[Following up for my own personal education so a bit OT!] Naively, I would have thought that package multcomp would be of use here. So I tried, for my own comprehension and education, to answer the OP's question using multcomp. Here's what I got:
## make this reproducible (I hope) set.seed(1234) s <- c(rpois(8, 4), rep(0, 4)) f <- rpois(12, 30) tr <- gl(3, 4) sf <- cbind(s,f) ## fit the glm mod <- glm(sf ~ tr, family=binomial) summary(mod) ## tr2 and tr3 not different from reference level tr1 anova(mod, test = "Chisq") ## tr is signif ## multiple comparison of levels of tr require(multcomp) mod.glht <- glht(mod, linfct = mcp(tr = "Tukey")) mod.glht summary(mod.glht) If I interpret this correctly, both summary(mod) and summary(mod.glht) suggest that there are no significant differences between the 3 levels of tr, but that tr, as a whole, is better than the Null model (as shown by anova(mod) )? Is my interpretation correct, for this specific example, or am I abusing multcomp and statistics in this case? Thanks for your time and indulgence of a more statistically-related than R-related question All the best, G On Wed, 2008-02-27 at 12:51 +0100, juli pausas wrote: > Thank you very much for your reply. > Then I understand that would not be correct to perform the test in > summary for testing the significance of the different levels of a > factor in relation to the first level, including when there are more > than 2 levels, as in my real case; at least for binomial regressions. > So here a more close-to-real example, with a 3-level factor > > s <- c(rpois(8, 4), rep(0, 4)) > f <- rpois(12, 30) > tr <- gl(3, 4) > sf <- cbind(s,f) > drop1(glm(sf ~ tr, family="binomial"), test="Chisq") # significant > summary(glm(sf ~ tr, family="binomial")) # the 3rd level > is not significant from the 1st > > So I understand that I need to explite the data and perform the two > tests separately: > > drop1(glm(sf ~ tr, family="binomial", subset=(tr %in% c("1", "2"))), > test="Chisq") # ns as expected > > drop1(glm(sf ~ tr, family="binomial", subset=(tr %in% c("1", "3"))), > test="Chisq") # significant, as expected > > Is this the correct approach? > Many thanks > > Juli > > On Wed, Feb 27, 2008 at 12:13 PM, Prof Brian Ripley > <[EMAIL PROTECTED]> wrote: > > On Wed, 27 Feb 2008, juli pausas wrote: > > > > > Dear all, > > > I have a question on glm, family binomial. I do not see significant > > > differences between the levels of a factor (treatment) if all data for > > > a level is 0; and replacing a 0 for a 1 (in fact reducing the > > > difference), then I detect the significant difference that I expected. > > > > This is because you are using the wrong test, one with negligible power. > > See MASS4 pp.197-8 -- you need to use the LRT, as in > > > > > drop1(glm(sf ~ tr, family="binomial"), test="Chisq") > > Single term deletions > > > > Model: > > sf ~ tr > > Df Deviance AIC LRT Pr(Chi) > > <none> 1.595 17.730 > > tr 1 24.244 38.379 22.649 1.944e-06 > > > > (and in your example you can replace 'drop1' by 'anova'). > > > > > > > Is there a way to overcome this problem? or this is an expected > > > behaviour ? Here is an example: > > > > > > s <- c(2,4,4,5,0,0,0,0) > > > f <- c(31,28,28,28,32,37,34,35) > > > tr <- gl(2, 4) > > > sf <- cbind(s,f) # numbers of successes and failures > > > summary(glm(sf ~ tr, family="binomial")) # tr ns > > > > > > sf[8,1] <- 1 > > > summary(glm(sf ~ tr, family="binomial")) # tr significative ** > > > > > > Thanks for any suggestion > > > > > > Juli > > > > > > -- > > > http://www.ceam.es/pausas > > > > > > ______________________________________________ > > > R-help@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-help > > > PLEASE do read the posting guide > > http://www.R-project.org/posting-guide.html > > > and provide commented, minimal, self-contained, reproducible code. > > > > > > > -- > > Brian D. Ripley, [EMAIL PROTECTED] > > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > > University of Oxford, Tel: +44 1865 272861 (self) > > 1 South Parks Road, +44 1865 272866 (PA) > > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > > > > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.