Lmer also has a predict() function. Or you can use lsmeans to get fitted values and se or ci for particular factor or covariate combos.
Boxplot the data first to check for zeroes and also ones though Good luck! On Feb 16, 2017 06:43, "Miguel Cañedo" <mcanedo....@gmail.com> wrote: > Hi Evan! > > Thank you so much! I had already removed species with less than 5 > occurrences. I even tried by only leaving those species with good model > performance. Yet, I get the same error. > > I have uploaded the files here (thanks for the advice!): > > https://drive.google.com/open?id=0B0sFWHdTbJiLeFhfdUlfSUJOUUE > > If anyone could have a quick look at the R code I would be really grateful. > > Best, Miguel. > > 2017-02-16 12:16 GMT+01:00 Evan Palmer-Young <ec...@cornell.edu>: > >> It looks like you have complete separation, meaning that some groups >> either have occurrences at every observation (p=1) or for no observations >> (p=0). >> >> Maybe you could combine some sites or treatments with low sample size >> >> Fyi attachments get scrubbed from the list. A link to a cloud file might >> work better >> >> Good luck! >> >> >> On Feb 16, 2017 03:26, "Miguel Cañedo" <mcanedo....@gmail.com> wrote: >> >> Hi! >> >> I am using the mars.csv function to predict the occurrences of diatoms in >> the Ebro basin (Spain) and I am finding some problems that I can´t solve. >> I >> get the following error: >> >> Creating predictions for subsets... >> glm.fit: fitted probabilities numerically 0 or 1 occurred >> >> I am attaching the predictors + species matrix (DiatomsCV.csv), the >> deviance resulting from applying the mars.glm function, the MARS functions >> and the R code. >> >> Can anyone take a quick look at it? I am really stuck... >> >> Thank you very much in advance! >> >> -- >> *“All things that are still to come lie in uncertainty; live >> straightway!” * >> >> *― Seneca <https://www.goodreads.com/author/show/4918776.Seneca>, On the >> Shortness of Life <https://www.goodreads.com/work/quotes/1374471>* >> >> *Miguel Cañedo-Argüelles* >> https://www.researchgate.net/profile/Miguel_Canedo-Argueelles/ >> http://www.linkedin.com/pub/miguel-cañedo-argüelles/23/4aa/249 >> >> *BETA Group, University of Vic* >> http://www.uvic.cat/es/centro-tecnol%C3%B3gico-beta >> <http://www.uvic.es/en/showrecerca/94> >> >> >> *FEM Group, University of Barcelona*http://www.ub.edu/fem/index.php >> <http://www.ub.edu/fem/> >> _______________________________________________ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> >> >> > > > -- > *“All things that are still to come lie in uncertainty; live > straightway!” * > > *― Seneca <https://www.goodreads.com/author/show/4918776.Seneca>, On the > Shortness of Life <https://www.goodreads.com/work/quotes/1374471>* > > *Miguel Cañedo-Argüelles* > https://www.researchgate.net/profile/Miguel_Canedo-Argueelles/ > http://www.linkedin.com/pub/miguel-cañedo-argüelles/23/4aa/249 > > *BETA Group, University of Vic* > http://www.uvic.cat/es/centro-tecnol%C3%B3gico-beta > <http://www.uvic.es/en/showrecerca/94> > > > *FEM Group, University of Barcelona*http://www.ub.edu/fem/index.php > <http://www.ub.edu/fem/> > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
