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:
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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')) |
Bug tracker:https://github.com/jeffreyhanson/raptr/issues
Last updated 9 months agofrom:f67fa73b31. Checks:ERROR: 1 OK: 2 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 26 2024 |
| R-4.5-win-x86_64 | OK | Oct 26 2024 |
| R-4.5-linux-x86_64 | OK | Oct 26 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 26 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 26 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 26 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 26 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 26 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 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 page | Topics |
|---|---|
| Extract amount held for a solution | amount.held amount.held.RapSolved |
| Amount targets | amount.target amount.target.RapData amount.target.RapUnsolOrSol amount.target<- amount.target<-.RapData amount.target<-.RapUnsolOrSol |
| Convert object to list | as.list as.list.GurobiOpts |
| Create new AttributeSpace object | AttributeSpace |
| AttributeSpace: An S4 class to represent an attribute space. | AttributeSpace-class |
| Create new AttributeSpaces object | AttributeSpaces |
| AttributeSpaces: An S4 class to represent a collection of attribute spaces for different species. | AttributeSpaces-class |
| Blank raster | blank.raster |
| Calculate boundary data for planning units | calcBoundaryData calcBoundaryData.PolySet calcBoundaryData.sf calcBoundaryData.SpatialPolygons |
| Calculate average value for species data in planning units | calcSpeciesAverageInPus calcSpeciesAverageInPus.sf calcSpeciesAverageInPus.SpatialPolygons calcSpeciesAverageInPus.SpatialPolygonsDataFrame |
| Case-study dataset for a conservation planning exercise | casestudy_data cs_pus cs_space cs_spp |
| Convert object to PolySet data | convert2PolySet convert2PolySet.sf convert2PolySet.SpatialPolygons convert2PolySet.SpatialPolygonsDataFrame |
| Create new DemandPoints object | DemandPoints |
| DemandPoints: An S4 class to represent demand points | DemandPoints-class |
| Subset demand points | dp.subset dp.subset.RapData dp.subset.RapUnsolOrSol |
| Create GurobiOpts object | GurobiOpts |
| GurobiOpts: An S4 class to represent Gurobi parameters | GurobiOpts-class |
| Test if Gurobi is installed | is.GurobiInstalled |
| Log file | logging.file logging.file.RapResults logging.file.RapSolved |
| Generate demand points for RAP | make.DemandPoints |
| Make data for RAP using minimal inputs | make.RapData |
| Create ManualOpts object | ManualOpts |
| ManualOpts: An S4 class to represent parameters for manually specified solutions | ManualOpts-class |
| Maximum targets | maximum.targets maximum.targets.RapUnsolOrSol |
| Names | names names.RapData names.RapUnsolOrSol names<-.RapData names<-.RapUnsolOrSol |
| Create new PlanningUnitPoints object | PlanningUnitPoints |
| PlanningUnitPoints: An S4 class to represent planning units in an attribute space | PlanningUnitPoints-class |
| Plot object | plot plot,RapSolved,missing-method plot,RapSolved,numeric-method plot,RapSolved,RapSolved-method |
| PolySet | PolySet PolySet-class |
| Print objects | print print.AttributeSpace print.AttributeSpaces print.GurobiOpts print.ManualOpts print.RapData print.RapReliableOpts print.RapResults print.RapSolved print.RapUnreliableOpts print.RapUnsolved |
| Subset probabilities above a threshold | prob.subset prob.subset.RapData prob.subset.RapUnsolOrSol |
| Subset planning units | pu.subset pu.subset.RapData pu.subset.RapUnsolOrSol |
| Sample random points from a SpatRaster | randomPoints |
| Generate prioritizations using RAP | rap |
| Create new RapData object | RapData |
| RapData: An S4 class to represent RAP input data | RapData-class |
| RapOpts class | RapOpts RapOpts-class |
| Create RapReliableOpts object | RapReliableOpts |
| RapReliableOpts: An S4 class to represent input parameters for the reliable formulation of RAP. | RapReliableOpts-class |
| Create RapResults object | RapResults |
| RapResults: An S4 class to represent RAP results | RapResults-class |
| Create new RapSolved object | RapSolved |
| RapSolved: An S4 class to represent RAP inputs and outputs | RapSolved-class |
| raptr: Representative and Adequate Prioritization Toolkit in R | raptr-package raptr |
| Deprecation notice | raptr-deprecated SpatialPolygons2PolySet |
| Create RapUnreliableOpts object | RapUnreliableOpts |
| RapUnreliableOpts: An S4 class to represent parameters for the unreliable RAP problem | RapUnreliableOpts-class |
| Create a new RapUnsolved object | RapUnsolved |
| RapUnsolved: An S4 class to represent RAP inputs | RapUnsolved-class |
| Proportion held using reliable RAP formulation. | rrap.proportion.held |
| Solution score | score score.RapResults score.RapSolved |
| Extract solution selections | selections selections.RapResults selections.RapSolved |
| Show objects | show 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 units | sim.pus |
| Simulate attribute space data for RAP | sim.space sim.space.sf sim.space.SpatialPolygons sim.space.SpatRaster |
| Simulate species distribution data for RAP | sim.species sim.species.sf sim.species.SpatialPolygons sim.species.SpatRaster |
| Simulated dataset for a conservation planning exercise | simulated_data sim_rs sim_ru |
| Solve RAP object | solve solve,RapUnsolOrSol,GurobiOpts-method solve,RapUnsolOrSol,logical-method solve,RapUnsolOrSol,matrix-method solve,RapUnsolOrSol,missing-method solve,RapUnsolOrSol,numeric-method |
| SolverOpts class | SolverOpts SolverOpts-class |
| Extract attribute space held for a solution | space.held space.held.RapSolved |
| Plot space | space.plot space.plot.RapData space.plot.RapSolved space.plot.RapUnsolved |
| Attribute space targets | space.target space.target.RapData space.target.RapUnsolOrSol space.target<- space.target<-.RapData space.target<-.RapUnsolOrSol |
| Plot species | spp.plot spp.plot.RapData spp.plot.RapSolved spp.plot.RapUnsolved |
| Subset species | spp.subset spp.subset.RapData spp.subset.RapUnsolOrSol |
| Summary of solutions | summary |
| Update object | update update.GurobiOpts update.ManualOpts update.RapData update.RapReliableOpts update.RapUnreliableOpts update.RapUnsolOrSol |
| Proportion held using unreliable RAP formulation. | urap.proportion.held |
