dismo: Species Distribution Modeling

Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites and the environment at these sites.

Install the latest version of this package by entering the following in R:
install.packages("dismo")
AuthorRobert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Date of publication2017-01-09 09:49:36
MaintainerRobert J. Hijmans <r.hijmans@gmail.com>
LicenseGPL (>= 3)
Version1.1-4
http://rspatial.org/sdm/

View on CRAN

Man pages

acaule: Solanum acaule data

bioclim: Bioclim

biovars: bioclimatic variables

boxplot: Box plot of model evaluation data

calc.deviance: Calculate deviance

circleHull: Circle hull model

circles: Circles range

convexHull: Convex hull model

dcEvaluate: Evaluate by distance class

density: density

dismo-package: Species distribution modeling

DistModel: Class "DistModel"

domain: Domain

ecocrop: Ecocrop model

ecolim: Ecolim model

evaluate: Model evaluation

evaluateROCR: Model testing with the ROCR package

gbif: Data from GBIF

gbm.data: Anguilla australis distribution data

gbm.fixed: gbm fixed

gbm.holdout: gbm holdout

gbm.interactions: gbm interactions

gbm.persp: gbm perspective plot

gbm.plot: gbm plot

gbm.plot.fits: gbm plot fitted values

gbm.simplify: gbm simplify

gbm.step: gbm step

geocode: Georeferencing with Google

geoDist: Geographic distance model

geoIDW: Inverse-distance weighted model

gmap: Get a Google map

gridSample: Stratified regular sample on a grid

kfold: k-fold partitioning

mahal: Mahalanobis model

maxent: Maxent

mess: Multivariate environmental similarity surfaces (MESS)

ModelEvaluation: Class "ModelEvaluation"

nicheEquivalency: Niche equivalency

nicheOverlap: Niche overlap

nullRandom: Random null model

pairs: Pair plots

plot: Plot predictor values

plotEval: Plot model evaluation data

pointValues: point values

predict: Distribution model predictions

prepareData: Prepare data for model fitting

pwdSample: Pair-wise distance sampling

randomPoints: Random points

rectHull: Rectangular hull model

response: response plots

ssb: Spatial sorting bias

threshold: Find a threshold

voronoi: Voronoi polygons

voronoiHulll: Voronoi hull model

Functions

acaule Man page
Anguilla_grids Man page
Anguilla_test Man page
Anguilla_train Man page
bioclim Man page
Bioclim-class Man page
bioclim,data.frame,missing-method Man page
bioclim,matrix,missing-method Man page
bioclim,Raster,data.frame-method Man page
bioclim,Raster,matrix-method Man page
bioclim,Raster,SpatialPoints-method Man page
bioclim,SpatialGridDataFrame,matrix-method Man page
bioclim,SpatialGridDataFrame,SpatialPoints-method Man page
biovars Man page
biovars,matrix,matrix,matrix-method Man page
biovars,Raster,Raster,Raster-method Man page
biovars,vector,vector,vector-method Man page
boxplot,ModelEvaluation-method Man page
calc.deviance Man page
circleHull Man page
CircleHull-class Man page
circleHull,data.frame-method Man page
circleHull,matrix-method Man page
circleHull,SpatialPoints-method Man page
circles Man page
circles,data.frame-method Man page
circles,matrix-method Man page
CirclesRange-class Man page
circles,SpatialPoints-method Man page
ConvexHull-class Man page
convHull Man page
convHull,data.frame-method Man page
convHull,matrix-method Man page
convHull,SpatialPoints-method Man page
dcEvaluate Man page
density Man page
density,DistModel-method Man page
density,ModelEvaluation-method Man page
dismo Man page
dismo-package Man page
DistModel-class Man page
domain Man page
Domain-class Man page
domain,data.frame,missing-method Man page
domain,matrix,missing-method Man page
domain,Raster,data.frame-method Man page
domain,Raster,matrix-method Man page
domain,Raster,SpatialPoints-method Man page
ecocrop Man page
ECOCROP-class Man page
ECOCROPcrop-class Man page
ECOcrops Man page
ecolim Man page
EcoLim-class Man page
ecolim,matrix,matrix-method Man page
evaluate Man page
evaluateROCR Man page
gbif Man page
gbm.fixed Man page
gbm.holdout Man page
gbm.interactions Man page
gbm.perspec Man page
gbm.plot Man page
gbm.plot.fits Man page
gbm.simplify Man page
gbm.step Man page
geocode Man page
geoDist Man page
geoDist,data.frame-method Man page
geoDist,matrix-method Man page
geoDist,SpatialPoints-method Man page
GeographicDistance-class Man page
geoIDW Man page
geoIDW,data.frame,data.frame-method Man page
geoIDW,matrix,matrix-method Man page
geoIDW,SpatialPoints,SpatialPoints-method Man page
getCrop Man page
gmap Man page
gridSample Man page
InvDistWeightModel-class Man page
kfold Man page
mahal Man page
Mahalanobis-class Man page
mahal,data.frame,missing-method Man page
mahal,matrix,missing-method Man page
mahal,Raster,data.frame-method Man page
mahal,Raster,matrix-method Man page
mahal,Raster,SpatialPoints-method Man page
maxent Man page
MaxEnt-class Man page
maxent,data.frame,vector-method Man page
maxent,missing,missing-method Man page
maxent,Raster,ANY-method Man page
MaxEntReplicates-class Man page
maxent,SpatialGridDataFrame,ANY-method Man page
Mercator Man page
mess Man page
ModelEvaluation-class Man page
nicheEquivalency Man page
nicheOverlap Man page
nullRandom Man page
pairs Man page
pairs,DistModel-method Man page
plot,Bioclim,missing-method Man page
plot,DistModel,numeric-method Man page
plot,ModelEvaluation,character-method Man page
points,DistModel-method Man page
pointValues Man page
predict Man page
predict,Bioclim-method Man page
predict,CircleHull-method Man page
predict,CirclesRange-method Man page
predict,ConvexHull-method Man page
predict,Domain-method Man page
predict,EcoLim-method Man page
predict,GeographicDistance-method Man page
predict,InvDistWeightModel-method Man page
predict,Mahalanobis-method Man page
predict,MaxEnt-method Man page
predict,MaxEntReplicates-method Man page
predict,RectangularHull-method Man page
predict,VoronoiHull-method Man page
prepareData Man page
pwdSample Man page
randomPoints Man page
RectangularHull-class Man page
rectHull Man page
rectHull,data.frame-method Man page
rectHull,matrix-method Man page
rectHull,SpatialPoints-method Man page
response Man page
response,ANY-method Man page
response,DistModel-method Man page
response,MaxEntReplicates-method Man page
ssb Man page
threshold Man page
threshold,ModelEvaluation-method Man page
voronoi Man page
voronoiHull Man page
VoronoiHull-class Man page
voronoiHull,data.frame,data.frame-method Man page
voronoiHull,matrix,matrix-method Man page
voronoiHull,SpatialPoints,SpatialPoints-method Man page

Files

inst
inst/ex
inst/ex/bio7.grd
inst/ex/biome.gri
inst/ex/biome.grd
inst/ex/bio17.gri
inst/ex/bio1.grd
inst/ex/bio12.gri
inst/ex/bio5.gri
inst/ex/bio17.grd
inst/ex/bradypus.csv
inst/ex/bio8.grd
inst/ex/bio6.gri
inst/ex/bio7.gri
inst/ex/bio6.grd
inst/ex/bio16.gri
inst/ex/bio1.gri
inst/ex/bio5.grd
inst/ex/bio16.grd
inst/ex/acaule.csv
inst/ex/bio8.gri
inst/ex/bio12.grd
inst/java
inst/java/dismo.jar
inst/doc
inst/doc/brt.Rnw
inst/doc/brt.R
inst/doc/sdm.pdf
inst/doc/sdm.Rnw
inst/doc/brt.pdf
inst/doc/sdm.R
src
src/percRank.c
NAMESPACE
data
data/ECOcrops.RData
data/acaule.RData
data/Anguilla_test.RData
data/Anguilla_grids.RData
data/Anguilla_train.RData
R
R/gbif.R R/reserves.R R/persp.R R/errorDetect.R R/convHull.predict.R R/bioclim.predict.R R/pointValues.R R/gbm.step.R R/prepareData.R R/boundRect.R R/mess.R R/geoDist.R R/gbm.perspec.R R/rectHull.R R/pointsToMatrix.R R/check.R R/onLoad.R R/evaluate.R R/convHull.R R/circles.predict.R R/pointInPolygon.R R/pwdSample.R R/plot.R R/gbm.interactions.R R/maxent.R R/nullRandom.R R/ecocrop.R R/threshold.R R/gbm.holdout.R R/voronoi.R R/circleHull.predict.R R/boxplot.R R/maxent.predict.R R/errorReport.R R/gbm.plot.R R/voronoiHull.predict.R R/nicheEquivelancy.R R/circles.R R/ssb.R R/geoIDW.predict.R R/Mahalanobis.predict.R R/precision.R R/estimators.R R/domain.R R/hullls.R R/nicheOverlap.R R/voronoiHull.R R/kauc.R R/gbm.plot.fits.R R/density.R R/randomPoints.R R/domain.predict.R R/gridSample.R R/geoDist.predict.R R/bioclim.R R/kfold.R R/bioclim.plot.R R/gbif_old.R R/dcEvaluate.R R/diversity.R R/gbm.simplify.R R/gbm.utils.R R/rectHull.predict.R R/calc.deviance.R R/biogeomancer.R R/geoIDW.R R/gmap.R R/geocode.R R/plotEval.R R/biovars.R R/AAAclasses.R R/gorilla.R R/ecolim.R R/gbm.fixed.R R/Mahalanobis.R R/mercator.R R/circleHull.R R/response.R R/pairs.R
vignettes
vignettes/brt.Rnw
vignettes/sdm.Rnw
MD5
java
java/mebridge.java
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/ssb.Rd man/geocode.Rd man/gbm.simplify.Rd man/threshold.Rd man/bioclim.Rd man/nicheEquivalency.Rd man/kfold.Rd man/gbif.Rd man/ModelEvaluation.Rd man/geoDist.Rd man/gbm.plot.Rd man/calc.deviance.Rd man/evaluate.Rd man/mess.Rd man/gbm.data.Rd man/maxent.Rd man/convexHull.Rd man/randomPoints.Rd man/voronoi.Rd man/gridSample.Rd man/predict.Rd man/pwdSample.Rd man/gmap.Rd man/pointValues.Rd man/pairs.Rd man/nullRandom.Rd man/ecolim.Rd man/acaule.Rd man/prepareData.Rd man/plotEval.Rd man/nicheOverlap.Rd man/dismo-package.Rd man/rectHull.Rd man/boxplot.Rd man/DistModel.Rd man/gbm.step.Rd man/gbm.interactions.Rd man/mahal.Rd man/gbm.persp.Rd man/ecocrop.Rd man/dcEvaluate.Rd man/biovars.Rd man/circleHull.Rd man/voronoiHulll.Rd man/gbm.fixed.Rd man/circles.Rd man/geoIDW.Rd man/plot.Rd man/response.Rd man/gbm.plot.fits.Rd man/evaluateROCR.Rd man/density.Rd man/domain.Rd man/gbm.holdout.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.