K. Fleischer
2008-Oct-15 07:33 UTC
[R] apply model predictions over larger area with predict()
Dear all, I have built glm models based on presences/absences and a number of predictor maps and would like to compute habitat suitability based on the modelled coefficients. I thought this is pretty straight forward and wanted to use predict() and supply the new data in a data frame, with one column for each predictor. However, I do get an error msg warning me that the number of rows for old and new data do not match. the script looks like that: model<-glm(species~temp+prec+elev,family=binomial(link=logit)) #whereby temp,prec,elev are in vector format and contain the elements on species presence/absence; species is vector of 0's and 1's (length=319) wholearea<-data.frame(cbind(as.vector(temperature),as.vector (precipitation),as.vector(elevation)) # (length=7526) predict(model, newdata=wholearea,type="response") Warning message: 'newdata' had 7526 rows but variable(s) found have 319 rows. Ive searched quite a while for the answer now, has anyone encountered that problem before?? thanx in advance. Katrin Fleischer MSc Student Computational Geo-ecology University of Amsterdam
Peter Dalgaard
2008-Oct-15 07:50 UTC
[R] apply model predictions over larger area with predict()
K. Fleischer wrote:> Dear all, > > I have built glm models based on presences/absences and a number of > predictor maps and would like to compute habitat suitability based on > the modelled coefficients. > > I thought this is pretty straight forward and wanted to use predict() > and supply the new data in a data frame, with one column for each > predictor. > > However, I do get an error msg warning me that the number of rows for > old and new data do not match. > > the script looks like that: > > model<-glm(species~temp+prec+elev,family=binomial(link=logit)) > #whereby temp,prec,elev are in vector format and contain the elements > on species presence/absence; species is vector of 0's and 1's > (length=319) > > wholearea<-data.frame(cbind(as.vector(temperature),as.vector > (precipitation),as.vector(elevation)) # (length=7526) > > predict(model, newdata=wholearea,type="response") > > Warning message: 'newdata' had 7526 rows but variable(s) found have > 319 rows. > > Ive searched quite a while for the answer now, has anyone encountered > that problem before?? thanx in advance.Your newdata does not contain the variables named temp, prec, and elev that your model refers to. (And you should get rid of that cbind, but that is not the problem.) -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
ONKELINX, Thierry
2008-Oct-15 07:57 UTC
[R] apply model predictions over larger area with predict()
Dear Katrin, Store the "old" data in a dataframe instead of vectors and supply the name of that dataframe to your model. eg Model <- glm(species ~ temp + prec + elev, data = your.data.frame, family = binomial(link = logit)) Notice that I've added some spaces which makes your code more easy to read. I think this will solve your problem. HTH, Thierry ------------------------------------------------------------------------ ---- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 Thierry.Onkelinx op inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -----Oorspronkelijk bericht----- Van: r-help-bounces op r-project.org [mailto:r-help-bounces op r-project.org] Namens K. Fleischer Verzonden: woensdag 15 oktober 2008 9:34 Aan: r-help op r-project.org Onderwerp: [R] apply model predictions over larger area with predict() Dear all, I have built glm models based on presences/absences and a number of predictor maps and would like to compute habitat suitability based on the modelled coefficients. I thought this is pretty straight forward and wanted to use predict() and supply the new data in a data frame, with one column for each predictor. However, I do get an error msg warning me that the number of rows for old and new data do not match. the script looks like that: model<-glm(species~temp+prec+elev,family=binomial(link=logit)) #whereby temp,prec,elev are in vector format and contain the elements on species presence/absence; species is vector of 0's and 1's (length=319) wholearea<-data.frame(cbind(as.vector(temperature),as.vector (precipitation),as.vector(elevation)) # (length=7526) predict(model, newdata=wholearea,type="response") Warning message: 'newdata' had 7526 rows but variable(s) found have 319 rows. Ive searched quite a while for the answer now, has anyone encountered that problem before?? thanx in advance. Katrin Fleischer MSc Student Computational Geo-ecology University of Amsterdam ______________________________________________ R-help op 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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.