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>).

Author
Jeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]
Date of publication
2016-11-25 13:00:00
Maintainer
Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
License
GPL-3
Version
0.0.3
URLs

View on CRAN

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