search for: simint

Using a "by() statement, I am preparing ANOVA's for multiple experiments, and using simint() to generate confidence intervals. This works fine. simint.by.fit <- by(analytes.dfr, list(Assay = analytes.dfr$analyte ), function(data) (simint(value ~ tx, data = data,type='Tukey' ) ) ) I can separately prepare plots of the confidence intervals, and I can prepare separate plots...

Dear R-listers, I am trying to compute simultaneous confidence intervals with simint from the package multcomp. 230 measures (abundance) have been taken in 23 sites (factor) of a data.frame (donnees: a file can be sent on request, saved with save(donnees,file="donnees")). I would like to get all pairwise comparisons with : mc<- simint(ren~ID,type="Tukey",dat...

Hi all, I've done some anovas, found some significance and proceeded to do the post hoc tests to determine the source of the significance. I used the multcmp package as suggested by Andy Liaw (thank you). I am, however, unsure how to interpret the results of the call to simint. Could someone help me with this? I've attached the code and the results it produced. There are 3 groups (ctrl,long,short) and I'm trying to see if the data in the Mean_12 column (in the example below) differs based on group membership. for (meanCol in meanColumns) { roi.err.aov<-aov...

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 p-values using the multcomp package and its simint function. The problem is that currently the simint function scales very badly for a large number of contrasts (&...

simint and TukeyHSD work for aov objects. Can someone point me to similar functions for lme objects? Dieter Menne

hi list, i have to ask you again, having tried and searched for several days... i want to do a TukeyHSD after an Anova, and want to get the adjusted p-values after the Tukey Correction. i found the p.adjust function, but it can only correct for "holm", "hochberg", bonferroni", but not "Tukey". Is it not possbile to get adjusted p-values after

...t temple.edu>. Burt Holland is the coauthor of the paper that the ?ptukey documentation references. R was used to run an example in our elementary Stat course. It was a one-way ANOVA, the factor `strategy' having 3 levels Price, Quality and Convenience. We issued the command summary(simint(sales ~ strategy, type="Tukey", data=Xm15.01s)) and received the output Coefficients: Estimate 2.5 % 97.5 % t value Std.Err. strategyPrice-strategyConvenience 31.10 -40.67 102.87 1.043 29.824 strategyQuality-strategyConvenience 75.45 3...

...11 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")) # Computes cimultaneous intervals using Tukey's method plot(fungus.cirec) # plots the data The plot function plots all the comparisons, I want to plot only part of the data since it clutters the graph. How do...

...m" "package:methods" [5] "package:stats" "package:utils" "package:graphics" "package:lattice" [9] "package:grid" "Autoloads" "package:base" > ## from R/rw1091alpha/library/multcomp/R-ex/simint.R > data(recovery) > lmmod <- lm(minutes ~ blanket, data=recovery, contrasts=list(blanket = + "contr.Dunnett")) > summary(simint(lmmod, psubset=2:4, conf.level=0.9, + alternative="less",eps=0.0001)) Simultaneous 90% confidence intervals:...

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 ../Murli [[alternative HTML version deleted]]

Hi, the function TukeyHSD gives incorrect results for balanced incomplete block designs, as the example below shows, but I can only half fix it. There are two problems, 1. It uses model.tables to estimate treatment means, 2. It uses the wrong standard error The first problem can be fixed using dummy.coef, if the lines > TukeyHSD.aov function (x, which = seq(along = tabs), ordered = FALSE,

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I have been using SAS for some time, and now I have discovered R. I am very happy with it, but I have not found out how to perform some of the multiple comparisons I was used to do in SAS. With the SAS/STAT, I generally used the MEANS (for comparison of arithmetic means) and the LSMEANS (for adjusted means) statements of the GLM procedure (I

Dear list, As a reply to my recent mail: > simint and TukeyHSD work for aov objects. > Can someone point me to similar functions for lme objects? Douglas Bates wrote There aren't multiple comparison methods for lme objects because it is not clear how to do multiple comparisons for these. I don't think the theory of multiple compariso...

I've never seen anything written about multiple comparisons, as in the multcomp package or with TukeyHSD, but using a glm. Do such procedures exist? Are they sensible? Are there any packages in R that implement such comparisons? Thank you. -- Ken Knoblauch Inserm U371 Cerveau et Vision 18 avenue du Doyen Lepine 69675 Bron cedex France Tel: +33 (0)4 72 91 34 77 Fax: +33 (0)4 72 91 34 61

I am trying to find the best way to save the follwoing object I am creating library(multcomp) data(recovery) Dcirec<-simint(minutes~blanket, data=recovery, conf.level=0.9, alternative="less") I am probably not doing it the most efficient way I think. Here is what I am doing a<-print(Dcirec) write(a,file="mult_test.dat", append=T) or save(Dcirec, file="mult.out") Which is the best...

Hi, I use glht to make multcomp, using Tukey, from a glm model. It is possible to get a more simplified output of result? Somethink like ordering by letters. Thanks Ronaldo -- Human kind cannot bear very much reality. -- T. S. Eliot, "Four Quartets: Burnt Norton" -- > Prof. Ronaldo Reis J?nior | .''`. UNIMONTES/Depto. Biologia Geral/Lab. de Ecologia | : :' :

This has a stats question and a R question. I am sure there are many core statisticians here how would know the answer to this simple question. In determining the significant comparisons using the methods in multcomp, the ones that are designated as significant are the ones that do not intersect the zero line. What is the physical meaning of this and why are those considered significant? I can

Dear R-users, In a randomized placebo-controlled within-subject design, subjects recieved a psycho-active drug and placebo. Subjects filled out a questionnaire containing 15 scales on four different time points after drug administration. In order to detect drug effects on each time point, I compared scale values between placebo and drug for all time conditions and scales, which sums up to

...en extended to general linear hypotheses in arbitrary parametric models and the most important function to check out is `glht()'. Multiple comparison of means procedures (for example Tukey all-pair comparisons) are contained in the framework as special cases. The old user interface (functions `simint()' and `simtest()') are still available, however deprecated, and the presentation of their output differs from older versions of `multcomp'. As always, feedback, feature requests and bug reports are more than welcome. Best wishes, Torsten __________________________________________...

Hi there, I am quite new to R and I would like to ask two questions: * is it possible to cancel the memory of the arrow up command? * I am running a glm to model animal abundance relating it to research effort and other variables. I have 10 years of data and I am treating year as a factor, R is comparing each year with the first year my data sheet, while I would like to compare each