[R-sig-Geo] Get importance variables in dismo package

[Ben Tupper]

Hi,

Along a similar vein, I have been assembling into a package some basic helper tools for working with dismo and in particular MaxEnt.  

https://github.com/BigelowLab/dismotools

> library(devtools)
> install_github("BigelowLab/dismotools")
> library(dismotools)
> maxent_get_results(me, "importance")
> maxent_get_results(me, "contribution")

Ben



> On Oct 10, 2016, at 4:48 AM, Ahmadou Dicko <dicko.ahmadou at gmail.com> wrote:
> 
> Hi Fabrice,
> 
> If you want to access variable contribution from a MaxEnt model, you can
> use still use the plot method.
> 
> var_imp <- plot(me)
> var_imp
> 
> Or build you own function based on the code of the plot method
> 
> var_contrib <- function(m, df = TRUE, ...) {
>  stopifnot(inherits(m,  "MaxEnt"))
>  res <- m at results[grep("contribution", rownames(m at results)), ]
>  names(res) <- gsub(".contribution", "", names(res))
>  if (df)
>    res <- data.frame(var = names(res), contrib = unname(res))
>  res
> }
> 
> var_contrib(me)
> 
> Hope it helps
> 
> 
> 
> 
> 
> On Mon, Oct 10, 2016 at 10:15 AM, Fabrice Vinatier <
> fabrice.vinatier.pro at gmail.com> wrote:
> 
>> Dear list members (and especially Robert J. Hijmans),
>> 
>> I am actually using the excellent "dismo" package for flora species
>> distribution modelling, and I am wondering if there is a way to get
>> importance of variables used in maxent, domain, mahal and bioclim
>> functions, to handle these importances in a table.
>> 
>> I tested all possible models included in https://cran.r-project.org/web
>> /packages/dismo/vignettes/sdm.pdf and I get easily the importance of
>> variables issued from Random Forest, GLM and RPART models using
>> "$importance", "$coefficients[-1], and "$variable.importance",
>> respectively, but it is more difficult to get the others, although there is
>> a possible indirect access to the importance variable of Maxent model using
>> plot(me) (if me is the fitted model).
>> 
>> Best regards,
>> 
>> Fabrice Vinatier
>> 
>> _______________________________________________
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>> 
> 
> 
> 
> -- 
> Ahmadou H. DICKO, PhD
> Data hacker and climate change economist
> Post-doctoral researcher
> CIRAD - UMR15 CIRAD/INRA Control of exotic and emerging diseases
> email : ahmadou-hamady.dicko at cirad.fr <ahmadou.dicko at ucad.edu.sn>
> twitter : @dickoah
> github : github/dickoa <https://github.com/dickoa>
> portable: +33 7 68 16 11 58
> 
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Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org