[R] apply model predictions over larger area with predict()

[K. Fleischer]

Dear all,

thanx for the quick reply but your ideas have not gotten me further 
unfortuantely..
after implementing the idea from Thierry my code looks like that now:

#b00all is the dataframe with only element used for model fitting
#variables .._zui contain the whole are over which to predict
veld<-b00all$veld00all_zui
water<-b00all$kmoi_water_zui
moeras<-b00all$kveg_moeras_zui
specvec<-b00all$specvec
mydata<-data.frame(specvec,veld,water,moeras)

b00all_mdl6<-glm(specvec~veld+water+moeras, 
data=mydata, family=binomial(link=logit))
veld<-veld00all_zui
water<-kmoi_water_zui
moeras<-kveg_moeras_zui
areadata<-data.frame(as.vector(veld),as.vector(water),as.vector(moeras))
zuid<-predict(b00all_mdl6,newdata=areadata,type="response")

Error: variables ‘veld’, ‘water’, ‘moeras’ were specified with 
different types from the fit
In addition: Warning message:
'newdata' had 7526 rows but variable(s) found have 106 rows 

So again the problem is as follows:

I have a dataframe with each column representing one predictor, whereby 
first columns contains species presence/absences and every row is one 
observation. 

now I want to take the model output and apply it over the whole area 
for which I have predictor values for, which are stored in .asc maps.

That cannot be too difficult I am sure!!

thanx again,
Katrin

MSc student
Computational Geo-Ecology
University of Amsterdam




----- Original Message -----
From: "ONKELINX, Thierry" <Thierry.ONKELINX at inbo.be>
Date: Wednesday, October 15, 2008 9:56 am
Subject: RE: [R] apply model predictions over larger area with predict()
To: "K. Fleischer" <K.Fleischer at student.uva.nl>, r-help at r-project.org

> 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 at inbo.be 
> www.inbo.be 
> 
> To call in the statistician after the experiment is done may be no 
> morethan 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 at r-project.org [mailto:r-help-bounces at r-
> project.org]Namens K. Fleischer
> Verzonden: woensdag 15 oktober 2008 9:34
> Aan: r-help at 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
> 
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