search for: multcomp

...ostatistical Analysis, 3rd. Ed., pg. 201 Example 10.11, pg. 288 Example 11.10). In the real world, I want to compare samples of fish length captured with different fishing gears. After using the Kruskal-Wallis test I want to check the differences between each two samples. I wrote the function multcomp (see below) and it?s working OK but I still have some doubts. To use it one must have a two-column dataframe with groups and measurements. 1) In line 20 (Results <- data.frame....) I create a dataframe to store the final results. It has a fixed row number but it would be better to have a var...

Hello all, Quick question: I want to do posthoc contrasts for a linear mixed effects model. However, when trying to use the csimtest function in multcomp package I receive an error message saying it cannot find the function, even after installing and loading package multcomp. Any pointers would be greatly appreciated Daniel

...20.83829053 Birch 22.9718181 Birch 22.28216829 Birch 24.23136797 Birch 22.32147961 Birch 20.30783598 Oak 27.24047258 Oak 29.7730014 Oak 30.12608508 Oak 25.76088669 Oak 30.14750974 Hornbeam 17.05307949 Hornbeam 15.32805111 Hornbeam 18.26920177 Hornbeam 21.30987049 Hornbeam 21.7173223 I am using the multcomp package to do multiple comparisons as follows library(multcomp) # loads the package fungus<-read.table("fungi.txt", Header=T) # Reads the data from file saved as fungi.txt fungus.cirec<-simint(Fungus.yield~Habitat, data=fungus,conf.level=0.95,type =c("Tukey")) # C...

Dear R-users, I'm currently using the multcomp package to produce plots of means with 95% confidence intervals i.e. mult<-glht(lm(response~treatment, data=statdata), linfct=mcp(treatment="Means")) plot(confint(mult,calpha = sig)) Unfortunately the y-axis on the plot appears to be fixed and hence if the labels on the y-axis (treat...

Hello, I'm a totally newbie to R and I'm taking a class using S+. In the class we use the multcomp command which takes a aov object and calculates confidence intervals for all pairwise differences by the Fisher least significant differences method. How can I do this in R. Thank you for taking the time with such a basic question. I've been looking on the net for a few days and I can't...

...CRAN soon. Thanks for the report! Torsten > > ---------- Forwarded message ---------- > Date: Sat, 3 Sep 2011 23:56:35 +0200 > From: Ulrich Halekoh <Ulrich.Halekoh at agrsci.dk> > To: "r-help at r-project.org" <r-help at r-project.org> > Subject: [R] glht (multcomp): NA's for confidence intervals using > univariate_calpha > > Hej, > > Calculation of confidence intervals for means > based on a model fitted with lmer > > using the package multcomp > > - yields results for calpha=adjusted_calpha > - NA's for...

I am trying to use multcomp to do a Tukey posthoc on growth increments among genetic crosstypes. #Fixed effect model m1 <- lm(inc ~ 0 + Age+ Crosstype + Sex, data = Data.age) summary(m1) RESULTS of the model: summary(m1) Call: lm(formula = inc ~ 0 + Age + Crosstype + Sex, data = Data.age) Residuals: Min 1Q...

...o do Tukey HSD comparisons on a repeated measures expt. I found the following example on r-help and quoted approvingly elsewhere. It is broken. Can anyone please tell me how to get it to work? I am using R 2.4.1. > require(MASS) ## for oats data set > require(nlme) ## for lme() > require(multcomp) ## for multiple comparison stuff > Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats) > Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats) > summary(Aov.mod) > anova(Lme.mod) > summary(Lme.mod) > summary(glht(Lme.mod, linfct=mcp(V="Tukey"))) Error in eval(...

...ler is set to "none" (default on Windows), # hence we cannot send the bug report directly from R. # Please copy the bug report (after finishing it) to # your favorite email program and send it to # # r-bugs@r-project.org # ###################################################### The multcomp functions work on "lm" objects as anticipated. They do not work on "aov" objects. Somehow the inheritance isn't being acknowledged. I can't spot where in the code the problem lies. Somewhere the df argument for "aov" objects is not defined. My workaround is t...

New package `multcomp' for general multiple comparisons written by Frank Bretz, Torsten Hothorn and Peter Westfall We've uploaded the package `multcomp' to CRAN. The R package allows for multiple comparisons of k groups in general linear models. We use the unifying representations of multiple contrast tes...

New package `multcomp' for general multiple comparisons written by Frank Bretz, Torsten Hothorn and Peter Westfall We've uploaded the package `multcomp' to CRAN. The R package allows for multiple comparisons of k groups in general linear models. We use the unifying representations of multiple contrast tes...

...xample 2", the function pmvt return NaN, so I cannot show this simtest result. Is there any solution? (I changed the variable "maxpts" to a large number in front of the function pmvt ... but, the function mvt returned an error. ) -- example 1 ------------------------------- require(multcomp) Loading required package: multcomp Loading required package: mvtnorm [1] TRUE y <- as.vector(t$int) f <- as.factor(t$group1) table(f) f 1 2 3 20988 20988 20988 dat <- cbind(as.data.frame(y),f) gc() summary(simtest(y ~ f, data=dat, type="Dunnett")) Simultane...

Dear useRs, `multcomp' version 0.991-1 will be shortly available from CRAN near you. Nearly all functionality contained in the package has been re-implemented from scratch. The focus of the package has been extended to general linear hypotheses in arbitrary parametric models and the most important function to chec...

I suppose that multcomp in R and multicomp in S-Plus are related and it appears that it is possible to use multicomp with lme in S-Plus given the following correspondence on s-news sally.rodriguez at philips.com 12:57 p.m. 24/04/03 -0400 7 [S] LME summary and multicomp.default() Is it possible to use multicomp with...

I used the multcomp package sometime back for doing multiple comparisons. I see that it has been updated and the methods like simint are no longer supported. When I run the program it prompts to me to use glht. How do I get the lower and upper conf int and the pValues using glht? Does anyone have an example? Thanks...

Hej, Calculation of confidence intervals for means based on a model fitted with lmer using the package multcomp - yields results for calpha=adjusted_calpha - NA's for calpha=univariate_calpha Example: library(lme4) library(multcomp) ### Generate data set.seed(8) d<-expand.grid(treat=1:2,block=1:3) e<-rnorm(3) names(e)<-1:3 d$y<-rnorm(nrow(d)) + e[d$block] d<-transform(d,tr...

Dear useRs, `multcomp' version 0.991-1 will be shortly available from CRAN near you. Nearly all functionality contained in the package has been re-implemented from scratch. The focus of the package has been extended to general linear hypotheses in arbitrary parametric models and the most important function to chec...

Something might have slipped by me, but I got into the following situation installing Rcmdr: < install.packages("Rcmdr",depend=TRUE) > Oodles of Output, until: * Installing *source* package 'multcomp' ... ** R ** data ** inst ** preparing package for lazy loading Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so': /home/bs/pd/Rlibrary/mvtnorm/libs/mvtnorm.so: cannot open shared object file...

...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 functions from library(nlme) and library(multcomp).. I would be thankful for receiving inputs on this script and let me know if I have modeled the lme formula correctly.. If the formula i have used is not the correct one i would appreciate receiving inputs on what is the correct formula for lme that I should use given the context of this example...

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)), B=factor(c('e','...