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
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
"Species"...
..I'll try it in the next days to provide the points as dataframe (not
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
Has anyone successfully tried dismo's maxent with multiple species
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
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
but if there is a way of doing them together I would be very
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
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
list into a training and testing dataset with:
kfold(occ.points, k = 5, by = occ.points$Species)
As I read in the orig. MaxEnt tutorial, it should be possible to use an
input file with multiple species. I'd like to know:
Does that accuatlly work also in the R-Maxent setup? Can a provide
maxent() spatial points of different species, or do I have to fit the
manually for each species (resp. in a loop?) How can I access the
of the single species (like the 'me' in the examples of maxent).
Another maxent related question: What happens if one of the predictor
rasters is not entirely populated with values resp. shows NA's? Are
cells just excluded from the model fit and prediction or will there be
problem with the entire model?
Thank you for your help,
Best regards,
Johannes
-------- Original-Nachricht --------
Datum: Fri, 27 Jan 2012 09:06:44 -0800
Von: "Robert J. Hijmans" <r.hijmans at gmail.com>
An: Johannes Radinger <JRadinger at gmx.at>
Betreff: Re: kfold question
An error occurs when you request a kfold for a single observation. I
will fix that, but the request obviously makes no sense. It is
straightforward to count the number of observations by species with
something like
table(data$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]) : ung?ltiges 'times' Argument
Zus?tzlich: Warnmeldungen:
1: In kfold(occ.fish, k = 5, by = occ.fish$Species) :
lowered k for by group: N.Gesamt.Amerikanischer.**Hundsfisch
the number of observations was 4
2: In kfold(occ.fish, k = 5, by = occ.fish$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
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
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