similar to: How Rcmdr or na.exclude blocks TukeyHSD

Hi, I am seeking help with an error when running the example from R Documentation for TukeyHSD. The error occurs with any example I run, from any text book or website. thank you... > plot(TukeyHSD(fm1, "tension")). Error in plot(confint(as.glht(x)), ylim = c(0.5, n.contrasts + 0.5), ...) : error in evaluating the argument 'x' in selecting a method for function

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

Hello, When plotting the results of a TukeyHSD multiple comparisons procedure with an ANOVA (lm) object, an extra line appears in the confidence intervals that contain 0. For example (this is straight from the TukeyHSD helpfile): > summary(fm1 <- aov(breaks ~ wool + tension, data = warpbreaks)) > TukeyHSD(fm1, "tension", ordered = TRUE) > plot(TukeyHSD(fm1,

Dear R community, I'm trying to understand this behavior of TukeyHSD. My goal is to obtain defensible, labelled multiple comparisons of an interaction term. Firstly, if I plot the TukeyHSD from the model that calculates its own interactions, then the y-axis labels appear to be reflected on their median when compared to the text output of the TukeyHSD statement. The labels are integers.

R Version 2.0.0 Under development (unstable) (2004-05-07) I have been wanting to use TukeyHSD for two and three way aov's, as they are especially simple for students to use correctly. I realize model simplification is usually a preferred methodology, but my disciplinary enertia and simplicity of TukeyHSD is also compelling. However, the lack of names on the comparisons for the higher order

Dear useRs, I'm working on multiple comparison design on two factor (2 3 levels) ANOVA. Each of the tests I have tried (Tukey, multcomp package) seem to do only with one factor at a time. fm1 <- aov(breaks ~ wool * tension, data = warpbreaks) tHSD <- TukeyHSD(fm1, "tension", ordered = FALSE) $tension diff lwr upr p adj M-L -10.000000 -19.35342

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

Hi All, I am wondering if their is a convenient way to export the results of the TukeyHSD function to Word or Excel. I have used capture.output(tukey.contrast, file="tukey.contrast.xls") and this works, but the data are not in a table form, and so it is sort of a pain to manipulate the output. I have be unable to find a more convenient way and any assistance would be greatly

I'm interested in restricting the pairwise comparisons of interaction effects in a multi-way factorial ANOVA, because I find comparisons of interactions between all different variables different to interpret. For example (supposing a p<0.10 cutoff just to be able to use this example): > summary(fm1 <- aov(breaks ~ wool*tension, data = warpbreaks)) Df Sum Sq Mean Sq F

Hey, I have this TukeyHSD output from which I would like to extract only the P-values (p adj, last number). The problem is that the test output is a character list. How can I "break" this sentence to separate the Pv? Tukey multiple comparisons of means 95% family-wise confidence level Fit: aov(formula = Fe1$Fe ~ Fe1$genotype) $`Fe1$genotype` diff lwr upr

Dear Sir, Many thanks for your reply. I have a query. I have a whole set of distributions which should be made normal / homoscedastic. Take for instance the warpbreaks data set. We have the following boxplots for the warpbreaks dataset: a. boxplot(breaks ~ wool) b. boxplot(breaks ~ tension) c. boxplot(breaks ~ interaction(wool,tension)) d. boxplot(breaks ~ wool @ each level of tension) e.

Dear Ashim, I?ll address your questions briefly but they?re really not appropriate for this list, which is for questions about using R, not general statistical questions. (1) The relevant distribution is within cells of the wool x tension cross-classification because it?s the deviations from the cell means that are supposed to be normally distributed with equal variance. In the warpbreaks data

Dear All, I want a transformation which will make the spread of the response at all combinations of 2 factors the same. See for example : boxplot(breaks ~ tension * wool, warpbreaks) The closest I can do is : spreadLevelPlot(breaks ~tension , warpbreaks) spreadLevelPlot(breaks ~ wool , warpbreaks) I want to do : spreadLevelPlot(breaks ~tension * wool, warpbreaks) But I get : >

I am wondering how to customize a pairwise comparisons plot of a factorial ANOVA, without doing a lot of manual manipulation of a TukeyHSD object. The customizations I'd like are: 1. The aov used log-transformed response data, but I'd like to plot the intervals on their original, untransformed scales 2. Plot all the main and interaction effects together, rather than in a separate

Dear Ashim, Try spreadLevelPlot(breaks ~ interaction(tension, wool), data=warpbreaks) . I hope this helps, John ----------------------------- John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada Web: socialsciences.mcmaster.ca/jfox/ > -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Ashim > Kapoor > Sent:

Dear All, we need to do : library(car) for the spreadLevelPlot function I forgot to say that. Apologies, Ashim On Sun, Jan 7, 2018 at 10:37 AM, Ashim Kapoor <ashimkapoor at gmail.com> wrote: > Dear All, > > I want a transformation which will make the spread of the response at all > combinations > of 2 factors the same. > > See for example : > >

I'm manipulating a large dataset and need to eliminate some observations based on specific identifiers. This isn't a problem in and of itself (using which.. or subset..) but an imprint of the deleted observations seem to remain, even though they have 0 observations. This is causing me problems later on. I'll use the dataset warpbreaks to illustrate, I apologize if this isn't in

Hi! I'm failing to understand the value of the intercept value in a multiple linear regression with categorical values. Taking the "warpbreaks" data set as an example, when I do: > lm(breaks ~ wool, data=warpbreaks) Call: lm(formula = breaks ~ wool, data = warpbreaks) Coefficients: (Intercept) woolB 31.037 -5.778 I'm able to understand that the value of

Hello, I am trying to determine the most appropriate way to run post-hoc comparisons on my lme model. I had originally planned to use Tukey HSD method as I am interested in all possible comparisons between my treatment levels. TukeyHSD, however, does not work with lme. The only other code that I was able to find, and which also seems to be widely used, is glht specified with Tukey:

Hello, I have some data in a data.frame where for each of a number of subjects, I have scores for all of a number of symptoms. Subjects are subdivided in a number of groups, which have unequal sizes. I'd like to plot between-group differences in the scores on the various symptoms. Ideally, that would be in a form as would be produced by > bwplot( Score~Symptom ) but I'm not sure