SDMPlay: Species Distribution Modelling Playground

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Functions provided by this pedagogic package allow to compute models with two popular machine learning approaches, BRT (Boosted Regression Trees) and MaxEnt (Maximum Entropy) applied on sets of marine biological and environmental data. They include the possibility of managing the main parameters for the construction of the models. Classic tools to evaluate model performance are provided (Area Under the Curve, omission rate and confusion matrix, map standard deviation) and are completed with tools to perform null models. The biological dataset includes original occurrences of two species of the class Echinoidea (sea urchins) present on the Kerguelen Plateau and that show contrasted ecological niches. The environmental dataset includes the corresponding statistics for 15 abiotic and biotic descriptors summarized for the Kerguelen Plateau and for different periods in a raster format. The package can be used for practicals to teach and learn the basics of species distribution modelling. Maps of potential distribution can be produced based on the example data included in the package, which brings prior observations of the influence of spatial and temporal heterogeneities on modelling performances. The user can also provide his own datasets to use the modelling functions.

Author
Guillaumot Charlene [aut, cre], Martin Alexis [aut], Eleaume Marc [aut], Saucede Thomas [aut]
Date of publication
2016-08-08 19:09:02
Maintainer
Guillaumot Charlene <charleneguillaumot21@gmail.com>
License
GPL-3
Version
1.0

View on CRAN

Man pages

brisaster.antarcticus
Records of _Brisaster antarcticus_ echinoid presences on the...
compute.brt
Compute BRT (Boosted Regression Trees) model
compute.maxent
Compute MaxEnt model
ctenocidaris.nutrix
Records of _Ctenocidaris nutrix_ echinoid presences on the...
delim.area
RasterStack preparation for modelling
null.model
Compute null model
predictors1965_1974
Environmental descriptors for 1965-1974 on the Kerguelen...
predictors2005_2012
Environmental descriptors for 2005-2012 on the Kerguelen...
predictors2200AIB
IPCC environmental descriptors predicted for 2200 (AIB...
SDMdata.quality
Evaluate dataset quality
SDMeval
Evaluate species distribution models
SDMtab
Compile species distribution dataset for modelling

Files in this package

SDMPlay
SDMPlay/inst
SDMPlay/inst/java
SDMPlay/inst/java/maxent.jar
SDMPlay/inst/extdata
SDMPlay/inst/extdata/model.RData
SDMPlay/inst/extdata/pred2000.gri
SDMPlay/inst/extdata/pred2000.grd
SDMPlay/inst/extdata/pred.gri
SDMPlay/inst/extdata/SDMdata1500.csv
SDMPlay/inst/extdata/pred.grd
SDMPlay/tests
SDMPlay/tests/testthat.R
SDMPlay/tests/testthat
SDMPlay/tests/testthat/test.R
SDMPlay/NAMESPACE
SDMPlay/data
SDMPlay/data/ctenocidaris.nutrix.rda
SDMPlay/data/datalist
SDMPlay/data/brisaster.antarcticus.rda
SDMPlay/data/predictors2005_2012.rda
SDMPlay/data/predictors2200AIB.rda
SDMPlay/data/predictors1965_1974.rda
SDMPlay/R
SDMPlay/R/Environmental_data_1965_1974_description.R
SDMPlay/R/SDMdata.quality.R
SDMPlay/R/compute.brt.R
SDMPlay/R/delim_area.R
SDMPlay/R/Environmental_data_2005_2012_description.R
SDMPlay/R/ctenocidaris.nutrix.R
SDMPlay/R/brisaster.antarcticus.R
SDMPlay/R/compute.maxent.R
SDMPlay/R/SDMeval.R
SDMPlay/R/null.model.R
SDMPlay/R/SDMtab.R
SDMPlay/R/Environmental_data_2200_A1B_description.R
SDMPlay/MD5
SDMPlay/java
SDMPlay/java/maxent.jar
SDMPlay/DESCRIPTION
SDMPlay/man
SDMPlay/man/SDMtab.Rd
SDMPlay/man/ctenocidaris.nutrix.Rd
SDMPlay/man/predictors2005_2012.Rd
SDMPlay/man/predictors2200AIB.Rd
SDMPlay/man/SDMdata.quality.Rd
SDMPlay/man/null.model.Rd
SDMPlay/man/brisaster.antarcticus.Rd
SDMPlay/man/compute.brt.Rd
SDMPlay/man/compute.maxent.Rd
SDMPlay/man/delim.area.Rd
SDMPlay/man/SDMeval.Rd
SDMPlay/man/predictors1965_1974.Rd