Package: wallace 2.1.3

Mary E. Blair

wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

The 'shiny' application Wallace is a modular platform for reproducible modeling of species niches and distributions. Wallace guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface. An extensive vignette, which guides users through most package functionality can be found on the package's GitHub Pages website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.

Authors:Bethany A. Johnson [aut], Jamie M. Kass [aut], Gonzalo E. Pinilla-Buitrago [aut], Andrea Paz [aut], Valentina Grisales-Betancur [aut], Dean Attali [aut], Matthew E. Aiello-Lammens [aut], Cory Merow [aut], Mary E. Blair [aut, cre], Robert P. Anderson [aut], Sarah I. Meenan [ctb], Olivier Broennimann [ctb], Peter J. Galante [ctb], Brian S. Maitner [ctb], Hannah L. Owens [ctb], Sara Varela [ctb], Bruno Vilela [ctb], Robert Muscarella [ctb]

wallace_2.1.3.tar.gz
wallace_2.1.3.tar.gz(r-4.5-noble)wallace_2.1.3.tar.gz(r-4.4-noble)
wallace_2.1.3.tgz(r-4.4-emscripten)wallace_2.1.3.tgz(r-4.3-emscripten)
wallace.pdf |wallace.html✨
wallace/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/wallaceecomod/wallace/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

3.89 score 79 scripts 1.6k downloads 4 mentions 49 exports 231 dependencies

Last updated 4 months agofrom:2f9d19cf76. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-linuxOKNov 16 2024

Exports:clearAllcreate_moduleecoClimate_getdataecoClimate_selectecospat.plot.nicheDEVenvs_ecoClimateenvs_userEnvsenvs_worldclimespace_nicheOvespace_occDensespace_pcafmtSpNgetRasterValshlSppmodel_bioclimmodel_maxentmxNonzeroCoefsoccs_queryDboccs_userOccspart_partitionOccspenvs_bgExtentpenvs_bgMaskpenvs_bgSamplepenvs_drawBgExtentpenvs_userBgExtentpoccs_removeByIDpoccs_selectOccspoccs_thinOccspolyZoompopUpContentpredictMaxnetprintVecAsisregister_moduleremEnvsValsNAreverseLabelrun_wallacesmartProgressspNamespuriousvis_bioclimPlotwrite_csv_robustwriteLogxfer_areaxfer_drawxfer_messxfer_timexfer_userEnvsxfer_userExtentzoom2Occs

Dependencies:abindade4adehabitatHRadehabitatLTadehabitatMAapeaskpassassertthatbackportsbase64encBHbibtexBIENbiomod2bitbit64blobbootbroombslibcachemcallrcellrangercheckmateCircStatsclassclassIntclicliprclustercodetoolscolorspacecommonmarkconflictedcowplotcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdigestdismodoParalleldoSNOWdotCall64dplyrDTdtplyre1071ecodistecospatENMevalevaluatefansifarverfasterizefastmapfieldsFNNfontawesomeforcatsforeachforeignFormulafsgarglegbmgenericsgeodatageojsonsfgeometriesggplot2glmnetgluegoogledrivegooglesheets4gridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpcodehttpuvhttridsigraphisobanditeratorsjquerylibjsonifyjsonlitekableExtrakernlabKernSmoothknitcitationsknitrkslabelinglaterlatticelazyevalleafemleafletleaflet.extrasleaflet.providerslifecyclelubridatemagrittrmapsmarkdownMASSMatrixmatrixStatsmaxnetmclustmemoisemgcvmimemodelrmulticoolmunsellmvtnormnabornlmennetoaiopensslpermutepillarpixmappkgconfigplyrpngpoibinpracmaPresenceAbsenceprettyunitspROCprocessxprogresspromisesproxypspurrrR6raggrangeModelMetadatarapidjsonrrappdirsrasterRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrebirdRefManageRrematchrematch2reprexreshapereshape2rgbifridigbiorJavarlangrmarkdownrpartRPostgreSQLrstudioapirvertnetrvests2sassscalesselectrsfsfheadersshapeshinyshinyalertshinyjsshinyWidgetssnowsourcetoolsspspamspoccspThinstringistringrsurvivalsvglitesyssystemfontsterratextshapingtibbletidyrtidyselecttidyversetimechangetinytextriebeardtzdbunitsurltoolsutf8uuidvctrsveganviridisviridisLitevroomwhiskerwithrwkxfunxml2xtableyamlzip

Readme and manuals

Help Manual

Help pageTopics
_Wallace_: A modular platform for reproducible ecological modelingwallace-package wallace
Create a Wallace modulecreate_module
ecoClimate_getdataecoClimate_getdata
ecoClimate_selectecoClimate_select
envs_ecoClimate Obtain ecoClimate variablesenvs_ecoClimate
envs_userEnvsenvs_userEnvs
envs_worldclim Obtain WorldClim variablesenvs_worldclim
espace_nicheOv Niche Overlapespace_nicheOv
Occurrence density gridespace_occDens
espace_pca Principal component analysisespace_pca
model_bioclim Generate Bioclim modelmodel_bioclim
model_maxent Generate maxent.jar or maxnet modelmodel_maxent
occs_queryDb Query online database for species occurrence records.occs_queryDb
occs_userOccs Loads user provided occurrence recordsoccs_userOccs
part_partitionOccs Partition occurrence datapart_partitionOccs
penvs_bgExtent Generate background extentpenvs_bgExtent
penvs_bgMask Mask environmental datapenvs_bgMask
penvs_bgSample Sample background pointspenvs_bgSample
penvs_drawBgExtent: Draw background extentpenvs_drawBgExtent
penvs_userBgExtent: user provided background extentpenvs_userBgExtent
poccs_removeByID Remove occurrence by IDpoccs_removeByID
poccs_selectOccs Remove occurrences outside of polygonpoccs_selectOccs
poocs_thinOccs Thin occurrencespoccs_thinOccs
Register a Wallace moduleregister_module
Run _Wallace_ Applicationrun_wallace
vis_bioclimPlot Visualize bivariate plot of BIOCLIM modelvis_bioclimPlot
xfer_area Transfer model to a new areaxfer_area
xfer_draw Draw extent of transferxfer_draw
xfer_mess generate MESS map for transferred rasterxfer_mess
xfer_time Transfer model to a new timexfer_time
xfer_userEnvs Transfer model to user specified area and timexfer_userEnvs
xfer_userExtent: user provided extent of transferxfer_userExtent