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

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.

Functions

amount.held Man page
amount.held.RapSolved Man page
amount.target Man page
amount.target<- Man page
amount.target<-.RapData Man page
amount.target.RapData Man page
amount.target<-.RapUnsolOrSol Man page
amount.target.RapUnsolOrSol Man page
as.list Man page
as.list.GurobiOpts Man page
AttributeSpace Man page
AttributeSpace-class Man page
AttributeSpaces Man page
AttributeSpaces-class Man page
basemap Man page
basemap.RapData Man page
basemap.RapSolved Man page
blank.raster Man page
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
calcBoundaryData.PolySet Man page
calcBoundaryData.SpatialPolygons Man page
calcSpeciesAverageInPus Man page
calcSpeciesAverageInPus.SpatialPolygons Man page
calcSpeciesAverageInPus.SpatialPolygonsDataFrame Man page
casestudy_data Man page
cs_pus Man page
cs_space Man page
cs_spp Man page
DemandPoints Man page
DemandPoints-class Man page
dp.subset Man page
dp.subset.RapData Man page
dp.subset.RapUnsolOrSol Man page
GurobiOpts Man page
GurobiOpts-class Man page
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
is.GurobiInstalled Man page
logging.file Man page
logging.file.RapResults Man page
logging.file.RapSolved Man page
make.DemandPoints Man page
make.RapData Man page
ManualOpts Man page
ManualOpts-class Man page
maximum.targets Man page
maximum.targets.RapUnsolOrSol Man page
names Man page
names<-.RapData Man page
names.RapData Man page
names<-.RapUnsolOrSol Man page
names.RapUnsolOrSol Man page
PlanningUnitPoints Man page
PlanningUnitPoints-class Man page
plot Man page
plot,RapSolved,missing-method Man page
plot,RapSolved,numeric-method Man page
plot,RapSolved,RapSolved-method Man page
PolySet Man page
PolySet-class Man page
print Man page
print.AttributeSpace Man page
print.AttributeSpaces Man page
print.GurobiOpts Man page
print.ManualOpts Man page
print.RapData Man page
print.RapReliableOpts Man page
print.RapResults Man page
print.RapSolved Man page
print.RapUnreliableOpts Man page
print.RapUnsolved Man page
prob.subset Man page
prob.subset.RapData Man page
prob.subset.RapUnsolOrSol Man page
pu.subset Man page
pu.subset.RapData Man page
pu.subset.RapUnsolOrSol Man page
randomPoints Man page
rap Man page
RapData Man page
RapData-class Man page
RapOpts Man page
RapOpts-class Man page
RapReliableOpts Man page
RapReliableOpts-class Man page
RapResults Man page
RapResults-class Man page
RapSolved Man page
RapSolved-class Man page
raptr Man page
raptr-package Man page
RapUnreliableOpts Man page
RapUnreliableOpts-class Man page
RapUnsolved Man page
RapUnsolved-class Man page
rasterizeGDAL Man page
read.RapResults Man page
rrap.proportion.held Man page
score Man page
score.RapResults Man page
score.RapSolved Man page
selections Man page
selections.RapResults Man page
selections.RapSolved Man page
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
sim_rs Man page
sim_ru Man page
sim.space Man page
sim.space.RasterLayer Man page
sim.space.SpatialPolygons Man page
sim.species Man page
sim.species.RasterLayer Man page
sim.species.SpatialPolygons 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
SolverOpts Man page
SolverOpts-class Man page
space.held Man page
space.held.RapSolved Man page
space.plot Man page
space.plot.RapData Man page
space.plot.RapSolved Man page
space.plot.RapUnsolved Man page
space.target Man page
space.target<- Man page
space.target<-.RapData Man page
space.target.RapData Man page
space.target<-.RapUnsolOrSol Man page
space.target.RapUnsolOrSol Man page
SpatialPolygons2PolySet Man page
SpatialPolygons2PolySet.SpatialPolygons Man page
SpatialPolygons2PolySet.SpatialPolygonsDataFrame Man page
spp.plot Man page
spp.plot.RapData Man page
spp.plot.RapSolved Man page
spp.plot.RapUnsolved Man page
spp.subset Man page
spp.subset.RapData Man page
spp.subset.RapUnsolOrSol Man page
summary Man page
update Man page
update.GurobiOpts Man page
update.ManualOpts Man page
update.RapData Man page
update.RapReliableOpts Man page
update.RapUnreliableOpts Man page
update.RapUnsolOrSol Man page
urap.proportion.held Man page

Files

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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