Displaying 20 results from an estimated 12000 matches similar to: "help with interpreting what nnet() output gives:"
2011 Jun 29
0
XML parsing
Hi,
i want to parse a XML-File.
I made some Tutorial but with my special Format it don't work.
An Example of my format:
<?xml version="1.0" encoding="ISO-8859-1"?>
<mzML xmlns="http://psi.hupo.org/ms/mzml"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://psi.hupo.org/ms/mzml
2011 Jun 30
2
volcano plot.r
Hello.
My name is Akashah. i work at metabolic laboratory. From my study, i found that volcano plot can help a lot in my section.
i already studied about the volcano plot and get the coding to run in R software, unfortunately, there is may be something wrong with the coding. This is because no graph appear, but no error (blue color text) was shown on the R console. Below is the coding for
2011 Jun 20
2
(no subject)
HELLO, anybody... could you help me to check the below coding for volcano.
what is the mistake?
what the plot could not display?
# volcano_plot.r
#
# Author: Amsha Nahid, Jairus Bowne, Gerard Murray
# Purpose: Produces a volcano plot
#
# Input: Data matrix as specified in Data-matrix-format.pdf
# Output: Plots log2(fold change) vs log10(t-test P-value)
#
#
2007 Aug 21
0
pvals.fnc unhappy about lmer objects
Dear folks (or Dear Professor Bates),
I'm quite confused as to the current status of some of the available
functions applicable to lmer objects. Following the examples in Baayen,
Davidson, Bates (2006), my plan is to run mcmcsamp on a random effect
model created by lmer in package lme4, then use the (perhaps outdated)
pvals to estimate p-value. But then I couldn't find pvals anywhere.
2008 Nov 26
1
Problem with aovlmer.fnc in languageR
Dear R list,
I have a recurring problem with the languageR package, specifically the
aovlmer.fnc function. When I try to run the following code (from R. H.
Baayen's textbook):
# Example 1:
library(languageR)
latinsquare.lmer <- lmer(RT ~ SOA + (1 | Word) + (1 | Subject),
data = latinsquare)
x <- pvals.fnc(latinsquare.lmer,
2008 Oct 01
1
pvals.fnc in lme4 and languageR
Hi everybody!
I was using the function pvals.fnc from package 'languageR' until April.
I do not know which version. Yesterday I updated all my packages
and tried to run my loop again. Now I get the following error message:
error in pvals.fnc(mm, nsim = 1000) :
MCMC sampling is not yet implemented in lme4_0.999375-27
for models with random correlation parameters
I guess it?s because of
2010 Dec 22
0
fdrtool help
Hello,
I am using fdrtool(x, statistic="pvalue") where x is a vector of chisq
p-values.
I can get this command to work with some x, but not with others.
When it does NOT work, I get the following screen output:
> fdrtool(pvals$Chi2.pval, statistic="pvalue")
Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values
2011 Apr 21
1
Error running pvals.fnc in R version 2.13.0
Dear R-help:
I've been trying to run pvals.fnc in the newest version of R (2.13.0). The
function lmer worked fine, but when I tried to use pvals.fnc on the lmer
object, I got the following error:
"Error in pvals.fnc(elogr.subj.dys.sum.3x3.p, nsim = 10000) :
trying to get slot "coefs" from an object (class "summaryDefault") that is
not an S4 object."
How can I
2010 Apr 01
3
pvals.fnc() with language R does not work with R 2.10.1
Hi Everyone,
I am using R 2.10.1. lmer function works properly, however pvals.fnc
() does not despite the fact that I uploaded:
- library(lme4)
- library(coda)
- library(languageR)
This is the error message I get
pvals.fnc(lexdec3.lmerE2, nsim=10000)$fixed
Error in pvals.fnc(lexdec3.lmerE2, nsim = 10000) :
MCMC sampling is not yet implemented in lme4_0.999375
for models with random
2009 Jul 06
0
R won't recognize the order
Dear R experts,
I was just wondering why R is not picking up the order that I am putting in.
Total ordering is the first argument of the sinDAG function from the package
'SIN'.
Description of sinDAG
This function computes the matrix of simultaneous p-values for SIN model
selection for acyclic
directed graphs (DAGs). SIN assumes that a total ordering of the variables
is available (e.g.,
2007 Jun 25
1
LanguageR pvals.fnc error message
Hi. I get an error message about not converging when I try and use the
pvals.fnc from the languageR library. The LMER analysis worked fine (See
below).
I am not an expert so I don't understand why the LMER worked but not the
pvals.fnc
Any help gratefully received.
- Mike
AIC BIC logLik MLdeviance REMLdeviance
-7324 -7254 3673 -7451 -7346
Random effects:
Groups
2007 May 11
0
incorrect MCMC CIs in pvals.fnc (languageR) ?
library(lme4)
library(coda)
library(languageR)
fit = lmer(Reaction~Days + (1|Subject) + (0+Days|Subject),
data=sleepstudy)
pvals.fnc(fit)$random
# compare with...
samp = mcmcsamp(fit, n=10000, trans=FALSE)
HPDinterval(samp)
densityplot(samp, plot=F)
# 'pvals.fnc' reports sigma instead of sigma^2, but it looks like the
# Sbjc.(In) and Sbjc.Days are also sqrt compared with the
2011 Sep 14
1
how to get a row with its its p value below 0.01 ??
Hi all,
I'm analyzing micro array data.. it has produced a file (to be specific
matrix) withdimension of 35556 2.
first few lines of the matrix are as below..
probe_name control.fdr.pvals.present
10338001 0.000440001
10338002 0.000583093
10338003 0.000528449
10338004 0.000610362
10338005 0.000151825
10338006 0.0001733
10338007 0.000152924
Now, i want only rows whose
2005 Jul 15
1
Adjusted p-values with TukeyHSD (patch)
Dear R-developeRs,
Attached follows a patch against svn 34959 that adds the
printing of p-values to the TukeyHSD.aov function in stats package. I
also updated the corresponding documentation file and added a 'see also'
reference to the simint function of the multcomp package.
As it was already brought up in a previous thread [1] in R-help,
one can obtain the adjusted
2012 Mar 20
0
Running BayesFst in R
Hi All,
I am trying to plot outlier loci in R from data generated by BayesFst. The
developers provide the code which I use but I can't seem to get it to work
consistently. Sometimes I can get R to generate a plot (without confidence
intervals or loci IDs) and other times I cannot even generate P-values using
the code supplied.
I am wondering if any one has used R to plot the BayesFst
2009 Jan 29
0
lmer for a binary dependent variable
Hi,
I am trying to use the lmer function from the lme4 package in R 2.8.0. to fit a generalized mixed-effects model for a dependent variable with a binomial distribution (for more info on my experiment, look below). However, I encounter a major problem: How is it possible to find the general test statistic and see the relative importance of the predictors? The methods which I found described in
2012 Apr 26
0
Correlated random effects: comparison unconditional vs. conditional GLMMs
In a GLMM, one compares the conditional model including covariates with the
unconditional model to see whether the conditional model fits the data
better.
(1) For my unconditional model, a different random effects term fits better
(independent random effects) than for my conditional model (correlated
random effects). Is this very uncommon, and how can this be explained? Can
I compare these models
2009 Jun 15
1
multcomp: contrasts for count data
Hi,
I would like to derive p-values for pair-wise comparison (Tukey's) of
effects when the response is a count.
I am trying a test case where y ~ Po( lambda(x) ). x has three
levels : A, B and C with lambda(x) = 10, 20 and 20 respectively.
Hence, p-values for the contrast C - B should distribute uniformally.
I have implemented this test case as below but do not get uniform
2014 Jun 13
3
p values con LMER
Hola Manuel
lo he tratado de hacer pero me sale
Error: unexpected string constante in:
"anova(a,as,test=Chisq")
no tengo ni idea de por qué...
Me resulta alucinante no poder contar ya con pvals.fnc. ¿Será imposible hacerse con ello?
Saludos,
Miguel
--------------------------------------------
El vie, 13/6/14, Manuel Azcárate <mazcarategarcia en gmail.com> escribió:
2005 Apr 29
0
Anscombe-Glynn, Bonett-Seier, D'Agostino
Dear useRs,
I was searching CRAN for implementation of kurtosis and skewness tests,
and found that there is some kind of lack on it.
So, I have written three functions:
1. Anscombe-Glynn test for kurtosis
2. Bonett-Seier test based on Geary's kurtosis (which is not widely
known, but I was inspired by original paper describing it, found
coincidentally in Elsevier database)
3.