The model is including the extra terms, but they are folded into, well, somewhere. The -1 only removes the intercept from the Time effect: the other factors still have to be contrasts to something. Doesn't Crawley's book explain this? If not, I wrote a paper a few years ago that might help: <http://www.sekj.org/PDF/anz46-free/anz46-124.pdf>
Bob On 23 July 2013 20:53, Leif Rasmuson <rasmu...@uoregon.edu> wrote: > Hi All, > > I am working on re-analyzing per a reviewers request. > > The goal of the project was to determine if the presence of predatory > fishes caused female crabs to delay the release of larvae. Number of > releases were recorded at three time periods: 1 hour before the simulated > tide, 3 hours after the simulated tide and 6 hours after the tide. > Predators were introduced at high tide and removed just following the 3 > hour observation. Thus we have two categorical variables with three levels > each. Time: pre-introduction, after introduction and after removal. > Predator: no-predator, predator of adults and predator of larvae. > > The number of females was not consistent between trials so my initial > method was to use the SRH extension of the Kruskal wallace test to examine > the percent of of larvae released. > > A reviewer suggested that I use a GLM with a binomial distribution and > logit link to analyze the larval release patterns. I used Crawley's book to > analyze the data based on proportions. See code below. The problem I am > running into is that the model is not including the predator control and > interaction is excluding the predator control and the introduction time > periods. Is this just the nature of using a binomial distribution (and/or > our small sample size) or is there a way to force R to include all the > factors and run all the interactions? > > Thanks, > Leif > > N=GLM$NumFemale-GLM$**NumFemaleRelease > y=GLM$NumFemaleRelease > rv <-cbind(y,N) > > > model1=glm(y~GLM$Time*GLM$**Treatment-1,family=binomial) > > summary(model1) > > Call: > glm(formula = y ~ GLM$Time * GLM$Treatment - 1, family = binomial) > > Deviance Residuals: > Min 1Q Median 3Q Max > -1.6024 -0.7146 -0.4284 -0.2512 3.9885 > > Coefficients: > Estimate Std. Error z value Pr(>|z|) > GLM$TimeAfterIntroduction -1.8289 0.2297 -7.963 1.68e-15 *** > GLM$TimeAfterRemoval -3.6571 0.5064 -7.222 5.14e-13 *** > GLM$TimePreIntro -5.0626 1.0029 -5.048 4.46e-07 *** > GLM$TreatmentPlanktivore -0.0123 0.3211 -0.038 0.969 > GLM$TreatmentPredator -0.1589 0.3311 -0.480 0.631 > GLM$TimeAfterRemoval:GLM$**TreatmentPlanktivore 0.5339 0.7132 0.749 0.454 > GLM$TimePreIntro:GLM$**TreatmentPlanktivore 0.6561 1.2708 0.516 0.606 > GLM$TimeAfterRemoval:GLM$**TreatmentPredator -0.1791 0.8399 -0.213 0.831 > GLM$TimePreIntro:GLM$**TreatmentPredator 1.7496 1.1496 1.522 0.128 > --- > Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 > > (Dispersion parameter for binomial family taken to be 1) > > Null deviance: 1720.2 on 270 degrees of freedom > Residual deviance: 258.3 on 261 degrees of freedom > AIC: 378.23 > > Number of Fisher Scoring iterations: 6 > > T > > -- > Leif K. Rasmuson > > Doctoral Candidate > Oregon Institute of Marine Biology > Phone: (253)961-1763 > E-Mail: rasmu...@uoregon.edu > >> <((((º>`·.¸¸.·´¯`·...¸><((((º> >> > > ______________________________**________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide http://www.R-project.org/** > posting-guide.html <http://www.R-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. > -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 798 40226 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://occamstypewriter.org/boboh/ Journal of Negative Results - EEB: www.jnr-eeb.org [[alternative HTML version deleted]]
______________________________________________ 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.
