maxent | R Documentation |
Build a "MaxEnt" (Maximum Entropy) species distribution model (see references below). The function uses environmental data for locations of known presence and for a large number of 'background' locations. Environmental data can be extracted from raster files. The result is a model object that can be used to predict the suitability of other locations, for example, to predict the entire range of a species.
Background points are sampled randomly from the cells that are not NA
in the first predictor variable, unless background points are specified with argument a
.
This function uses the MaxEnt species distribution model software by Phillips, Dudik and Schapire.
## S4 method for signature 'Raster,ANY'
maxent(x, p, a=NULL, factors=NULL, removeDuplicates=TRUE, nbg=10000, ...)
## S4 method for signature 'SpatialGridDataFrame,ANY'
maxent(x, p, a=NULL, removeDuplicates=TRUE, nbg=10000, ...)
## S4 method for signature 'data.frame,vector'
maxent(x, p, args=NULL, path, ...)
## S4 method for signature 'missing,missing'
maxent(x, p, silent=FALSE, ...)
x |
Predictors. Raster* object or SpatialGridDataFrame, containing grids with predictor variables. These will be used to extract values from for the point locations. |
p |
Occurrence data. This can be a data.frame, matrix, SpatialPoints* object, or a vector. If If |
a |
Background points. Only used if |
nbg |
Number of background points to use. These are sampled randomly from the cells that are not |
factors |
character. Which (if any) variables should be considered as categorical? Either by (layer)name or by index. Only used when argument 'x' is a Raster* object because it is not needed in other cases as you can set the appropriate class to the variables in the data.frame |
args |
charater. Additional argument that can be passed to MaxEnt. See the MaxEnt help for more information. The R maxent function only uses the arguments relevant to model fitting. There is no point in using args='outputformat=raw' when *fitting* the model; but you can use arguments relevant for *prediction* when using the predict function. Some other arguments do not apply at all to the R implementation. An example is 'outputfiletype', because the 'predict' function has its own 'filename' argument for that |
removeDuplicates |
Boolean. If |
path |
character. Optional argument to set where you want the MaxEnt output files to be stored. This allows you to permanently keep these files. If not supplied the MaxEnt files will be stored in a temporary file. These are the files that are shown in a browser when typing the model name or when you use "show(model)" |
silent |
Boolean. If |
... |
Additional arguments |
An object of class 'MaxEnt' (inherits from DistModel-class
). Or a 'MaxEntReplicates' object if you use 'replicates=' as part of the args
argument. If the function is run without any arguments a boolean value is returned (TRUE
if maxent.jar was found).
Steven Phillips and Robert J. Hijmans
https://biodiversityinformatics.amnh.org/open_source/maxent/
Steven J. Phillips, Miroslav Dudik, Robert E. Schapire, 2004. A maximum entropy approach to species distribution modeling. Proceedings of the Twenty-First International Conference on Machine Learning. p. 655-662.
Steven J. Phillips, Robert P. Anderson, Robert E. Schapire, 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling 190:231-259.
Jane Elith, Steven J. Phillips, Trevor Hastie, Miroslav Dudik, Yung En Chee, Colin J. Yates, 2011. A statistical explanation of MaxEnt for ecologists. Diversity and Distributions 17:43-57. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1472-4642.2010.00725.x")}
predict
# test if you can use maxent
maxent()
if (maxent()) {
# get predictor variables
fnames <- list.files(path=paste(system.file(package="dismo"), '/ex', sep=''),
pattern='grd', full.names=TRUE )
predictors <- stack(fnames)
#plot(predictors)
# file with presence points
occurence <- paste(system.file(package="dismo"), '/ex/bradypus.csv', sep='')
occ <- read.table(occurence, header=TRUE, sep=',')[,-1]
# witholding a 20% sample for testing
fold <- kfold(occ, k=5)
occtest <- occ[fold == 1, ]
occtrain <- occ[fold != 1, ]
# fit model, biome is a categorical variable
me <- maxent(predictors, occtrain, factors='biome')
# see the maxent results in a browser:
me
# use "args"
# me2 <- maxent(predictors, occtrain, factors='biome', args=c("-J", "-P"))
# plot showing importance of each variable
plot(me)
# response curves
# response(me)
# predict to entire dataset
r <- predict(me, predictors)
# with some options:
# r <- predict(me, predictors, args=c("outputformat=raw"), progress='text',
# filename='maxent_prediction.grd')
plot(r)
points(occ)
#testing
# background data
bg <- randomPoints(predictors, 1000)
#simplest way to use 'evaluate'
e1 <- evaluate(me, p=occtest, a=bg, x=predictors)
# alternative 1
# extract values
pvtest <- data.frame(extract(predictors, occtest))
avtest <- data.frame(extract(predictors, bg))
e2 <- evaluate(me, p=pvtest, a=avtest)
# alternative 2
# predict to testing points
testp <- predict(me, pvtest)
head(testp)
testa <- predict(me, avtest)
e3 <- evaluate(p=testp, a=testa)
e3
threshold(e3)
plot(e3, 'ROC')
}
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