Displaying 20 results from an estimated 5000 matches similar to: "glht() and contrast() comparison"
2011 Mar 04
2
glht: Problem with symbolic contrast for factors with number-levels
Using a factor with 'number' levels the straightforward
symbolic formulation of a contrast in 'glht' of
the 'multcomp' package fails.
How can this problem be resolved without having to redefine the factor levels?
Example:
#A is a factor with 'number' levels
#B similar factor with 'letter' levels
dat<-data.frame(y=1:4,A=factor(c(1,1,2,2)),
2012 Dec 05
1
Using multcomp::glht() with Anova object
Hello everyone,
I've conducted a Type III repeated-measures ANOVA using Anova() from the
car package, based on the suggestions at
http://blog.gribblelab.org/2009/03/09/repeated-measures-anova-using-r/(option
3) and
http://languagescience.umd.edu/wiki/EEG#ERP_ANOVA_in_R. My ANOVA has two
factors: Condition (3 levels) and Region (6 levels) and their interaction.
Below is code to run the Anova
2012 Nov 05
0
Diference in results from doBy::popMeans, multcomp::glht and contrast::contrast for a lme model
Hello R users,
I'm analyzing an experiment in a balanced incomplet block design (BIB). The
effect of blocks are assumed to be random, so I'm using nlme::lme for this.
I'm analysing another more complex experiments and I notice some diferences
from doBy::popMeans() compared multcomp::glht() and contrast::contrast().
In my example, glht() and contrast() were equal I suspect popMeans()
2009 Mar 22
1
Multiple Comparisons for (multicomp - glht) for glm negative binomial (glm.nb)
Hi
I have some experimental data where I have counts of the number of
insects collected to different trap types rotated through 5 different
location (variable -location), 4 different chemical attractants [A, B,
C, D] were applied to the traps (variable - semio) and all were
trialled at two different CO2 release rates [1, 2] (variable CO2) I also
have a selection of continuous variables
2011 Aug 06
1
multcomp::glht() doesn't work for an incomplete factorial using aov()?
Hi R users,
I sent a message yesterday about NA in model estimates (
http://r.789695.n4.nabble.com/How-set-lm-to-don-t-return-NA-in-summary-td3722587.html).
If I use aov() instead of lm() I get no NA in model estimates and I use
gmodels::estimable() without problems. Ok!
Now I'm performing a lot of contrasts and I need correcting for
multiplicity. So, I can use multcomp::glht() for this.
2011 Mar 01
1
glht() used with coxph()
Hi, I am experimenting with using glht() from multcomp package together with
coxph(), and glad to find that glht() can work on coph object, for example:
> (fit<-coxph(Surv(stop, status>0)~treatment,bladder1))
coxph(formula = Surv(stop, status > 0) ~ treatment, data = bladder1)
coef exp(coef) se(coef) z p
treatmentpyridoxine -0.063 0.939 0.161
2008 Jan 10
1
general linear hypothesis glht() to work with lme()
Hi,
I am trying to test some contrasts, using glht() in
multcomp package on fixed effects in a linear mixed
model fitted with lme() in nlme package. The command I
used is:
## a simple randomized block design,
## type is fixed effect
## batch is random effect
## model with interaction
dat.lme<-lme(info.index~type, random=~1|batch/type,
data=dat)
glht(dat.lme, linfct = mcp(type
2012 Feb 06
2
glht (multicomparisons) with a binomial response variable
Hi,
I,ve a run a model like this
mcrm<-glm(catroj~month,binomial)
being catroj a binary response variable with two levels (infected and
non infected)
> anova(mcrm3,test="Chisq")
Df Deviance Resid. Df Resid. Dev P(>|Chi|)
NULL 520 149.81
mes 3 16.86 517 132.94 0.0007551 ***
When I?m trying to do a post
2008 Apr 15
2
glht with a glm using a Gamma distribution
Quick question about the usage of glht. I'm working with a data set
from an experiment where the response is bounded at 0 whose variance
increases with the mean, and is continuous. A Gamma error
distribution with a log link seemed like the logical choice, and so
I've modeled it as such.
However, when I use glht to look for differences between groups, I get
significant
2013 Jul 25
1
lme (weights) and glht
Dear R members,
I tried to fit an lme model and to use the glht function of multcomp.
However, the glht function gives me some errors when using
weights=varPower().
The glht error makes sense as glht needs factor levels and the model
works fine without weights=. Does anyone know a solution so I do not
have to change the lme model?
Thanks
Sibylle
--> works fine
2012 Jan 11
2
problems with glht for ancova
I've run an ancova, edadysexo is a factor with 3 levels,and log(lcc) is the
covariate (continous variable)
I get this results
> ancova<-aov(log(peso)~edadysexo*log(lcc))
> summary(ancova)
Df Sum Sq Mean Sq F value Pr(>F)
edadysexo 2 31.859 15.9294 803.9843 <2e-16 ***
log(lcc) 1 11.389 11.3887 574.8081 <2e-16 ***
2010 Jul 21
1
post hoc test for lme using glht ?
Hi,
I have a fairly simple repeated measures-type data set I've been attempting
to analyze using the lme function in the nlme package. Repeated searches
here and other places lead me to believe I have specified my model
correctly.
However, I am having trouble with post-hoc tests. From what I gather, other
people are successfully using the glht function from the multcomp package to
2008 Jan 18
1
how to specify a particular contrast
Hi, I am running a simple one-way ANOVA with an
independent factot variable "treat" (3 levels: a, b
and c) and a response variable "y". I want to test a
linear relationship of the response among the 3 levels
of the variable "treat" (ordered a->b->c). I used
glht() from multcomp package. Later I found out I need
to exclude the situation where the response at the
2007 Nov 21
1
multiple comparison (glht) problem
I am not sure whether there is a bug. When I tested the example given for "glht"
in the help, I entered the following error:
Running commands:
amod <- aov(minutes ~ blanket, data = recovery)
rht <- glht(amod, linfct = mcp(blanket = "Dunnett"),
alternative = "less")
Errors are:
Error in try(coef.(model)) : could not find function
2012 Nov 07
1
A warning message in glht
Dear all,
I was wondering if you could give me any suggestions/help on the following
issue. So I carried out the analysis of my data using generalized linear
model (glm). After that, to check for multiple comparisons, I applied the
glht function from the multcomp package in R. The output, however, gave me a
warning (please see below). So my question is whether this warning is smth
that I should
2012 Jan 13
1
GLHT in multcomp: Two similar models, one doesn't work
i ran this model
> model2<-glm(rojos~ageandsex+sector+season+sector:season,quasipoisson)
> glht(model2,linfct=mcp(ageandsex="Tukey"))
General Linear Hypotheses
Multiple Comparisons of Means: Tukey Contrasts
Linear Hypotheses:
Estimate
M - H == 0 0.2898
SUB - H == 0 -0.2261
SUB - M == 0 -0.5159
I tried to do the same changing factor season
2011 Jul 18
1
Multiple comparison test on selected contrasts
Dear Help-list, How can I do a multiple comparison test (mct) on selected contrasts from a linear model while using packages lme4 and multcomp? I am running R 2.13.0 under Windows 7. The following linear model and mct produces a global mct of 15 paired contrasts of the combined (Site, Position) factor SitePos of which only 9 are of interest. Model.G = lmer(log10(SrCa) ~ SitePos + (1 | Eel),
2012 Mar 28
1
discrepancy between paired t test and glht on lme models
Hi folks,
I am working with repeated measures data and I ran into issues where the
paired t-test results did not match those obtained by employing glht()
contrasts on a lme model. While the lme model itself appears to be fine,
there seems to be some discrepancy with using glht() on the lme model
(unless I am missing something here). I was wondering if someone could
help identify the issue. On
2010 May 17
1
Query on linear mixed model
Hi R Forum
I am a newbie to R and I have been amazed by what
I can get my team to accomplish just by
implementing Scripting routines of R in all my
team's areas of interest..
Recently i have been trying to adopt R scripting
routine for some analysis with longitudanal data..
I am presenting my R script below that I have
tried to make to automate data analysis for
longitudanal data by employing
2012 Apr 16
0
warning message: coxme with package multcomp
Hi
I'm encountering an error/warning when doing multiple comparisons with
the package multcomp on a coxme model.
My data:
I'm looking at the removal of brood from the nest according to three
treatments I applied on the brood.
The brood and the workers caring about the brood in the nest, belonged
to different colonies.
Factor: treatment (3 levels: tx,uv,meta)
Random effect 1: origin of