similar to: Creating composite factor and changing format from character to factor

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),

Hello, I am performing a BACI analysis with ANOVA using the following glm: fit1<-glm(log(Cucs_m+1)~(BA*Otter)+BA+Otter+ID+Primary, data=b1) The summary(aov(fit1)) shows significance in the interaction; however, now I would like to determine what combinations of BA and Otter are significantly different (each factor has two levels). ID and PRIMARY substrates are categorical and included in

I am running a linear model with achiev as the outcome and major as my iv (5 levels). The lm statement runs fine, but for the glht command I get the following error. I noted that someone else asked the same question a while back but received no reply. I am hoping someone might know what is happening. anovaf2<-lm(achiev ~ major, data=data_mcp) > pairwise<- glht(anovaf2,linfct =

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

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

Could you please help me on the following ANCOVA issue? This is a part of my dataset: sampling dist h 1 wi 200 0.8687212 2 wi 200 0.8812909 3 wi 200 0.8267464 4 wi 0 0.8554508 5 wi 0 0.9506721 6 wi 0 0.8112781 7 wi 400 0.8687212 8 wi 400 0.8414646 9 wi 400 0.7601675 10 wi 900 0.6577048 11 wi 900

I am trying to do post-hoc tests associated with a repeated measures analysis with on factor nested within respondents. The factor (SOI) has 17 levels. The overall testing is working fine, but I can''t seem to get the multiple comparisons to work. The first step is to "stack" the data. Then I used "lme" to specify and test the overall model. Finally

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

Hi all, I want to order a series that is included on the second column in MCT.csv. I do but R doesn?t order, could be because is a csv? I have prove MCT<-read.csv("MCT.csv") a<-order(MCTor[,2],2,decreasing = FALSE) a<-order(MCTor[,2],1,decreasing = FALSE) or the same with sort but didn?t worked. It is suposed that a will have the ordered on ascending or descending

Hello everybody, problem solved, there was a typo. I wrote Type instead of Material Best ----Messaggio originale---- Da: angelo.arcadi@virgilio.it Data: 22-giu-2012 11.05 A: <r-help@r-project.org> Ogg: Error with glht function: Error in mcp2matrix(model, linfct = linfct) : Variable(s) 'Type' have been specified in 'linfct' but cannot be found in 'model'!

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 ***

hey, how can i extract the values from the CI's when i use following code for a tukey test? the output shows three CI's and i know it should work with 'names but i don't really know how... thanks library(multcomp) data1$soort<-as.factor(data1$soort) amod<-aov(waarde~soort,data=data1) g<-glht(amod, linfct=mcp(soort = "Tukey")) confint(g) -- View this message in

Dear list members, I get the following error when using the glht function to perform a post hoc analysis for an ANOVA with repeated measures: require(nlme) lme_H2H_musicians = lme(H2H ~ Emotion*Material, data=musicians, random = ~1|Subject) require(multcomp) summary(glht(lme_H2H_musicians, linfct=mcp(Type = "Tukey")), test = adjusted(type = "bonferroni")) Error in

Hi all, I attach a picture, with my output plot. I put this command to obtain it: hist(MCT[,2],probability=TRUE,xlab=" ",ylab="Max",main="M distribution") lines(density(MCT[,2]), lwd = 2) The problem is that when I extract the "bell" is too high? And the higher part doesn?t appear in the plot. There is some trick to adjust the line on the plotted area?

Hi enthusiasts, Trying to create a single chart in lattice with different plotting definitions for the different series (two series should be drawn with lines and the other without them) I am using a dataset, which includes a grouping variable e.g. clinic with three levels, the variable "year" and a continous variable: "mct". In the graph the variable "year" is in

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

Dear r-help, I would like to select a subset of levels from a factor variable in a data frame and return a data frame. The data set consists of 3 variables, 2 of which are factors (Site, Fish) and one numeric (Datavalue) as follows: Site Fish Datavalue AB 2-1 2.3 AB 2-1 2.4 AB 2-1 2.2 AB 2-2 2.6 AB 2-2 2.5 AB 2-2 2.7 AB 2-3

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

Dear R-experts, I need to replace the values of a vector(tx) with a word ('Vehicle') when the value of the vector contains the word 'vehicle'. Sometimes, the value could be 'MCT vehicle', or 'control-vehicle', etc. I tried gsub like this treatment<-gsub('vehicle','Vehicle', tx, ignore.case=T) But then I end up with values like 'MCT

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)),