raptr: Representative and Adequate Prioritization Toolkit in R
Version 0.0.3

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 ). Additionally, the 'rgurobi' package can also be installed to provide extra functionality (obtained from ).

Browse man pages Browse package API and functions Browse package files

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
URL https://github.com/jeffreyhanson/raptr
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("raptr")

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.

Functions

AttributeSpace Man page Source code
AttributeSpace-class Man page
AttributeSpaces Man page Source code
AttributeSpaces-class Man page
DemandPoints Man page Source code
DemandPoints-class Man page
GurobiOpts Man page Source code
GurobiOpts-class Man page
ManualOpts Man page Source code
ManualOpts-class Man page
PlanningUnitPoints Man page Source code
PlanningUnitPoints-class Man page
PolySet Man page
PolySet-class Man page
RapData Man page Source code
RapData-class Man page
RapOpts Man page
RapOpts-class Man page
RapReliableOpts Man page Source code
RapReliableOpts-class Man page
RapResults Man page Source code
RapResults-class Man page
RapSolved Man page Source code
RapSolved-class Man page
RapUnreliableOpts Man page Source code
RapUnreliableOpts-class Man page
RapUnsolved Man page Source code
RapUnsolved-class Man page
SolverOpts Man page
SolverOpts-class Man page
SpatialPolygons2PolySet Man page Source code
SpatialPolygons2PolySet.SpatialPolygons Man page Source code
SpatialPolygons2PolySet.SpatialPolygonsDataFrame Man page Source code
affineTrans Source code
amount.held Man page Source code
amount.held.RapSolved Man page Source code
amount.target Man page Source code
amount.target.RapData Man page Source code
amount.target.RapUnsolOrSol Man page Source code
amount.target<- Man page
amount.target<-.RapData Man page
amount.target<-.RapUnsolOrSol Man page
as.list Man page
as.list.GurobiOpts Man page Source code
basemap Man page Source code
basemap.RapData Man page Source code
basemap.RapSolved Man page Source code
bimodal_niche Source code
blank.raster Man page Source code
brewerCols Source code
cache Man page
cache,RapData,character,ANY-method Man page
cache,RapData,character,missing-method Man page
cache,RapResults,character,ANY-method Man page
cache,RapResults,character,missing-method Man page
calcBoundaryData Man page Source code
calcBoundaryData.PolySet Man page Source code
calcBoundaryData.SpatialPolygons Man page Source code
calcSpeciesAverageInPus Man page Source code
calcSpeciesAverageInPus.SpatialPolygons Man page Source code
calcSpeciesAverageInPus.SpatialPolygonsDataFrame Man page Source code
casestudy_data Man page
categoricalLegend Source code
continuousLegend Source code
cs_pus Man page
cs_space Man page
cs_spp Man page
demand.points.density1d Source code
demand.points.density2d Source code
demand.points.hypervolume Source code
dp.subset Man page Source code
dp.subset.RapData Man page Source code
dp.subset.RapUnsolOrSol Man page Source code
dump_object Source code
emptyPolySet Source code
findGdalInstallationPaths Source code
hashCall Source code
is.GurobiInstalled Man page Source code
is.cached Man page
is.cached,RapData,character-method Man page
is.cached,RapResults,character-method Man page
is.comparable Man page
is.comparable,RapData,RapData-method Man page
is.comparable,RapData,RapUnsolOrSol-method Man page
is.comparable,RapUnsolOrSol,RapData-method Man page
is.comparable,RapUnsolOrSol,RapUnsolOrSol-method Man page
is.gdalInstalled Man page Source code
logging.file Man page Source code
logging.file.RapResults Man page Source code
logging.file.RapSolved Man page Source code
make.DemandPoints Man page Source code
make.RapData Man page Source code
maximum.targets Man page Source code
maximum.targets.RapUnsolOrSol Man page Source code
mergeRapResults Source code
names Man page
names.RapData Man page Source code
names.RapUnsolOrSol Man page Source code
names<-.RapData Man page
names<-.RapUnsolOrSol Man page
normal_niche Source code
onAttach Source code
onUnload Source code
parseArgs Source code
parseArgs2 Source code
plot Man page
plot,RapSolved,RapSolved-method Man page
plot,RapSolved,missing-method Man page
plot,RapSolved,numeric-method Man page
prettyGeoplot Source code
print Man page
print.AttributeSpace Man page Source code
print.AttributeSpaces Man page Source code
print.GurobiOpts Man page Source code
print.ManualOpts Man page Source code
print.RapData Man page Source code
print.RapReliableOpts Man page Source code
print.RapResults Man page Source code
print.RapSolved Man page Source code
print.RapUnreliableOpts Man page Source code
print.RapUnsolved Man page Source code
prob.subset Man page Source code
prob.subset.RapData Man page Source code
prob.subset.RapUnsolOrSol Man page Source code
pu.subset Man page Source code
pu.subset.RapData Man page Source code
pu.subset.RapUnsolOrSol Man page Source code
randomPoints Man page Source code
rap Man page Source code
raptr Man page
raptr-package Man page
rasterizeGDAL Man page Source code
rcpp_Polygons2PolySet Source code
rcpp_append_model_object Source code
rcpp_calcBoundaryDF Source code
rcpp_dump_character_object Source code
rcpp_dump_integer_object Source code
rcpp_dump_numeric_object Source code
rcpp_extract_model_object Source code
rcpp_generate_model_object Source code
rcpp_groupcombine Source code
rcpp_groupmean Source code
rcpp_proportion_held Source code
rcpp_rrap_proportion_held Source code
rcpp_rrap_squared_distance Source code
rcpp_squared_distance Source code
rcpp_sum_duplicates Source code
read.RapResults Man page Source code
rrap.proportion.held Man page Source code
rrap.squared.distance Source code
score Man page Source code
score.RapResults Man page Source code
score.RapSolved Man page Source code
selections Man page Source code
selections.RapResults Man page Source code
selections.RapSolved Man page Source code
show Man page
show,GurobiOpts-method Man page
show,ManualOpts-method Man page
show,RapData-method Man page
show,RapReliableOpts-method Man page
show,RapResults-method Man page
show,RapSolved-method Man page
show,RapUnreliableOpts-method Man page
show,RapUnsolved-method Man page
sim.pus Man page Source code
sim.space Man page Source code
sim.space.RasterLayer Man page Source code
sim.space.SpatialPolygons Man page Source code
sim.species Man page Source code
sim.species.RasterLayer Man page Source code
sim.species.SpatialPolygons Man page Source code
sim_rs Man page
sim_ru Man page
simulated_data Man page
solve Man page
solve,RapUnsolOrSol,GurobiOpts-method Man page
solve,RapUnsolOrSol,logical-method Man page
solve,RapUnsolOrSol,matrix-method Man page
solve,RapUnsolOrSol,missing-method Man page
solve,RapUnsolOrSol,numeric-method Man page
space.held Man page Source code
space.held.RapSolved Man page Source code
space.plot Man page Source code
space.plot.RapData Man page Source code
space.plot.RapSolved Man page Source code
space.plot.RapUnsolved Man page Source code
space.target Man page Source code
space.target.RapData Man page Source code
space.target.RapUnsolOrSol Man page Source code
space.target<- Man page
space.target<-.RapData Man page
space.target<-.RapUnsolOrSol Man page
spacePlot.1d Source code
spacePlot.2d Source code
spacePlot.3d Source code
spp.plot Man page Source code
spp.plot.RapData Man page Source code
spp.plot.RapSolved Man page Source code
spp.plot.RapUnsolved Man page Source code
spp.subset Man page Source code
spp.subset.RapData Man page Source code
spp.subset.RapUnsolOrSol Man page Source code
summary Man page
summary.RapResults Source code
summary.RapSolved Source code
uniform_niche Source code
update Man page
update.GurobiOpts Man page Source code
update.ManualOpts Man page Source code
update.RapData Man page Source code
update.RapReliableOpts Man page Source code
update.RapUnreliableOpts Man page Source code
update.RapUnsolOrSol Man page Source code
urap.proportion.held Man page Source code
urap.squared.distance Source code
zonalMean Source code
zonalMean.RasterLayerInMemory Source code
zonalMean.RasterLayerNotInMemory Source code

Files

inst
inst/doc
inst/doc/raptr.Rmd
inst/doc/raptr.html
inst/vign
inst/vign/raptr.Rmd
inst/vign/placeholder.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-02-misc.R
tests/testthat/test-10-RapData.R
tests/testthat/test-07-DemandPoints.R
tests/testthat/test-06-PlanningUnitPoints.R
tests/testthat/test-05-simulate-data.R
tests/testthat/test-01-rapr-internal-test.R
tests/testthat/test-03-SolverOpts.R
tests/testthat/functions.R
tests/testthat/test-11-RapUnsolved.R
tests/testthat/test-13-rap.R
tests/testthat/test-04-RapOpts.R
tests/testthat/test-12-RapSolved.R
tests/testthat/test-08-AttributeSpace.R
tests/testthat/test-09-AttributeSpaces.R
src
src/dump_object.cpp
src/rcpp_proportion_held.cpp
src/rcpp_squared_distance.cpp
src/rcpp_groupmean.cpp
src/rcpp_rrap_proportion_held.cpp
src/rcpp_append_model_object.cpp
src/functions.h
src/rcpp_generate_model_object.cpp
src/rcpp_Polygons2PolySet.cpp
src/functions.cpp
src/rcpp_groupcombine.cpp
src/rcpp_rrap_squared_distance.cpp
src/rcpp_extract_model_object.cpp
src/rcpp_sum_duplicates.cpp
src/RcppExports.cpp
src/rcpp_calcBoundaryDF.cpp
NAMESPACE
data
data/sim_ru.rda
data/cs_spp.rda
data/datalist
data/cs_space.rda
data/sim_rs.rda
data/cs_pus.rda
R
R/sim.space.R
R/calcSpeciesAverageInPus.R
R/ManualOpts.R
R/rap.R
R/sim.pus.R
R/PlanningUnitPoints.R
R/RapData.R
R/raptr.R
R/generics.R
R/AttributeSpace.R
R/dependencies.R
R/RapUnreliableOpts.R
R/DemandPoints.R
R/data.R
R/AttributeSpaces.R
R/raptr-internal.R
R/RcppExports.R
R/GurobiOpts.R
R/rrap.proportion.held.R
R/RapSolved.R
R/RapResults.R
R/calcBoundaryData.R
R/RapUnsolved.R
R/misc.R
R/SpatialPolygons2PolySet.R
R/zzz.R
R/RapReliableOpts.R
R/urap.proportion.held.R
R/sim.species.R
vignettes
vignettes/raptr.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/PlanningUnitPoints-class.Rd
man/GurobiOpts-class.Rd
man/amount.target.Rd
man/DemandPoints.Rd
man/space.held.Rd
man/sim.species.Rd
man/prob.subset.Rd
man/RapReliableOpts.Rd
man/show.Rd
man/AttributeSpace-class.Rd
man/calcSpeciesAverageInPus.Rd
man/score.Rd
man/casestudy_data.Rd
man/is.gdalInstalled.Rd
man/space.plot.Rd
man/solve.Rd
man/names.Rd
man/maximum.targets.Rd
man/is.cached.Rd
man/read.RapResults.Rd
man/rrap.proportion.held.Rd
man/RapUnsolved.Rd
man/make.DemandPoints.Rd
man/rap.Rd
man/simulated_data.Rd
man/PolySet-class.Rd
man/SolverOpts-class.Rd
man/sim.pus.Rd
man/update.Rd
man/RapReliableOpts-class.Rd
man/calcBoundaryData.Rd
man/randomPoints.Rd
man/DemandPoints-class.Rd
man/RapUnreliableOpts-class.Rd
man/PlanningUnitPoints.Rd
man/SpatialPolygons2PolySet.Rd
man/RapResults-class.Rd
man/ManualOpts.Rd
man/raptr.Rd
man/blank.raster.Rd
man/ManualOpts-class.Rd
man/dp.subset.Rd
man/AttributeSpaces-class.Rd
man/spp.subset.Rd
man/urap.proportion.held.Rd
man/amount.held.Rd
man/RapUnreliableOpts.Rd
man/GurobiOpts.Rd
man/cache.Rd
man/as.list.Rd
man/is.comparable.Rd
man/RapData-class.Rd
man/sim.space.Rd
man/logging.file.Rd
man/make.RapData.Rd
man/RapResults.Rd
man/is.GurobiInstalled.Rd
man/basemap.Rd
man/spp.plot.Rd
man/RapOpts-class.Rd
man/AttributeSpaces.Rd
man/rasterizeGDAL.Rd
man/print.Rd
man/RapData.Rd
man/pu.subset.Rd
man/plot.Rd
man/AttributeSpace.Rd
man/selections.Rd
man/RapSolved.Rd
man/RapUnsolved-class.Rd
man/RapSolved-class.Rd
man/summary.Rd
man/space.target.Rd
raptr documentation built on May 19, 2017, 11:46 p.m.