex
France.
Tél : 01.48.38.73.07
Tél :
Dear all,
I'm not able to solve easily the following simple problem.
I really hope someone can give me some hints.
I trained an svm (e1071). Now I'd like to show the results graphically.
I used plot.svm and I'd like to add some other objects to the plot:
points, (coloured) ellipses to indicate
Thanks for the help.
The variables do all come from a frame but with various transformations
and manipulations. I prefer not to stick them all into a new frame just
to call one function.
Thanks again,
Murray Jorgensen
Prof Brian Ripley wrote:
On 14 May 2004, Peter Dalgaard wrote:
Murray
Darren Shaw [EMAIL PROTECTED] writes:
Dear R-helpers
I have a problem related to the use of NLME
I think is simply a matter of getting the nlme coding correct, but i
cannot get my brain around it
I am analysing some 24 growth curves of some cells , and i wanted to
say that there are
Hi all;
I've got temporal series of data. And I'm plotting it with the type 'l', and
with a interpolating slipe.
Could you advise me about the best way to calculate the area under any of
these curves.
I know it is very easy to calculate the first one, although have no idea of
the second
On 14 May 2004 at 10:13, Ulrich Leopold wrote:
Dear list,
I would like to export the summary statistics of a regression to latex
code. Is there an easy way of doing that?
Ulrich
See function latex() in package
Hmisc
Kjetil Halvorsen
--
On 14 May 2004 at 11:45, Karla Meurk wrote:
Hi, I would like to plot a graph which sits in the background as a
watermark with other plots in the foreground - on top. I have looked
through the threads on the r-project website but they seem to concern
background colours rather than actual
On 14 May 2004 at 11:11, Darren Shaw wrote:
Dear R-helpers
I have a problem related to the use of NLME
I think is simply a matter of getting the nlme coding correct, but i
cannot get my brain around it
I am analysing some 24 growth curves of some cells , and i wanted to
say that there
You probably won't be able to do that without modifying plot.svm(). It
calls filled.contour() like this:
filled.contour(xr, yr, matrix(as.numeric(preds),
nr = length(xr), byrow = TRUE), plot.axes = {
axis(1)
axis(2)
On Fri, 14 May 2004 10:13:47 +0200
Ulrich Leopold [EMAIL PROTECTED] wrote:
Dear list,
I would like to export the summary statistics of a regression to latex
code. Is there an easy way of doing that?
Ulrich
Depending on the regression model and the summary statistics, you can use
the
I run R 1.9.0 on windows 2000, and have the following libraries installed:
affydata_1.3.1
affy_1.4.23
Biobase_1.4.10
DynDoc_1.3.14
gcrma_1.0.6
hgu133acdf_1.4.3
hgu95av2cdf_1.4.3
hgu95av2probe_1.0
matchprobes_1.0.7
moe430acdf_1.4.3
multcomp_0.4-6
mvtnorm_0.6-6
rae230acdf_1.4.3
reposTools_1.3.29
Hi,
I have begun to use R some months ago. I have solved many problems, but now
I do not reach my aim.
I have written a function ?Tranmer.cor? with the parameters x, y and N, which
calculates weighted correlation coefficients. It works, when I define the
parameters each time I want to run it. But
Dear John,
I checked for the uniquenesses from factanal() and found out that these
estimates need an a priori assumption about the number of latent factors
(and they depend strongly on that assumption). What I want is an estimate of
reliablity independent of such an assumption. Is it possible
This is a bioconductor issue, and better suited for that list.
Li, James [PRDUS Non-JJ] [EMAIL PROTECTED] writes:
I run R 1.9.0 on windows 2000, and have the following libraries installed:
affydata_1.3.1
affy_1.4.23
Biobase_1.4.10
DynDoc_1.3.14
gcrma_1.0.6
hgu133acdf_1.4.3
Isn't this a report on problems with Bioconductor packages? If so, please
ask the Bioconductor list as people there will have a much better idea of
what you are trying to do.
On Fri, 14 May 2004, Li, James [PRDUS Non-JJ] wrote:
I run R 1.9.0 on windows 2000, and have the following libraries
If you want pairwise correlations for the cols of matrix x and N
is some parameter to your routine that does not vary throughout
the calculation then:
apply(x,2,function(a)apply(x,2,function(b)Transmer.cor(a,b,N)))
Replace both occurrences of 2 with 1 if you want rows.
Ruedi Epple ruedi.epple
hi: would it be useful to build into R an optional mechanism that
typechecks arguments? for example,
sum.across - function ( inpmatrix : matrixtype( dim[1]1, dim[2]3
) ) : vector { }
# this would define a sum.across function that can take matrices
or data sets, but not vectors,
Hello everyone,
I got a problem to change the default output on the screen and I use
Xemacs ESS and R.
When I happen to show a data.frame with thousands of records (type a
variable name and return), the screen just freeze or keep scrolling for
minutes, because of the large quantity of
Ivo --
The stopifnot statement can be used to do this sort of check. For
example, if you need to check that one of your arguments is a vector with
length = N, you can add
stopifnot(is.vector(myarg))
stopifnot(length(myarg) = N)
To the beginning of your function. This will throw an error if
If its just arg 1 then you can use S3 generics for this. Here it is
but we have extended it to data frames too which isn't so easy
if you can only specify one type:
sum.across - function(x) UseMethod(sum.across)
sum.across.matrix - function(x) { stopifnot(is.numeric(x)); c(rowMeans(x)) }
Dear R list,
I have been trying to do a linear model, extracting the effect of a
covariate and the results do not match, when I do it with other programs
(e.g. minitab) so it is obvious that I was doing something wrong.
Whan I do it with minitab, I have this results: (sector is a
From the output you've shown, Minitab and R give the same thing when you ask
for the same thing. In Minitab,
Source DF Seq SS Adj SS Adj MS F P
sector 6 9.0605 2.9989 0.49981.21 0.297
depth 134.207211.997311.9973
But R does not call show() to print, it calls print() unless you have an
object with a formal class. You can try setting a new data.frame method
for print, but an S3 method, please.
On Fri, 14 May 2004, Song Baiyi wrote:
I got a problem to change the default output on the screen and I use
S4 methods take care of some of this checking (more specification
needed).
best,
-tony
ivo welch [EMAIL PROTECTED] writes:
hi: would it be useful to build into R an optional mechanism that
typechecks arguments? for example,
sum.across - function ( inpmatrix : matrixtype( dim[1]1,
I asked a couple of weeks ago about how to write an S4 method for sum, or
another member of the Summary group generics. This prompted an informed and
somewhat over my head email discussion off list, but for the benefit of
posterity the current answer is
1) Redefine the generic for sum as
Hi,
I am trying to do the following aggregation :
data - data.frame(a=rep(2,10),b=rep(a,10))
aggregate(data$a, by=list(a1=data$a, b1=data$b), NROW)
but I have the following error message
Error in names-.default(`*tmp*`, value = c(names(by), names(x))) :
names attribute [3] must be the
Hi,
I am doing a barplot, and the fist bar is very big (high values) and
the rest of the bars are quite small (small values). So - is there any
way to make the Y scale logarithmic so that i have a wider
distance from 0 to 50 for example than for 50 to 100, and so on?
Thanks in advance for
Someone forgot drop=FALSE was needed. Fixed in R-patched.
BTW, calling an object `data' is not a good idea.
On Fri, 14 May 2004, Philippe Hupé wrote:
Hi,
I am trying to do the following aggregation :
data - data.frame(a=rep(2,10),b=rep(a,10))
aggregate(data$a, by=list(a1=data$a,
Dear Jens,
One of the nice features of maximum-likelihood factor analysis, implemented
in factanal(), is that you can test for the number of common factors.
More generally, the estimated uniquenesses will depend upon the number of
common factors. Using sem() requires a stronger initial
I would like to generate a vector having the same length
as the number of rows in a matrix. The vector should contain
an integer indicating the group of the row, where identical
matrix rows are in a group, and a unique row has a unique integer.
Thus, for
a - c(1,2)
b - c(1,3)
c - c(1,2)
d -
Here's one possibility:
index - as.numeric(factor(apply(mat, 1, paste, collapse=:)))
index
[1] 1 2 1 1 2 3
There's probably some better way though...
Andy
From: Scott Waichler
I would like to generate a vector having the same length
as the number of rows in a matrix. The vector should
Scott Waichler [EMAIL PROTECTED] writes:
I would like to generate a vector having the same length
as the number of rows in a matrix. The vector should contain
an integer indicating the group of the row, where identical
matrix rows are in a group, and a unique row has a unique integer.
Thus,
The trick is to collapse the rows, as Andy Liaw pointed out and
unique.matrix (and .data.frame) does. Once you have the collapsed rows as
character vectors, unique and match will do a fast job (via internal
hashing). (Andy's solution via factor() is the same thing with a bit of
extra baggage.)
The shortest expression I can think of is:
as.numeric(interaction(mat[,1],mat[,2],drop=T))
Completing the thought of those who suggested dist or
unique:
N - nrow(mat)
dd - as.matrix(dist(rbind(mat,unique(mat[-seq(N),seq(N)]
apply(dd,2,function(x)match(0,x))
Scott Waichler scott.waichler
R Version 2.0.0 Under development (unstable) (2004-05-07)
I have been wanting to use TukeyHSD for two and three way aov's, as
they are especially simple for students to use correctly. I realize
model simplification is usually a preferred methodology, but my
disciplinary enertia and simplicity
Thanks to all of you who responded to my help request.
Here is the very efficient upshot of your advice:
mat2 - apply(mat, 1, paste, collapse=:)
vec - match(mat2, unique(mat2))
vec
[1] 1 2 1 1 2 3
P.S. I found that Andy Liaw's method didn't preserve the
index order that I wanted; it yields
Waichler, Scott R Scott.Waichler at pnl.gov writes:
Thanks to all of you who responded to my help request.
Here is the very efficient upshot of your advice:
mat2 - apply(mat, 1, paste, collapse=:)
vec - match(mat2, unique(mat2))
vec
[1] 1 2 1 1 2 3
P.S. I found that Andy Liaw's
I seem to be running into a machine precision issue below.
Should I be using a different method to calculate this or should I do
some kind of validity check
(i.e. max(tapply(resp,data$Split,var,na.rm=TRUE),na.rm=TRUE)0)
in an 'if' statement before the call to anova?
Or is there some
I just can't get it to work... I've got a data.frame that looks like,
ata
age.class acres
1 0 94.25871
2 10 202.58106
3 20 254.74497
4 30 326.43598
5 40 170.75596
6 50 146.50230
7 60 76.84737
8 70 90.65786
9 80
Hello,
I've a problem with a self written routine taking a lot of memory (1.2Gb). Maybe you
can suggest some enhancements, I'm pretty sure that my implementation is not optimal
...
I'm creating many linear models and store coefficients, anova p-values ... all I need
in different lists which
Data frames are supposed to have unique rownames but it
seems xtable does not know that so just set them all
to anyways on a copy of ata that you throw away later:
ata2 - ata
rownames(ata2) - rep(,nrow(ata2))
xtable(ata2)
rm(ata2)
Jeff D. Hamann jeff.hamann at forestinformatics.com writes:
:
On Fri, 2004-05-14 at 12:11, Monica Palaseanu-Lovejoy wrote:
Hi,
I am doing a barplot, and the fist bar is very big (high values) and
the rest of the bars are quite small (small values). So - is there any
way to make the Y scale logarithmic so that i have a wider
distance from 0 to 50
Real rough estimate ... looks like you're trying to store about 38 million
numbers in the data frame. Do you need all of the models in the dataframe
at the end or are you just trying to generate the output and look at it
later?
Perhaps you could save intermediate results to file, that is, create
The problem with interaction() is that it doesn't scale with increasing
number of columns:
set.seed(1)
mat2 - matrix(sample(20,5e4,rep=T), 1e4)
invisible(gc()); system.time(z0 - f0(mat2))
[1] 1.58 0.01 1.85 NA NA
invisible(gc()); system.time(z1 - f1(mat2))
[1] 1.57 0.00 1.66 NA NA
Hello:
The website
http://ourworld.compuserve.com/homepages/jsuebersax/tetra.htm might
provide you with further hints and information on implementing
polychoric correlations. Further information related to your inquiry can
also be found on http://www.unt.edu/rss/class/rich/5840/
In addition,
OK. Good point. I have revised the interaction solution (which is
now unfortunately not as short) but it is nearly an order of
magnitude faster than the other two using 5 columns. It is solution
f4, below:
R set.seed(1)
R mat - matrix(sample(20,10,rep=T),nc=5)
R
R f0 - function(mat) {
+
rownames are for a matrix.
row.names are for a data frame.
I think you have confused your helpers. Try coercing to a matrix first.
I am not sure it will `work fine': it does still seem to have an empty
column for the row names. This is hard-coded in print.xtable in the lines
cols -
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