[R-sig-eco] SDM (MaxEnt) per Species, package dismo

Fri Feb 3 16:24:46 CET 2012

Hi Robert,

thank you for your answer. Will the feature of fitting multiple
species models with one dismo::maxent run be implementent in future?
I am asking because the resulting html file provides following  link:
Results for all species modeled in the same Maxent run, with summary statistics and (optionally) jackknife results
I guess that is just the normal output of maxent and is not created
by dismo:maxent.

Anyway I managed to run multiple models in a loop resp. use lapply to
get the singel model objects into a list.

Thank you very much and I really appreciate your work you have provided
with the dismo package.

Best regards,
Johannes

-------- Original-Nachricht --------
> Datum: Wed, 1 Feb 2012 21:07:14 -0800
> Von: "Robert J. Hijmans" <r.hijmans at gmail.com>
> An: Johannes Radinger <JRadinger at gmx.at>
> CC: Mieke Zwart <m.c.zwart at newcastle.ac.uk>, r-sig-ecology at r-project.org
> Betreff: Re: [R-sig-eco] SDM (MaxEnt) per Species, package dismo

> Johannes & Mieke,
> 
> No it is not possible to fit models for multiple species with one call to
> dismo::maxent. This may be possible with the Java program MaxEnt,
> but dismo::maxent behaves more like other R model functions. Also, it is
> straightforward to fit many models using a loop.
> 
> Robert
> 
> 
> On Tue, Jan 31, 2012 at 6:00 AM, Johannes Radinger <JRadinger at gmx.at>
> wrote:
> 
> > Hello,
> >
> > theoretically it should work (at least in the original MaxEnt according
> to
> > the tutorial) to use
> > multiple species as input. When I try to run it with multiple species as
> > spatial points, the
> > species are ignored (treated all as one). In the html output there is a
> > link to the csv file
> > for the single model results but there I can find only one species
> called
> > "Species"...
> >
> > ..I'll try it in the next days to provide the points as dataframe (not 
> as
> > spatial points), maybe that makes
> > a difference. Maybe the spatial points are transformed incorrectly in
> > dismo so that maxent can't read the name column (but thats just a
> guess).
> > Has anyone successfully tried dismo's maxent with multiple species
> already?
> >
> >
> > Best regards,
> > johannes
> >
> >
> > Am 30.01.2012 um 15:12 schrieb Mieke Zwart:
> >
> >  Hi,
> >>
> >> I would like to know this answer as well as I am doing a very similar
> >> thing. I am currently working with enfa (package adehabitat) for
> Species
> >> Distribution Models but will also look at the results with maxent.
> >>
> >> I also have multiple species on my site and was thinking of doing a
> loop,
> >> but if there is a way of doing them together I would be very
> interested!
> >>
> >> Best,
> >>
> >> Mieke
> >>
> >> Mieke Zwart
> >> PhD student
> >> Room 4.53
> >> School of Biology
> >> Ridley 2
> >> Newcastle University
> >> Newcastle upon Tyne
> >> NE1 7RU
> >> United Kingdom
> >>
> >> Tel extension: 5952
> >>
> >>
> >>
> >>
> >> -----Original Message-----
> >> From:
> r-sig-ecology-bounces at r-**project.org<r-sig-ecology-bounces at r-project.org>[mailto:
> >>
> r-sig-ecology-bounces@**r-project.org<r-sig-ecology-bounces at r-project.org>]
> >> On Behalf Of Johannes Radinger
> >> Sent: 30 January 2012 11:25
> >> To: r-sig-ecology at r-project.org
> >> Subject: [R-sig-eco] SDM (MaxEnt) per Species, package dismo
> >>
> >> Hello SIG-ECO list,
> >>
> >> I am want to perform Species Distribution Models with R's dismo package
> >> (function: maxent()). Of course this topic is a spatial topic
> (R-SIG-GEO
> >> related) but I think it fits better to the ECO list.
> >>
> >> For my analysis (MaxEnt)I have a Rasterstack of predictor variables and
> >> the species occurence points as spatial points (sp-class).
> >>
> >> My list of observations has several different species. And I divided
> the
> >> list into a training and testing dataset with:
> >> kfold(occ.points, k = 5, by = occ.points$Species)
> >>
> >> As I read in the orig. MaxEnt tutorial, it should be possible to use an
> >> input file with multiple species. I'd like to know:
> >> Does that accuatlly work also in the R-Maxent setup? Can a provide
> >> maxent() spatial points of different species, or do I have to fit the
> model
> >> manually for each species (resp. in a loop?) How can I access the
> results
> >> of the single species (like the 'me' in the examples of maxent).
> >>
> >> Another maxent related question: What happens if one of the predictor
> >> rasters is not entirely populated with values resp. shows NA's? Are
> these
> >> cells just excluded from the model fit and prediction or will there be
> a
> >> problem with the entire model?
> >>
> >> Thank you for your help,
> >>
> >> Best regards,
> >> Johannes
> >>
> >>
> >> -------- Original-Nachricht --------
> >>
> >>> Datum: Fri, 27 Jan 2012 09:06:44 -0800
> >>> Von: "Robert J. Hijmans" <r.hijmans at gmail.com>
> >>> An: Johannes Radinger <JRadinger at gmx.at>
> >>> Betreff: Re: kfold question
> >>>
> >>
> >>  Johannes,
> >>>
> >>> An error occurs when you request a kfold for a single observation. I
> >>> will fix that, but the request obviously makes no sense. It is
> >>> straightforward to count the number of observations by species with
> >>> something like
> >>> table(data$species)
> >>>
> >>> Best,
> >>> Robert
> >>>
> >>> On Fri, Jan 27, 2012 at 1:56 AM, Johannes Radinger <JRadinger at gmx.at>
> >>> wrote:
> >>>
> >>>  Dear Mr Hijmans,
> >>>>
> >>>> I tried to use your package dismo's function: kfold() I want to
> >>>> split my dataset into 5 parts by species.
> >>>> Of course it is not possible to split records of a species with less
> >>>> the 5 observation into 5 parts... That is the reason why I get a
> >>>> warning message...
> >>>> It'd be okay when these species are devided by their maximum number
> >>>> of records (1,2,3,4).
> >>>> But somehow I also get an error message. I think that might be
> >>>> related to that. Of course it doesn't make sense to devide a species
> >>>> with 1 record by 1. Is this the reason for the error message (sorry
> >>>> it is in German) or is it just something totally different?
> >>>>
> >>>> Fehler in rep(j, times = times[j]) : ungültiges 'times' Argument
> >>>> Zusätzlich: Warnmeldungen:
> >>>> 1: In kfold(occ.fish, k = 5, by = occ.fish$Species) :
> >>>>  lowered k for by group: N.Gesamt.Amerikanischer.**Hundsfisch 
> because
> >>>> the number of observations was  4
> >>>> 2: In kfold(occ.fish, k = 5, by = occ.fish$Species) :
> >>>>  lowered k for by group: N.Gesamt.Flunder  because the number of
> >>>> observations was  3
> >>>> 3: In kfold(occ.fish, k = 5, by = occ.fish$Species) :
> >>>>  lowered k for by group: N.Juvenil.Flunder  because the number of
> >>>> observations was  1
> >>>>
> >>>>>
> >>>>>
> >>>> ...which would mean Error in rep(j, times = times[j]) : invalid
> 'times'
> >>>> argument
> >>>>
> >>>> How do you usually handle such datasets?Probably excluding these
> >>>> species at all and subsetting the dataset (I have to think how to do
> >>>> that in R).
> >>>>
> >>>>
> >>>> best regards,
> >>>> johannes
> >>>> --
> >>>> "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ...
> >>>> Jetzt GMX TopMail testen:
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> >>>>
> >>>>
> >> --
> >>
> >>
> >>
> >>
> >> --
> >>
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> >>
> >
> >

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