Hello,
When I try to to obtain the expected risk for a new dataset using coxph in the
survival package I get an error. Using the example from ?coxph:
test1 - list(time= c(4, 3,1,1,2,2,3),+
status=c(1,NA,1,0,1,1,0),+ x= c(0, 2,1,1,1,0,0),+
when I load my data file in txt format into the R workstation I lose about
6000 rows, this is a problem. Is there a limit to the display capabilities
for the workstation? is all the information there and I just can't see the
first couple thousand rows?
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I need to compute a high dimensional integral. Currently I'm using the
function adapt in R package adapt. But this method is kind of slow to me.
I'm wondering if there are other solutions. Thanks.
Zhongwen
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Hi,
I got the following problem when I type make. The error is not enough
verbose to me so I can find the problem. Please cc me, I'm not
subscribed.
Thanks,
Mathieu
---
make[4]: `vfonts.so' is up to date.
building system startup profile
building package 'base'
all.R is
Reid Tingley r_tingley at hotmail.com writes:
When I try to to obtain the expected risk for a new dataset using coxph in the
survival package I get an error.
Using the example from ?coxph:
# Example rewritten by DM; please do not use HTML mail
library(survival)
test1 - list(time= c(4,
On Fri, Jun 6, 2008 at 10:30 PM, RobertsLRRI [EMAIL PROTECTED] wrote:
when I load my data file in txt format into the R workstation I lose about
6000 rows, this is a problem. Is there a limit to the display capabilities
for the workstation? is all the information there and I just can't see
On Fri, 6 Jun 2008, hadley wickham wrote:
On Fri, Jun 6, 2008 at 6:23 PM, Achim Zeileis
[EMAIL PROTECTED] wrote:
On Fri, 6 Jun 2008, Michael Friendly wrote:
In an R graphic, I'm using
cond.col - c(green, yellow, red)
to represent a quantitative variable, where green means 'OK', yellow
Rebecca Sela rsela at stern.nyu.edu writes:
When I use a model fit with LME, I get an error if I try to use predict with
a dataset consisting of a single line.
For example, using this data:
simpledata
Y t D ID
23 4.359511097 3 1 6
24 6.165419699 4 1 6
This
John Fox jfox at mcmaster.ca writes:
I intend at some point to extend the effects package to linear and
generalized linear mixed-effects models, probably using lmer() rather
than lme(), but as you discovered, it doesn't handle these models now.
It wouldn't be hard, however, to do the
On Fri, 6 Jun 2008, ZT2008 wrote:
I need to compute a high dimensional integral. Currently I'm using the
function adapt in R package adapt. But this method is kind of slow to me.
I'm wondering if there are other solutions. Thanks.
What does 'high' mean? Numerical quadrature will be slow in
Thanks Daniel. Appreciate your info.
- G.V.
On Fri, Jun 6, 2008 at 9:51 PM, Daniel Folkinshteyn [EMAIL PROTECTED] wrote:
according to the helpfile, comment only takes one character, so you'll have
to do some 'magic' :)
i'd suggest to first run mydata through sed, and replace one of the
Muhammad Azam wrote:
Dear R users
I have a very basic question. I tried but could not find the required result.
using
dat - pima
f - table(dat[,9])
f
0 1
500 268
i want to find that class say 0 having maximum frequency i.e 500. I used
which.max(f)
which provide
0
1
How can
You need to read the file into an object:
dat - read.table(file=C:\\Documents and Settings\\Owner\\My
Documents\\colon cancer1.txt,header=T,row.names=1)
On Sat, Jun 7, 2008 at 12:56 AM, Paul Adams [EMAIL PROTECTED] wrote:
Hello everyone,
I have two problems which I am unable to solve :
1.I
try:
yr1bp$TreeTag[1501]-sub(1.00, 1, as.character(yr1bp$TreeTag[1501]))
Since it appears that TreeTag is a factor. This can be verified with 'str'.
On Fri, Jun 6, 2008 at 11:22 PM, john.polo [EMAIL PROTECTED] wrote:
Daniel Folkinshteyn wrote:
works for me:
sub('1.00', '1', '1.00E-20')
Actually change the TreeTag to characters first because you are trying to
store in a new factor value that is not there
yr1bp$TreeTag - as.character(yr1bp$TreeTag)
yr1bp$TreeTag[1501]-sub(1.00, 1, yr1bp$TreeTag[1501])
# change back to a factor if desired
yr1bp$TreeTag - factor(yr1bp$TreeTag)
I'm trying to do a linear regression between the columns of matrices. In
example below I want to regress column 1 of matrix xdat with column1 of ydat
and do a separate regression between the column 2s of each matrix. But the
output I get seems to give correct slopes but incorrect intercepts and
Hello
Is there exists a package for multivariate random forest, namely for
multivariate response data ? It seems to be impossible with the
randomForest function and I did not find any information about this
in the help pages ...
party:::cforest can do, here is an example:
y -
On Sat, 7 Jun 2008, Dieter Menne wrote:
Rebecca Sela rsela at stern.nyu.edu writes:
When I use a model fit with LME, I get an error if I try to use predict with
a dataset consisting of a single line.
For example, using this data:
simpledata
Y t D ID
23 4.359511097 3 1 6
On Jun 7, 2008, at 8:13 AM, jonboym wrote:
I'm trying to do a linear regression between the columns of
matrices. In
example below I want to regress column 1 of matrix xdat with
column1 of ydat
and do a separate regression between the column 2s of each matrix.
But the
output I get
Hi,
I'm relatively new to R, so I don't know the full list of base (or
popular add-on packages) functions and tools available. For example, I
tripped across mention of rle() in a message about some other problem.
rle() turned out to be a handy shortcut to splitting some of my data by
Yes, I knew I have to use gmake instead of the BSD one. So, I have set
the export MAKE=gmake before the installation process. Your reply
reminder me of the possibility that I have failed to install some
other related components. After install the GUN version of automake,
the problem is solved.
Hi all,
I found this snippet in a gene expression
clustering code.
__BEGIN__
temp - readLines(GSE1110_series_matrix.txt);
cat(temp[-grep(^!|^\$, temp)], file=GSE1110clean.txt, sep=\n);
mydata - read.delim(GSE1110clean.txt, header=T, sep=\t)
mydatascale - t(scale(t(mydata)))
I am wondering, in
The two sets of packages I use a lot for their utility functions and for
making my day-to-day analysis and reporting easier are Hmisc and Design
by Frank Harrell and {gdata,gmodels,gplots} by Greg Warnes. Frank's
packages have good documentation and cover a pretty good range of
regression
Type ?scale in R for the answer :)
Gundala Viswanath wrote:
Hi all,
I found this snippet in a gene expression
clustering code.
__BEGIN__
temp - readLines(GSE1110_series_matrix.txt);
cat(temp[-grep(^!|^\$, temp)], file=GSE1110clean.txt, sep=\n);
mydata - read.delim(GSE1110clean.txt, header=T,
Which packages you need is crucially dependent on what you want
to do. There is not likely a general answer. Googling for CRAN Task Views
should get you to package views which list packages applicable to
different areas.
Prior to installing any R packages yourself
library()
will list the
Hi,
I got the following problem when I type make. The error is not enough
verbose to me so I can find the problem. Please cc me, I'm not
subscribed.
Thanks,
Mathieu
---
make[4]: `vfonts.so' is up to date.
building system startup profile
building package 'base'
all.R is
When a variance components mixed model is run in Stata, if some of the
variance components are zero, the model may not converge, for rational
reasons. However, when the same model is run in SAS, the models with
variance components that estimate to zero nonetheless converge. If I'm
Hi All,
I was using the function bugs() in package R2WinBUGS to call WinBUGS
under Linux, and the WInBUGS window always hangs up until the program
finishes. This causes a little inconvenience if I run a program which
takes a long time (a couple of days), because I cannot use nohup
[command] and
I'm working with a genomic data-set with ~31k end-points and have
performed an F-test across 5 groups for each end-point. The QA
measurments on the individual micro-arrays all look good. One of the
first things I do in my work-flow is take a look at the p-valued
distribution. it is my
Nanye Long wrote:
Hi All,
I was using the function bugs() in package R2WinBUGS to call WinBUGS
under Linux, and the WInBUGS window always hangs up until the program
finishes. This causes a little inconvenience if I run a program which
takes a long time (a couple of days), because I cannot use
Dear Dieter,
I don't know whether I qualify as a master, but here's my brief take on
the subject: First, I dislike the term least-squares means, which seems to
me like nonsense. Second, what I prefer to call effect displays are just
judiciously chosen regions of the response surface of a model,
Dear R users,
I am analyzing several response variables (all scaled to [0;1]) using a
multivariate linear model.
After fitting the model, I set up a hypothesis matrix to test specific
contrasts for these response variables; for example: a always increases
significantly more than b when regressed
Thanks to Dieter Menne for suggesting cph in the Design package. I had been
looking at cph, but I can't seem to find an analog to the expected argument
in the survival package. Am I missing something? I am using R 2.6.1 and Windows
XP. Cheers,Reid To: [EMAIL PROTECTED] From: [EMAIL PROTECTED]
Dear Mark,
try out the example code below. Such a p-value distribution often occurs
if you have batch effects, i.e. if the between-group variability is
in fact less than the within-group variability.
In the example below, I do, for each row of x, a t-test between the
values in the even
On Sat, Jun 7, 2008 at 3:02 PM, John Fox [EMAIL PROTECTED] wrote:
Dear Dieter,
I don't know whether I qualify as a master, but here's my brief take on
the subject: First, I dislike the term least-squares means, which seems to
me like nonsense. Second, what I prefer to call effect displays are
Dear Christoph,
To answer your question directly, F statistics are ratios of mean squares,
not of sums of squares. You have to divide the hypothesis and error sums of
squares by their respective degrees of freedom to form the mean squares
before computing the F statistic for each test. Assuming
Hi (Hadley): Do you still have the ggplot2 book being published this summer?
Felipe D. Carrillo Fishery Biologist Department of the Interior US Fish
Wildlife Service California, USA
__
R-help@r-project.org mailing list
On Fri, 6 Jun 2008, RobertsLRRI wrote:
when I load my data file in txt format into the R workstation I lose about
6000 rows, this is a problem. Is there a limit to the display capabilities
for the workstation? is all the information there and I just can't see the
first couple thousand rows?
Hi:
I have a data file in the following format. The first three digits stand
for the ID of a respondent such as 402, 403. Different respondents may have the
same ID. Followed the ID are 298 single digit number ranging from 1 to 5. My
question is how to read this data file into R. I tried
Hello everyone,
I have a data frame in which I am wanting to eliminate the row labels and then
relabel the rows with
g1-g2000.I have used the following code:
dat-read.table(file=C:\\Documents and Settings\\Owner\\My Documents\\colon
cancer1.txt,header=T,row.names=1)
file.show(file=C:\\Documents
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