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 package (obtained from <http://www.gurobi.com/>). Additionally, the 'rgurobi' package can also be installed to provide extra functionality (obtained from <http://github.com/jeffreyhanson/rgurobi>).

AuthorJeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]
Date of publication2016-11-25 13:00:00
MaintainerJeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
LicenseGPL-3
Version0.0.3
https://github.com/jeffreyhanson/raptr

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Man pages

amount.held: Extract amount held for a solution

amount.target: Amount targets

as.list: Convert object to list.

AttributeSpace: Create new AttributeSpace object

AttributeSpace-class: AttributeSpace: An S4 class to represent an attribute space.

AttributeSpaces: Create new AttributeSpaces object

AttributeSpaces-class: AttributeSpaces: An S4 class to represent a collection of...

basemap: Basemap

blank.raster: Blank raster

cache: Get and set cache Methods

calcBoundaryData: Calculate boundary data for planning units

calcSpeciesAverageInPus: Calculate average value for species data in planning units

casestudy_data: Case-study dataset for a conservation planning exercise

DemandPoints: Create new DemandPoints object

DemandPoints-class: DemandPoints: An S4 class to represent demand points

dp.subset: Subset demand points

GurobiOpts: Create GurobiOpts object

GurobiOpts-class: GurobiOpts: An S4 class to represent Gurobi parameters

is.cached: Test if hash is cached in a Rap object

is.comparable: Compare Rap objects

is.gdalInstalled: Test if GDAL is installed on computer

is.GurobiInstalled: Test if Gurobi is installed on computer

logging.file: Log file

make.DemandPoints: Generate demand points for RAP

make.RapData: Make data for RAP using minimal inputs

ManualOpts: Create ManualOpts object

ManualOpts-class: ManualOpts: An S4 class to represent parameters for manually...

maximum.targets: Maximum targets

names: Names

PlanningUnitPoints: Create new PlanningUnitPoints object

PlanningUnitPoints-class: PlanningUnitPoints: An S4 class to represent planning units...

plot: Plot object

PolySet-class: PolySet

print: Print objects

prob.subset: Subset probabilities above a threshold

pu.subset: Subset planning units

randomPoints: Sample random points from a RasterLayer

rap: Generate prioritisations using RAP

RapData: Create new RapData object

RapData-class: RapData: An S4 class to represent RAP input data

RapOpts-class: RapOpts class

RapReliableOpts: Create RapReliableOpts object

RapReliableOpts-class: RapReliableOpts: An S4 class to represent input parameters...

RapResults: Create RapResults object

RapResults-class: RapResults: An S4 class to represent RAP results

RapSolved: Create new RapSolved object

RapSolved-class: RapSolved: An S4 class to represent RAP inputs and outputs

raptr: raptr: Representative and Adequate Prioritisation Toolkit in...

RapUnreliableOpts: Create RapUnreliableOpts object

RapUnreliableOpts-class: RapUnreliableOpts: An S4 class to represent parameters for...

RapUnsolved: Create a new RapUnsolved object

RapUnsolved-class: RapUnsolved: An S4 class to represent RAP inputs

rasterizeGDAL: Rasterize polygon data using GDAL

read.RapResults: Read RAP results

rrap.proportion.held: Proportion held using reliable RAP formulation.

score: Solution score

selections: Extract solution selections

show: Show objects

sim.pus: Simulate planning units

sim.space: Simulate attribute space data for RAP

sim.species: Simulate species distribution data for RAP

simulated_data: Simulated dataset for a conservation planning exercise

solve: Solve RAP object

SolverOpts-class: SolverOpts class

space.held: Extract attribute space held for a solution

space.plot: Plot space

space.target: Attribute space targets

SpatialPolygons2PolySet: Convert SpatialPolygons to PolySet data

spp.plot: Plot species

spp.subset: Subset species

summary: Summary of solutions

update: Update object

urap.proportion.held: Proportion held using unreliable RAP formulation.

Files in this package

raptr
raptr/inst
raptr/inst/doc
raptr/inst/doc/raptr.Rmd
raptr/inst/doc/raptr.html
raptr/inst/vign
raptr/inst/vign/raptr.Rmd
raptr/inst/vign/placeholder.Rmd
raptr/tests
raptr/tests/testthat.R
raptr/tests/testthat
raptr/tests/testthat/test-02-misc.R
raptr/tests/testthat/test-10-RapData.R
raptr/tests/testthat/test-07-DemandPoints.R
raptr/tests/testthat/test-06-PlanningUnitPoints.R
raptr/tests/testthat/test-05-simulate-data.R
raptr/tests/testthat/test-01-rapr-internal-test.R
raptr/tests/testthat/test-03-SolverOpts.R
raptr/tests/testthat/functions.R
raptr/tests/testthat/test-11-RapUnsolved.R
raptr/tests/testthat/test-13-rap.R
raptr/tests/testthat/test-04-RapOpts.R
raptr/tests/testthat/test-12-RapSolved.R
raptr/tests/testthat/test-08-AttributeSpace.R
raptr/tests/testthat/test-09-AttributeSpaces.R
raptr/src
raptr/src/dump_object.cpp
raptr/src/rcpp_proportion_held.cpp
raptr/src/rcpp_squared_distance.cpp
raptr/src/rcpp_groupmean.cpp
raptr/src/rcpp_rrap_proportion_held.cpp
raptr/src/rcpp_append_model_object.cpp
raptr/src/functions.h
raptr/src/rcpp_generate_model_object.cpp
raptr/src/rcpp_Polygons2PolySet.cpp
raptr/src/functions.cpp
raptr/src/rcpp_groupcombine.cpp
raptr/src/rcpp_rrap_squared_distance.cpp
raptr/src/rcpp_extract_model_object.cpp
raptr/src/rcpp_sum_duplicates.cpp
raptr/src/RcppExports.cpp
raptr/src/rcpp_calcBoundaryDF.cpp
raptr/NAMESPACE
raptr/data
raptr/data/sim_ru.rda
raptr/data/cs_spp.rda
raptr/data/datalist
raptr/data/cs_space.rda
raptr/data/sim_rs.rda
raptr/data/cs_pus.rda
raptr/R
raptr/R/sim.space.R raptr/R/calcSpeciesAverageInPus.R raptr/R/ManualOpts.R raptr/R/rap.R raptr/R/sim.pus.R raptr/R/PlanningUnitPoints.R raptr/R/RapData.R raptr/R/raptr.R raptr/R/generics.R raptr/R/AttributeSpace.R raptr/R/dependencies.R raptr/R/RapUnreliableOpts.R raptr/R/DemandPoints.R raptr/R/data.R raptr/R/AttributeSpaces.R raptr/R/raptr-internal.R raptr/R/RcppExports.R raptr/R/GurobiOpts.R raptr/R/rrap.proportion.held.R raptr/R/RapSolved.R raptr/R/RapResults.R raptr/R/calcBoundaryData.R raptr/R/RapUnsolved.R raptr/R/misc.R raptr/R/SpatialPolygons2PolySet.R raptr/R/zzz.R raptr/R/RapReliableOpts.R raptr/R/urap.proportion.held.R raptr/R/sim.species.R
raptr/vignettes
raptr/vignettes/raptr.Rmd
raptr/README.md
raptr/MD5
raptr/build
raptr/build/vignette.rds
raptr/DESCRIPTION
raptr/man
raptr/man/PlanningUnitPoints-class.Rd raptr/man/GurobiOpts-class.Rd raptr/man/amount.target.Rd raptr/man/DemandPoints.Rd raptr/man/space.held.Rd raptr/man/sim.species.Rd raptr/man/prob.subset.Rd raptr/man/RapReliableOpts.Rd raptr/man/show.Rd raptr/man/AttributeSpace-class.Rd raptr/man/calcSpeciesAverageInPus.Rd raptr/man/score.Rd raptr/man/casestudy_data.Rd raptr/man/is.gdalInstalled.Rd raptr/man/space.plot.Rd raptr/man/solve.Rd raptr/man/names.Rd raptr/man/maximum.targets.Rd raptr/man/is.cached.Rd raptr/man/read.RapResults.Rd raptr/man/rrap.proportion.held.Rd raptr/man/RapUnsolved.Rd raptr/man/make.DemandPoints.Rd raptr/man/rap.Rd raptr/man/simulated_data.Rd raptr/man/PolySet-class.Rd raptr/man/SolverOpts-class.Rd raptr/man/sim.pus.Rd raptr/man/update.Rd raptr/man/RapReliableOpts-class.Rd raptr/man/calcBoundaryData.Rd raptr/man/randomPoints.Rd raptr/man/DemandPoints-class.Rd raptr/man/RapUnreliableOpts-class.Rd raptr/man/PlanningUnitPoints.Rd raptr/man/SpatialPolygons2PolySet.Rd raptr/man/RapResults-class.Rd raptr/man/ManualOpts.Rd raptr/man/raptr.Rd raptr/man/blank.raster.Rd raptr/man/ManualOpts-class.Rd raptr/man/dp.subset.Rd raptr/man/AttributeSpaces-class.Rd raptr/man/spp.subset.Rd raptr/man/urap.proportion.held.Rd raptr/man/amount.held.Rd raptr/man/RapUnreliableOpts.Rd raptr/man/GurobiOpts.Rd raptr/man/cache.Rd raptr/man/as.list.Rd raptr/man/is.comparable.Rd raptr/man/RapData-class.Rd raptr/man/sim.space.Rd raptr/man/logging.file.Rd raptr/man/make.RapData.Rd raptr/man/RapResults.Rd raptr/man/is.GurobiInstalled.Rd raptr/man/basemap.Rd raptr/man/spp.plot.Rd raptr/man/RapOpts-class.Rd raptr/man/AttributeSpaces.Rd raptr/man/rasterizeGDAL.Rd raptr/man/print.Rd raptr/man/RapData.Rd raptr/man/pu.subset.Rd raptr/man/plot.Rd raptr/man/AttributeSpace.Rd raptr/man/selections.Rd raptr/man/RapSolved.Rd raptr/man/RapUnsolved-class.Rd raptr/man/RapSolved-class.Rd raptr/man/summary.Rd raptr/man/space.target.Rd

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