Displaying 20 results from an estimated 900 matches similar to: "Extraction from an output"
2007 Nov 01
1
Help me in Cochran armitage trend test Coding
Dear sir,
I am Shibu John from Thrombosis Research Institute India. It is a
multidisciplinary organisation concerned with the interrelated problems of
thrombosis and atherosclerosis.
I was searching for Cochran armitage trend test program in R. Then I had
seen your R coding for C-A trend test. I tried that in the R software.
But I can?t run the program due the [Error: could not find function
2006 Dec 28
0
Cochran-Armitage statistics
Dear R-enthusiasts,
I am trying to do a Cochran-Armitage test for trend in R. After consulting
google I found Torsten Hothorn's remark that the 'coin' library could be
used.
lungtumor <- data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)),
tumor = c(rep(c(0, 1), c(38, 2)),
rep(c(0, 1), c(43, 7)),
2010 May 30
2
Question about package coin
Anyone know if coin can run a permutation test based on a (user-defined) statistic other than the mean difference? The function independence_test does the permutation t-test via difference in means. I'm wondering if it's possible to use independence_test to run a permutation test for some other statistic than the difference in means. For example, I'd like to run a permutation test
2009 Oct 25
1
A naive question about permutation tests in the coin package
Dear R helpers,
I am trying to understand how to use the independence_test function in
the coin package. I think I suffer from a misunderstanding about what
the package does. Either that or I do not understand how to use it
properly. Specifically, I cannot understand if I can test independence
of arbitrary statistics.
Take the following example:
set.seed(10)
d <- data.frame(y = c(rnorm(10,
2005 Aug 04
2
p-values
HI R-users,
I am trying to repeat an example from Rayner and Best "A contingency
table approach to nonparametric testing (Chapter 7, Ice cream example).
In their book they calculate Durbin's statistic, D1, a dispersion
statistics, D2, and a residual. P-values for each statistic is
calculated from a chi-square distribution and also Monte Carlo p-values.
I have found similar p-values
2009 Sep 23
1
dotchart to barplots
Hi,
I am trying to plot the following data so that it can be visually represented well. I tried the dotchart but I felt it was too spread out. Then I tried the barplot which is good enough for me. Is there a way to give the labels for the y-axis as in the dot chart? Also, I feel the grey level is confusing, so is there options for designs within the bars? I cannot use color as the journal wants
2012 Jul 19
2
Subsetting problem data, 2
Hello,
I didn't give enough information when I sent an query before, so I'm trying
again with a more detailed explanation:
In this data set, each patient has a different number of measured variables
(they represent tumors, so some people had 2 tumors, some had 5, etc). The
problem I have is that often in later cycles for a patient, tumors that
were originally measured are now missing (or
2008 Jul 20
0
coin package (conditional inference / permutation): parameter teststat
Dear R-list members,
This is in fact a question about statistics, not directly
about the R software.
The coin package, for conditional inference through permutation
methods, has as it main function the function independence_test.
One of its parameters is teststat, about which the package
documentation says:
teststat: "a character, the type of test statistic to be applied:
either a
2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
Hi,
The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub.
Unfortunately we don't use qsub anymore so can't test it, but it should be as follows:
R-script eg. test.R:
> ##First read in the arguments listed at the command line
> args=(commandArgs(TRUE))
>
> ##args is now a list of
2006 Aug 18
0
[Fwd: Trend test and test for homogeneity of odd-ratios]
I partly answered my question since independence_test() function in coin package apparently do
Cochran-Armitage trend test just like Eric Lecoutre's function tabletrend() - slightly modified here:
> independence_test(pheno ~ geno, data = dat2, teststat = "quad", scores = list(geno = c(0, 1, 2)))
Asymptotic General Independence Test
data: pheno by groups 1 < 2
2017 Jul 12
2
submitting R scripts with command_line_arguments to PBS HPC clusters
Dear all,
please could you advise me on the following : I've written a R script that
reads 3 arguments from the command line, i.e. :
" args <- commandArgs(TRUE)
TUMOR <- args[1]
GERMLINE <- args[2]
CHR <- args[3] ".
when I submit the R script to a PBS HPC scheduler, I do the following
(below), but ... I am getting an error message.
(I am not posting the error message,
2017 Jul 12
0
submitting R scripts with command_line_arguments to PBS HPC clusters
This sounds like an operating system specific question, in that "submit the R script to a PBS HPC scheduler" would be the kind of action that would run R with very different environment variables and possibly different access credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC
2012 Jun 27
1
trend in incidence rate
I would like to compare the incidence rates of three groups. They are
supposed to have different risks so I would like to test whether there is a
increasing trend in the incidence rates. Does R or any packages provide a
trend test for incidence rates? I checked epiR and epitools. It seems they
do not have this function.
Thank you for the help.
--
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2009 Feb 19
4
problem with comparing a part of string with whole string
Hi all,
I got one problem with comparing strings like if any string is like
"*RIGHT, EPICARDIUM: FOCUS, GRAY-WHITE, SINGLE, APPROX 0.6 CM IN DIAMETER*."
and i have to compare "*GRAY-WHITE*" with the above string
or otherwise i have to compare " *TUMOR BENIGN*" this string
with
"*MEDULLRY TUMOR BENIGN,TYP PHEOCHROMOCYTOMA*"
i
2007 Jun 07
3
How to load a big txt file
Dear list,
I need to read a big txt file (around 130Mb; 23800 rows and 49 columns)
for downstream clustering analysis.
I first used "Tumor <- read.table("Tumor.txt",header = TRUE,sep = "\t")"
but it took a long time and failed. However, it had no problem if I just put
data of 3 columns.
Is there any way which can load this big file?
Thanks for any suggestions!
2007 Aug 07
1
Classifly problems
Hello,
I am trying to explore a classification with GGobi. I am trying to
generate additional data according to the model so I can draw the
decision boundaries on the GGobi plot. The problem is that I always get
the same error: Error in predict.lda(model,data): wrong number of
variables, even if I know that I used the same number of variables for
the model generation (6) and for the additional
2010 Dec 16
1
defining a formula method for a weighted lm()
In the vcdExtra package on R-Forge, I have functions and generic methods
for calculating log odds ratios
for R x C x strata tables. I'd like to define methods for fitting
weighted lm()s to the resulting loddsratio objects,
but I'm having problems figuring out how to do this generally.
# install.packages("vcdExtra", repos="http://R-Forge.R-Project.org")
2008 Feb 27
2
problem with creation of eSet
Hi,
I am having troubles with creating an eSet and would appreciate any help on
the following problem.
I am trying to create an eSet using the following code
pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);
colnames(pd) <- c("type","tumor","time","id");
pdN <- list(type =
2003 Apr 25
2
About qvalue
Hello,
I'm apologize to have made failure before.
I wrote this : p<-scan("teststat.txt") on R and R returns Error in scan
("teststat.txt") : "scan" expected a real, got "x". I don't really
understand,because teststat has been created, so........
Thanks a lot.
Sandrine
2007 Aug 20
1
LDA decission boundaries
Hello,
I would like to plot the results of a LDA analysis plotting the
discriminant scores with the decission boundaries on it with rggobi. I
have GGobi already installed on my computer. I have three classes, so
the plot would be LD1xLD2 plus the decission boundaries. Here there is
the code I use make the plot:
library(MASS)
data <- zgcppr273K.pca$x[,1:7]
Tumor <-