Dear friends,
My dataset have many zeros, so i must use fisher exact test .
Unfortunately, the fisher.test(stats) function fail to do it.
Anybody knows how to do the fisher exact test with many zeros in the
dataset?
My dataset is:
Dear boot.ers,
I ran a small program for training purposes and ended with problems in
boot.ci
bush - c(rep(1, 840), rep(0, 660))
f.mean - function(y, id) {mean(y[id])}
bushB - boot(bush, f.mean, 1000)
boot.ci(bushB, conf = 0.95, type = c('perc', 'bca'))
Error in bca.ci(boot.out, conf,
Hi R Users!
Thanks in advance.
I am using R-2.5.1 on Windows XP and I have installed all necessary tools
such as perl and tools.exe.
I am trying to use sample(1:100, 3, rep=F) in C. How can I use this R
function in C?
Once again thank you very much for your time.
Hi!
Could you please explain the difference between prior and weight in
rpart? It seems to be the same. But in this case why including a weight
option in the latest versions? For an unbalanced sampling what is the
best to use : weight, prior or the both together?
Thanks a lot.
Aurélie
Hello everyone,
I have a set of data in the following form, which are stored in an Excel
file:
nick john peter
lesson1 0.465 0.498 0.473
lesson2 0.422 0.44 0.134
lesson3 0.45 0.35 0.543
Original Message
Subject: [R] help on fisher.test(stats)?
From: zhijie zhang [EMAIL PROTECTED]
To: R-help@stat.math.ethz.ch
Date: 09.07.2007 09:03
Dear friends,
My dataset have many zeros, so i must use fisher exact test .
Unfortunately, the fisher.test(stats) function fail
hello,
to display a data.frame I use this syntax
dir.create(file.path(tempdir(),R2HTML))
target - HTMLInitFile(file.path(tempdir(),R2HTML),filename=sample,
BackGroundColor=#EE)
HTML(brDon't forget to use the CSS file in order to benefit from fixed-width
font,file=target)
tmp -
Dear Jian,
This came up on R-help recently; I haven't got time to find the thread
for you, but it shouldn't take too much hunting out.
I suggested the following approach, based on the swap method of Roberts
and Stone (1990) Island-sharing by archipelago species. Oecologia 85:
560-567. The code
On 09-Jul-07 02:20:47, Marcus Vinicius wrote:
Dear all,
I need to use the EM algorithm where data are missing.
Example:
x- c(60.87, NA, 61.53, 72.20, 68.96, NA, 68.35, 68.11, NA, 71.38)
May anyone help me?
Thanks.
Marcus Vinicius
The Dempster, Laird Rubin reference given by Simon
Edna Bell wrote:
Hi again!
How do I create the Latex and HTML files for documentation for a new
package, please?
Is there something in the R CMD stuff that would do it, or do I need
to produce by hand, pleaes?
As the manual Writing R Extensions suggests, please write your
ggplot2
===
ggplot2 is a plotting system for R, based on the grammar of graphics,
which tries to take the good parts of base and lattice graphics and
avoid bad parts. It takes care of many of the fiddly details
that make plotting a hassle (like drawing legends) as
Dear Friends,
I want to extract the records from A according to B, but the results are
not correct because R says :
The length of long object is not integer times on the length of short
object.
Anybody have met the same problem? How to do it correctly?
length(A)=47
length(B)=6
This is just a quick confirmation to let you know that we received your
message below at [EMAIL PROTECTED]
Your input is important to us and we will get back to you as soon as we can.
If you have any other questions please feel free to send us email or call
our customer service department
zhijie zhang wrote:
Dear Friends,
I want to extract the records from A according to B, but the results are
not correct because R says :
The length of long object is not integer times on the length of short
object.
Anybody have met the same problem? How to do it correctly?
On Sun, 8 Jul 2007, Aurélie Davranche wrote:
Hi!
Could you please explain the difference between prior and weight in
rpart? It seems to be the same. But in this case why including a weight
option in the latest versions? For an unbalanced sampling what is the best to
use : weight, prior or
AB - with(B, subset(A, coords.x1 %in% X1))
AB
coords.x1 coords.x2
0 542250.9 3392404
7 541512.5 3394722
8 541479.3 3394878
9 538903.4 3395943
18 543274.0 3389919
19 543840.8 3392012
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On
Dear useRs,
I'm trying to use ggplot2 in Sweave (R 2.5.1). The plots use the alpha
channel, so I need to use pdf version 1.4. Search the mailinglist
archive I found two solutions: \SweaveOpts{echo = FALSE,
pdf.version=1.4} and explicit writing to a pdf 1.4 file. The latter
works but the first
Hi folks,
I thought I recalled a request for turning a character string into an
object name as in:
x$as.name(y)-1:4
OR
x-data.frame(as.name(y)=1:4)
However, as.name and a few other uninformed attempts didn't even come
close. A search of character to name produced no helpful functions.
This
Hi, people.
I am using R-2.5.0 now, when tried the function aggregate with sum, it
showed an error as following:
a - gl(3,10)
b - rnorm(30)
aggregate(b,list(a),sum)
# here is the error message, it complained that an error in FUN(X[[1L]],
missing INDEX, and no defaults value.
but the tapply
On Mon, 2007-07-09 at 20:14 +0800, jingjiang yan wrote:
Hi, people.
I am using R-2.5.0 now, when tried the function aggregate with sum, it
showed an error as following:
a - gl(3,10)
b - rnorm(30)
aggregate(b,list(a),sum)
# here is the error message, it complained that an error in
Is one of these alternatives what you want?
# 1
x - list()
x[[y]] - 1:4
x - as.data.frame(x)
x
# 2
x - data.frame(1:4)
names(x) - y
x
# 3
x - as.data.frame(sapply(y, function(x, y) y, 1:4, simplify = FALSE))
x
On 7/9/07, Jim Lemon [EMAIL PROTECTED] wrote:
Hi folks,
I thought I recalled a
I am not sure exactly what you want but see if this
will work. It will give you a dotchart.
Assume your data.frame is dat
First give the lessons column a name. See ?names
convert numbers in data.frame to a matrix for dotchart
dmat - as.matrix(dat[,2:4])
Draw dotchart using dat$lessons as a
Hi R-helpers,
I am new in programming and R, so this may be basic. I need to speed up
a procedure where I minimize some function on different partitions of
the data. I can do this with a loop, as for instance in:
i-1
meanmin-Inf
while (ilength(x)) {
ind-xxord[i]
if (some
Take for example the following data.frame:
a-c(1,1,5)
b-c(3,2,3)
c-c(5,1,5)
sample.data.frame-data.frame(a=a,b=b,c=c)
I'd like to be able to use unique(sample.data.frame), but have
unique() ignore column a when determining the unique elements.
However, I figured that this would be setting for
On 7/9/07, Andrew Yee [EMAIL PROTECTED] wrote:
Take for example the following data.frame:
a-c(1,1,5)
b-c(3,2,3)
c-c(5,1,5)
sample.data.frame-data.frame(a=a,b=b,c=c)
I'd like to be able to use unique(sample.data.frame), but have
unique() ignore column a when determining the unique
Thanks. But in this specific case, I would like the output to include
all three columns, including the ignored column (in this case, I'd
like it to ignore column a).
Thanks,
Andrew
On 7/9/07, hadley wickham [EMAIL PROTECTED] wrote:
On 7/9/07, Andrew Yee [EMAIL PROTECTED] wrote:
Take for
Hi,
2007/7/8, Marc Schwartz [EMAIL PROTECTED]:
[snip]
There exists the xlsReadWrite package on CRAN by Hans-Peter Suter, which
is restricted to Windows, since it utilizes the non-FOSS MS Office API
to write the Excel formats.
The non-FOSS API is not the problem(#) but its implementation is:
I can't use the HTML.data.frame function maybe because the good package should
however be charged I charged R2HTML and HTMLapplets could you indicate to me in
which package this function is?
_
Thanks all of you guys for your help. It will most helpful.
[EMAIL PROTECTED] a écrit :
On 7/7/07, Sébastien [EMAIL PROTECTED] wrote:
Dear R users,
Here is a couple a quick questions, for which I was unable to not find
any answer in the list archives and in the help:
[...]
2- When a log
Dear Bjorn,
Do you know that mean(xy*ind)+mean(xy*!ind) yields the same value for
all i? Maybe you meant mean(xy[ind]) + mean(xy[!ind])
sapply(xord, function(xordi, xy = x){
ind - xy xordi
mean(xy*ind)+mean(xy*!ind)
})
Cheers,
Thierry
Andrew Yee wrote:
Thanks. But in this specific case, I would like the output to include
all three columns, including the ignored column (in this case, I'd
like it to ignore column a).
df[!duplicated(df[,c(a,c)]),]
or perhaps
df[!duplicated(df[-2]),]
Thanks,
Andrew
On 7/9/07, hadley
Dear useRs,
a new package for computing distance and similarity matrices made it to
CRAN, and will propagate to the mirrors soon.
It includes an enhanced version of dist() with support for more than
40 popular similarity and distance measures, both for auto- and
cross-distances. Some
On Mon, 9 Jul 2007, Jim Lemon wrote:
Hi folks,
I thought I recalled a request for turning a character string into an
object name as in:
Yes. It's a FAQ.
-thomas
x$as.name(y)-1:4
OR
x-data.frame(as.name(y)=1:4)
However, as.name and a few other uninformed attempts didn't even
Hi Olivier,
You can call scagnostics either with two vectors, or a data.frame (in
which case it computes all pairwise scagnostics).
I just double checked to make sure I didn't accidentally misname the
vector of scagnostics in R, and it doesn't look like I did, so could
you please send me a
On 7/9/07, Peter Dalgaard [EMAIL PROTECTED] wrote:
Andrew Yee wrote:
Thanks. But in this specific case, I would like the output to include
all three columns, including the ignored column (in this case, I'd
like it to ignore column a).
df[!duplicated(df[,c(a,c)]),]
or perhaps
On Mon, 9 Jul 2007, Andrew Yee wrote:
Thanks. But in this specific case, I would like the output to include
all three columns, including the ignored column (in this case, I'd
like it to ignore column a).
sample.data.frame[!duplicated(sample.data.frame[-1]), ]
(index to exclude columns as
On 7/6/07, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Wed, 4 Jul 2007, hadley wickham wrote:
On 7/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Tue, 3 Jul 2007, hadley wickham wrote:
Hi Stephane,
The problem is that the windows graphics device doesn't support
On Mon, 2007-07-09 at 16:42 +0300, Hans-Peter wrote:
Hi,
2007/7/8, Marc Schwartz [EMAIL PROTECTED]:
[snip]
There exists the xlsReadWrite package on CRAN by Hans-Peter Suter, which
is restricted to Windows, since it utilizes the non-FOSS MS Office API
to write the Excel formats.
The
Announcing...
Planet R - a weblog aggregator for statistical computing
Q: What is it?
A: An aggregator for weblog posts about statistical computing topics,
focused primarily around the R community.
Q2: Where is it?
A2: For now, at http://planetr.stderr.org
Q3: What's it good for?
A3:
Note that there already is a function, read.xls, in gdata that uses Perl.
On 7/9/07, Marc Schwartz [EMAIL PROTECTED] wrote:
On Mon, 2007-07-09 at 16:42 +0300, Hans-Peter wrote:
Hi,
2007/7/8, Marc Schwartz [EMAIL PROTECTED]:
[snip]
There exists the xlsReadWrite package on CRAN by
Thanks, this works perfectly.
On 7/9/07, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Mon, 9 Jul 2007, Andrew Yee wrote:
Thanks. But in this specific case, I would like the output to include
all three columns, including the ignored column (in this case, I'd
like it to ignore column a).
Dear R help,
In limma package, contrasts.fit() function is very useful. I am
wondering whether there is a similar function for lme object, which
means given a mixed linear model fit, compute estimated coefficients
and standard errors for a given set of contrasts.
Thanks,
Shirley
Hi Hadley,
thank you for providing this scagnostics primer
I was trying to do some basic testing, and I see that I probably missed
some points :
first it's not clear for me if the argument of scagnostics should be
raw data or processed data (results of calling splom or whatever...).
If the
Since the covariance is zero (i.e. you have independent normals), you can
simplify your problem so that you just need to perform one-dimensional
integration. Here is how you can do it:
trial2 - function(input) {
#pmvnorm(lower = c(0,0), upper = c(10, 10), mean = input, sigma =
matrix(c(.01, 0,
Shirley,
The contrast package can do this. The method of specifying the contrast
conditions/coefficients is different (and I think easier).
Max
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of shirley zhang
Sent: Monday, July 09, 2007 11:16 AM
To:
Hi Max,
Thanks for your prompt reply. Actually I have already checked contrast
package, but I still could not figure out how to set the contrast
matrix for a 2x2 factorial design.
I would like to set a contrast exactly similar to the limma's user
guide, 8.7 Factorial Designs (page 45). For
Gabor Grothendieck wrote:
Note that there already is a function, read.xls, in gdata that uses Perl.
Note that Marc talked about *writing* in his original message.
Uwe Ligges
On 7/9/07, Marc Schwartz [EMAIL PROTECTED] wrote:
On Mon, 2007-07-09 at 16:42 +0300, Hans-Peter wrote:
Hi,
Uwe- thanks. After a little trial and error, I created these two very simple
custom functions that calculate the t.stat and p.value of columns in a
dataframe.
I think they work correctly and as intended. I welcome comments critiques.
myfn.t.stat - function(df) { apply(df,2,function(x)
Announcing CRANberries -- An RSS feed about New and Updated CRAN packages
A new RSS feed [1] is now available that summarizes uploads to CRAN. This
makes it possibly to quickly obtain concise information about which (of the
now over one thousand !!) packages were added or updated at CRAN and
Dirk Eddelbuettel wrote:
but the easiest way may just be to subscribe to Elijah's wonderful 'Planet R'
feed aggregator
My favourite RSS reader at the moment is the RSS cat caption generator:
http://lol.ianloic.com/feed/dirk.eddelbuettel.com/cranberries/index.rss
Barry
Reshape version 0.8
http://had.co.nz/reshape
Reshape is an R package for flexibly restructuring and aggregating
data. It's inspired by Excel's pivot tables, and it (hopefully) makes
it very easy to get your data into the shape that you want. You can find out
more at http://had.co.nz/reshape
Shirley,
Well, you picked the type of contrast that proves my statement wrong.
The interface in the contrast package (and the Design package) may not
be well suited for the type that you are interested in (or other types,
such as SAS's lsmeans type contrasts).
The good news is that the function
Hello everyone,
This is my first time posting to the list, thanks in advance.
I am calculating the smoothed periodogram for the residuals of an AR model
that I fit to EEG data. The autocorrelation plot of the residuals shows the
series is now approximately white (i.e. ACF = 1 at lag 0, and
My apologies for cross-postings
Hi all,
I am interested in performing a cluster analysis on ecological data from
forests in Pennsylvania. I would like to develop definitions for forest
types (red maple forests, upland oak forests, etc.(AH AR in attached table))
based on measured attributes in
Jim Lemon wrote:
Hi folks,
I thought I recalled a request for turning a character string into an
object name as in:
x$as.name(y)-1:4
...
Thanks to those who replied to this eminently dumb question.
OT:
I put this down to the Euthermic Model of Cognitive Efficiency. This
model,
Hi all,
I am interested in performing a cluster analysis on ecological data from
forests in Pennsylvania. I would like to develop definitions for forest
types (red maple forests, upland oak forests, etc.(AH AR in attached table))
based on measured attributes in each forest type. To do this, I
Hi.
It seems that nearly every time I try to use factanal I get the following
response:
faa2db1-factanal(mretdb1,factors=2,method=mle,control=list(nstart=25))
Error in factanal(mretdb1, factors = 2, method = mle, control =
list(nstart = 25)) :
unable to optimize from these starting
I am executing a Repeated Measures Analysis of Variance with 1 DV (LOCOMOTOR
RESPONSE), 2 Within-Subjects Factors (AGE, ACOUSTIC CONDITION), and 1
Between-Subjects Factor (SEX).
Does anyone know whether the between-subjects factor (SEX) belongs in the
Error Term of the aov or not? And if it does
Weijun and I corresponded off-list so that I could
get a copy of the data.
On a relatively modest machine with 2G of RAM, 10G swap,
dual core 1Ghz 64bit AMDs, the code below takes approximately
100 seconds. It is not optimized in any particular way, so
there is room for improvement.
doc -
On 7/8/07, Paul Matthias Diderichsen
[EMAIL PROTECTED] wrote:
Hi Deepayan,
Deepayan Sarkar [EMAIL PROTECTED] schrieb am 06.07.2007
02:05:02:
On 7/5/07, Paul Matthias Diderichsen
[EMAIL PROTECTED] wrote:
library(lattice)
xyplot(speed~dist|speed, data=cars, layout=c(3,3))
If this is
Alex Baugh wrote:
I am executing a Repeated Measures Analysis of Variance with 1 DV (LOCOMOTOR
RESPONSE), 2 Within-Subjects Factors (AGE, ACOUSTIC CONDITION), and 1
Between-Subjects Factor (SEX).
Does anyone know whether the between-subjects factor (SEX) belongs in the
Error Term of the aov
factanal() does not have an argument method=mle.
Trying to do factor analysis on 1000 columns is quite unrealistic, but you
may find rescaling the matrix helps.
On Mon, 9 Jul 2007, Talbot Katz wrote:
Hi.
It seems that nearly every time I try to use factanal I get the following
response:
Meanwhile I have recognized, that the breaks-option enforces density as
the default. But if I try to force frequencies (freq=TRUE) I get the
following feedback:
Warning message:
the AREAS in the plot are wrong -- rather use freq=FALSE in:
plot.histogram(r, freq = freq, col = col, border = border,
Chris:
yes, this is indeed a bug (in predict.svm) - will be fixed in the next
release of e1071.
Thanks for pointing this out,
David
--
Hello all,
I am trying to use the svm method provided by e1071 (Version: 1.5-16)
together with a matrix provided by the SparseM
Since I wrote the xls2csv.pl and read.xls() code for gdata, a perl
module for writing MS-Excel files has come on the scene. I don't
have the time at the moment to create an csv2xls.pl file, but it
should be straightforward, and I would gladly add it to the gdata
package.
-G
On Jul 9,
Is this you want?
library(gplots)
n
-(0.465,0.422,0.45,0.59,0.543,0.498,0.44,0.35,0.64,0.5,0.473,0.134,0.543,0.
11,0.32)
graph - matrix(n, nrow=5, ncol=3)
colnames(graph) - c(Nick, John, Peter)
rownames(graph) - c(Lesson1,Lesson2,Lesson3, Lesson4,Lesson5)
g - barplot2(graph, beside = TRUE,
Dear everybody!
If I have an array of numbers e.g. the points my students got at an
examination, and a key to group the numbers, e.g. the key which
interval corresponds with which mark (two arrays of the same length or
one 2x(number of marks)), how can I get the array of absolute
frequencies of
Hello All,
I have a question, which somehow I think it is easy, however, I just couldn't
get it.
I want to histogram each row of a 1000*2 matrix( means it has 1000 rows), and
I want to see those 1000 pictures together. How can I do this? Am I able to
split a graph into 1000 parts and in
Hi All,
I have strings made up of an unknown number of letters, digits, and
spaces. Strings always start with one or two letters, and always end
with one or two digits. A set of letters (one or two letters) is always
followed by a set of digits (one or two digits), possibly with one or
more
Jessie:
How many pixels would you need to allocate for each of these 1000 parts? Is
that feasible?
Charles Annis, P.E.
[EMAIL PROTECTED]
phone: 561-352-9699
eFax: 614-455-3265
http://www.StatisticalEngineering.com
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
Hi all,
sorry for the misleading in the previous email. here is my function to
calculate the maximum likelihood function for a multinormial distribution:
mymle - function (sigmaX, sigmaY, constraints, env){
# build omega
omegaX = abs(sigmaX) * kin + abs(env) * diag(1.0, n, n)
Well, how about an example of what you are doing, and a
description of what the results you get and the results you
want are?
When I do a histogram, I get frequencies.
Sarah
On 7/9/07, Mag. Ferri Leberl [EMAIL PROTECTED] wrote:
Meanwhile I have recognized, that the breaks-option enforces
How many columns do you have? Is it 2 or 1000; can not tell from your
email. A histogram of 2 values does not seem meaningful.
Do you want 1000 separate histograms, one per page, or multiple per
page? Yes you can do it, the question is what/how do you want to do
it.
On 7/9/07, tian shen
strapply in package gsubfn can do that. The following matches the
indicated regular expression against x and applies the function
given in formula notation (which removes spaces) to each match,
outputting the result as a list:
library(gsubfn)
x - c(AB10B10, A10 B5, AB 10 CD 12, A10CD2EF3)
Is this what you want:
x - A10B10A10 B5AB 10 CD 12A10CD2EF3
x - gsub( , , x) # remove blanks
y - gregexpr([A-Z]+\\s*[0-9]+, x )[[1]]
substring(x, y, y + attr(y, 'match.length') - 1)
[1] A10 B10 A10 B5 AB10 CD12 A10 CD2 EF3
On 7/9/07, Drescher, Michael (MNR) [EMAIL PROTECTED]
Hi all,
I am working on cluster, I am trying to evaluate a within and between
matrix. Is there any facility for that ? I did my own function, but I
am not a programmer, so I am affraid I am not really able to programme
efficiant and fast function...
Thanks
Christophe
It would be nice if you could supply an example of what your input
looks like and then what you would like your output to look like. You
would probably use 'tapply', but I would have to see what you data
looks like.
On 7/9/07, Mag. Ferri Leberl [EMAIL PROTECTED] wrote:
Dear everybody!
If I
thank you. This is definitely doable. - adschai- Original Message
-From: David Meyer Date: Friday, July 6, 2007 6:34 amSubject: Re: [R]
Question for svm function in e1071To: [EMAIL PROTECTED]:
r-help@stat.math.ethz.ch Adschai: The function is written in C++, so
debugging the source
Try this I used today
aggregate(data, by=list(factor.name=data$FACTOR.NAME), sum)
Norm Good
CMIS/e-Health Research Centre
A joint venture between CSIRO and the Queensland Government
Lvl 20, 300 Adelaide Street BRISBANE QLD 4000
PO Box 10842 Adelaide Street BRISBANE QLD 4000
Ph: 07 3024
Unless you want to do this millions of times, efficiecy is probably not
a big issue here, but simplicity always pays off.
I'm presuming you are dealing with a single classification setup.
Let f (n x 1) be a *factor* defining the classes
Let X (n x p) be the data matrix.
Then the steps I would
LOL!
-roger
On 7/9/07, Barry Rowlingson [EMAIL PROTECTED] wrote:
Dirk Eddelbuettel wrote:
but the easiest way may just be to subscribe to Elijah's wonderful 'Planet
R'
feed aggregator
My favourite RSS reader at the moment is the RSS cat caption generator:
Looks like rggobi can't find GGobi. Make sure that PKG_CONFIG_PATH contains
the path to your ggobi.pc file. For example:
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
I would have assumed, however, that the ggobi package would have installed
to the /usr prefix, in which case pkg-config should
On 9 July 2007 at 22:38, Michael Lawrence wrote:
| Looks like rggobi can't find GGobi. Make sure that PKG_CONFIG_PATH contains
| the path to your ggobi.pc file. For example:
|
| export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
|
| I would have assumed, however, that the ggobi package would have
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