Package: enmSdmX 1.1.6

enmSdmX: Species Distribution Modeling and Ecological Niche Modeling

Implements species distribution modeling and ecological niche modeling, including: bias correction, spatial cross-validation, model evaluation, raster interpolation, biotic "velocity" (speed and direction of movement of a "mass" represented by a raster), interpolating across a time series of rasters, and use of spatially imprecise records. The heart of the package is a set of "training" functions which automatically optimize model complexity based number of available occurrences. These algorithms include MaxEnt, MaxNet, boosted regression trees/gradient boosting machines, generalized additive models, generalized linear models, natural splines, and random forests. To enhance interoperability with other modeling packages, no new classes are created. The package works with 'PROJ6' geodetic objects and coordinate reference systems.

Authors:Adam B. Smith [cre, aut]

enmSdmX_1.1.6.tar.gz
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enmSdmX.pdf |enmSdmX.html✨
enmSdmX/json (API)
NEWS

# Install 'enmSdmX' in R:
install.packages('enmSdmX', repos = c('https://adamlilith.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/adamlilith/enmsdmx/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:
  • crss - Coordinate reference systems (CRSs) and nicknames
  • lemurs - Lemur occurrences from GBIF
  • mad0 - Madagascar spatial object
  • mad1 - Madagascar spatial object

On CRAN:

bias-correctionbiogeographyecological-niche-modelingecological-niche-modellingniche-modelingniche-modellingspecies-distribution-modeling

49 exports 21 stars 2.33 score 97 dependencies 22 scripts 486 downloads

Last updated 3 months agofrom:0148f00677. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 20 2024
R-4.5-winOKAug 20 2024
R-4.5-linuxOKAug 20 2024
R-4.4-winOKAug 20 2024
R-4.4-macOKAug 20 2024
R-4.3-winOKAug 20 2024
R-4.3-macOKAug 20 2024

Exports:bioticVelocitycompareResponsecoordImprecisioncountPointscustomAlberscustomLambertcustomVNSdecimalToDmsdmsToDecimalelimCellDuplicatesevalAUCevalContBoyceevalMultiAUCevalThresholdevalThresholdStatsevalTjursR2evalTSSextentToVectgeoFoldgeoFoldContrastgeoThingetCRSgetValueByCellglobalxinterpolateRastslongLatRastsmodelSizenearestEnvPointsnearestGeogPointsnicheOverlapMetricsplotExtentpredictEnmSdmpredictMaxEntpredictMaxNetsampleRastsetValueByCellspatVectorToSpatialsquareCellRastsummaryByCrossValidtrainBRTtrainByCrossValidtrainESMtrainGAMtrainGLMtrainMaxEnttrainMaxNettrainNStrainRFweightByDist

Dependencies:AICcmodavgbase64encbootbslibcachemclassclassIntclicodetoolscolorspacecommonmarkcrayoncrosstalkdata.tableDBIdigestdoParallelDTe1071evaluatefarverfastmapFNNfontawesomeforeachfsgbmglmnetgluehighrhtmltoolshtmlwidgetshttpuviteratorsjquerylibjsonlitekernlabKernSmoothknitrkslabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixmaxnetmclustmemoisemgcvmimeminqamulticoolmunsellmvtnormnlmenloptromnibuspracmapredictspromisesproxyR6rangerrappdirsRColorBrewerRcppRcppArmadilloRcppEigenrJavarlangrmarkdowns2sassscalessfshapeshinysourcetoolsspstatisfactorysurvivalterratinytexTMBunitsunmarkedVGAMviridisLitewithrwkxfunxtableyaml

Readme and manuals

Help Manual

Help pageTopics
Velocity of shifts in densities across a series of rastersbioticVelocity
Vector outline of Canadacanada
Compare two response curves along one or more predictorscompareResponse
Calculate the precision of a geographic coordinatecoordImprecision
Number of points in a "spatial points" objectcountPoints
Coordinate reference systems (CRSs) and nicknamescrss
Custom coordinate reference system WKT2 stringcustomAlbers customLambert customVNS
Convert geographic coordinates in decimal format to degrees-minutes-seconddecimalToDms
Convert geographic coordinates in degrees-minutes-second to decimal formatdmsToDecimal
Thin spatial points so that there is but one per raster cellelimCellDuplicates
Weighted AUCevalAUC
Continuous Boyce Index (CBI) with weightingevalContBoyce
Calculate multivariate weighted AUCevalMultiAUC
Weighted thresholds for predictionsevalThreshold
Thresholded evaluation statisticsevalThresholdStats
Weighted Tjur's R2evalTjursR2
Weighted True Skill Statistic (TSS)evalTSS
Convert extent to a spatial polygonextentToVect
Assign geographically-distinct k-foldsgeoFold
Assign geographically-distinct k-folds to background/absence sitesgeoFoldContrast
Thin geographic points deterministically or randomlygeoThin
WKT string for a named coordinate reference system or a spatial objectgetCRS
Get or assign values to cells in a rastergetValueByCell setValueByCell
"Friendly" wrapper for terra::global() for calculating raster statisticsglobalx
Interpolate values from a series of rastersinterpolateRasts
Lemur occurrences from GBIFlemurs
Generate rasters with cell values equal to cell longitude or latitudelongLatRasts
Madagascar spatial objectmad0
Madagascar spatial objectmad1
Present-day climate rasters for MadagascarmadClim
Future climate rasters for MadagascarmadClim2030
Future climate rasters for MadagascarmadClim2050
Future climate rasters for MadagascarmadClim2070
Future climate rasters for MadagascarmadClim2090
Number of response data in a model objectmodelSize
Extract "most conservative" environments from points and/or polygonsnearestEnvPoints
Minimum convex polygon from a set of spatial polygons and/or pointsnearestGeogPoints
Metrics of niche overlapnicheOverlapMetrics
Create spatial polygon same size as a plotplotExtent
Generic predict function for SDMs/ENMspredictEnmSdm
Predict a MaxEnt model object (with optional feature-level permutation)predictMaxEnt
Predictions from a MaxNet modelpredictMaxNet
Sample random points from a raster with/out replacementsampleRast
Convert SpatVector to Spatial*spatVectorToSpatial
Create a raster with square cellssquareCellRast
Summarize distribution/niche model cross-validation objectsummaryByCrossValid
Calibrate a boosted regression tree (generalized boosting machine) modeltrainBRT
Calibrate a distribution/niche model using cross-validationtrainByCrossValid
Calibrate an ensemble of small modelstrainESM
Calibrate a generalized additive model (GAM)trainGAM
Calibrate a generalized linear model (GLM)trainGLM
Calibrate a MaxEnt (ver 3.3.3+ or "maxent") model using AICctrainMaxEnt
Calibrate a MaxNet (MaxEnt) model using AICctrainMaxNet
Calibrate a natural splines modeltrainNS
Calibrate a random forest modeltrainRF
Troubleshooting parallel operationstroubleshooting_parallel_operations
Proximity-based weighting for occurrences to correct for spatial biasweightByDist