Package: raptr 1.0.1

raptr: Representative and Adequate Prioritization Toolkit in R

Biodiversity is in crisis. The overarching aim of conservation is to preserve biodiversity patterns and processes. To this end, protected areas are established to buffer species and preserve biodiversity processes. But resources are limited and so protected areas must be cost-effective. This package contains tools to generate plans for protected areas (prioritizations), using spatially explicit targets for biodiversity patterns and processes. To obtain solutions in a feasible amount of time, this package uses the commercial 'Gurobi' software (obtained from <https://www.gurobi.com/>). For more information on using this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.

Authors:Jeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]

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raptr.pdf |raptr.html
raptr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/jeffreyhanson/raptr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • sim_rs - Simulated dataset for a conservation planning exercise
  • sim_ru - Simulated dataset for a conservation planning exercise

On CRAN:

5.46 score 7 stars 82 scripts 864 downloads 45 exports 122 dependencies

Last updated 10 months agofrom:f67fa73b31. Checks:ERROR: 1 OK: 2 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILOct 26 2024
R-4.5-win-x86_64OKOct 26 2024
R-4.5-linux-x86_64OKOct 26 2024
R-4.4-win-x86_64NOTEOct 26 2024
R-4.4-mac-x86_64NOTEOct 26 2024
R-4.4-mac-aarch64NOTEOct 26 2024
R-4.3-win-x86_64NOTEOct 26 2024
R-4.3-mac-x86_64NOTEOct 26 2024
R-4.3-mac-aarch64NOTEOct 26 2024

Exports:amount.heldamount.targetamount.target<-AttributeSpaceAttributeSpacesblank.rastercalcBoundaryDatacalcSpeciesAverageInPusconvert2PolySetDemandPointsdp.subsetGurobiOptsis.GurobiInstalledlogging.filemake.DemandPointsmake.RapDataManualOptsmaximum.targetsPlanningUnitPointsprob.subsetpu.subsetrandomPointsrapRapDataRapReliableOptsRapResultsRapSolvedRapUnreliableOptsRapUnsolvedrrap.proportion.heldscoreselectionssim.pussim.spacesim.speciessolvespace.heldspace.plotspace.targetspace.target<-SpatialPolygons2PolySetspp.plotspp.subsetsummaryurap.proportion.held

Dependencies:abindade4adehabitatHRadehabitatLTadehabitatMAassertthatBHbootcaretCircStatsclassclassIntcliclockcodetoolscolorspacecpp11crayondata.tableDBIdiagramdigestdoParalleldplyre1071fansifarverfastclusterFNNforeachfuturefuture.applygenericsgeometryggplot2globalsgluegowergtablehardhathitandrunhmshypervolumeipredisobanditeratorskernlabKernSmoothkslabelinglatticelavalifecyclelinproglistenvlpSolvelubridatemagicmagrittrmapsMASSMatrixmclustmgcvModelMetricsmulticoolmunsellmvtnormnlmennetnumDerivpalmerpenguinsparallellypbapplyPBSmappingpdistpillarpixmappkgconfigplyrpracmaprettyunitspROCprodlimprogressprogressrproxypurrrR6rasterrcddRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressrecipesreshape2rlangrparts2scalessfshapespSQUAREMstringistringrsurvivalterratibbletidyrtidyselecttimechangetimeDatetzdbunitsutf8vctrsviridisLitewithrwk

raptr: Representative and Adequate Prioritization Toolkit in R

Rendered fromraptr.Rmdusingknitr::rmarkdown_notangleon Oct 26 2024.

Last update: 2023-03-13
Started: 2016-07-19

Readme and manuals

Help Manual

Help pageTopics
Extract amount held for a solutionamount.held amount.held.RapSolved
Amount targetsamount.target amount.target.RapData amount.target.RapUnsolOrSol amount.target<- amount.target<-.RapData amount.target<-.RapUnsolOrSol
Convert object to listas.list as.list.GurobiOpts
Create new AttributeSpace objectAttributeSpace
AttributeSpace: An S4 class to represent an attribute space.AttributeSpace-class
Create new AttributeSpaces objectAttributeSpaces
AttributeSpaces: An S4 class to represent a collection of attribute spaces for different species.AttributeSpaces-class
Blank rasterblank.raster
Calculate boundary data for planning unitscalcBoundaryData calcBoundaryData.PolySet calcBoundaryData.sf calcBoundaryData.SpatialPolygons
Calculate average value for species data in planning unitscalcSpeciesAverageInPus calcSpeciesAverageInPus.sf calcSpeciesAverageInPus.SpatialPolygons calcSpeciesAverageInPus.SpatialPolygonsDataFrame
Case-study dataset for a conservation planning exercisecasestudy_data cs_pus cs_space cs_spp
Convert object to PolySet dataconvert2PolySet convert2PolySet.sf convert2PolySet.SpatialPolygons convert2PolySet.SpatialPolygonsDataFrame
Create new DemandPoints objectDemandPoints
DemandPoints: An S4 class to represent demand pointsDemandPoints-class
Subset demand pointsdp.subset dp.subset.RapData dp.subset.RapUnsolOrSol
Create GurobiOpts objectGurobiOpts
GurobiOpts: An S4 class to represent Gurobi parametersGurobiOpts-class
Test if Gurobi is installedis.GurobiInstalled
Log filelogging.file logging.file.RapResults logging.file.RapSolved
Generate demand points for RAPmake.DemandPoints
Make data for RAP using minimal inputsmake.RapData
Create ManualOpts objectManualOpts
ManualOpts: An S4 class to represent parameters for manually specified solutionsManualOpts-class
Maximum targetsmaximum.targets maximum.targets.RapUnsolOrSol
Namesnames names.RapData names.RapUnsolOrSol names<-.RapData names<-.RapUnsolOrSol
Create new PlanningUnitPoints objectPlanningUnitPoints
PlanningUnitPoints: An S4 class to represent planning units in an attribute spacePlanningUnitPoints-class
Plot objectplot plot,RapSolved,missing-method plot,RapSolved,numeric-method plot,RapSolved,RapSolved-method
PolySetPolySet PolySet-class
Print objectsprint print.AttributeSpace print.AttributeSpaces print.GurobiOpts print.ManualOpts print.RapData print.RapReliableOpts print.RapResults print.RapSolved print.RapUnreliableOpts print.RapUnsolved
Subset probabilities above a thresholdprob.subset prob.subset.RapData prob.subset.RapUnsolOrSol
Subset planning unitspu.subset pu.subset.RapData pu.subset.RapUnsolOrSol
Sample random points from a SpatRasterrandomPoints
Generate prioritizations using RAPrap
Create new RapData objectRapData
RapData: An S4 class to represent RAP input dataRapData-class
RapOpts classRapOpts RapOpts-class
Create RapReliableOpts objectRapReliableOpts
RapReliableOpts: An S4 class to represent input parameters for the reliable formulation of RAP.RapReliableOpts-class
Create RapResults objectRapResults
RapResults: An S4 class to represent RAP resultsRapResults-class
Create new RapSolved objectRapSolved
RapSolved: An S4 class to represent RAP inputs and outputsRapSolved-class
raptr: Representative and Adequate Prioritization Toolkit in Rraptr-package raptr
Deprecation noticeraptr-deprecated SpatialPolygons2PolySet
Create RapUnreliableOpts objectRapUnreliableOpts
RapUnreliableOpts: An S4 class to represent parameters for the unreliable RAP problemRapUnreliableOpts-class
Create a new RapUnsolved objectRapUnsolved
RapUnsolved: An S4 class to represent RAP inputsRapUnsolved-class
Proportion held using reliable RAP formulation.rrap.proportion.held
Solution scorescore score.RapResults score.RapSolved
Extract solution selectionsselections selections.RapResults selections.RapSolved
Show objectsshow show,GurobiOpts-method show,ManualOpts-method show,RapData-method show,RapReliableOpts-method show,RapResults-method show,RapSolved-method show,RapUnreliableOpts-method show,RapUnsolved-method
Simulate planning unitssim.pus
Simulate attribute space data for RAPsim.space sim.space.sf sim.space.SpatialPolygons sim.space.SpatRaster
Simulate species distribution data for RAPsim.species sim.species.sf sim.species.SpatialPolygons sim.species.SpatRaster
Simulated dataset for a conservation planning exercisesimulated_data sim_rs sim_ru
Solve RAP objectsolve solve,RapUnsolOrSol,GurobiOpts-method solve,RapUnsolOrSol,logical-method solve,RapUnsolOrSol,matrix-method solve,RapUnsolOrSol,missing-method solve,RapUnsolOrSol,numeric-method
SolverOpts classSolverOpts SolverOpts-class
Extract attribute space held for a solutionspace.held space.held.RapSolved
Plot spacespace.plot space.plot.RapData space.plot.RapSolved space.plot.RapUnsolved
Attribute space targetsspace.target space.target.RapData space.target.RapUnsolOrSol space.target<- space.target<-.RapData space.target<-.RapUnsolOrSol
Plot speciesspp.plot spp.plot.RapData spp.plot.RapSolved spp.plot.RapUnsolved
Subset speciesspp.subset spp.subset.RapData spp.subset.RapUnsolOrSol
Summary of solutionssummary
Update objectupdate update.GurobiOpts update.ManualOpts update.RapData update.RapReliableOpts update.RapUnreliableOpts update.RapUnsolOrSol
Proportion held using unreliable RAP formulation.urap.proportion.held