SDMPlay: Species Distribution Modelling Playground

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.

AuthorGuillaumot Charlene [aut, cre], Martin Alexis [aut], Eleaume Marc [aut], Saucede Thomas [aut]
Date of publication2016-08-08 19:09:02
MaintainerGuillaumot Charlene <charleneguillaumot21@gmail.com>
LicenseGPL-3
Version1.0

View on CRAN

Files

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

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