# Representative and Adequate Prioritization Toolkit in R

## Documentation for package ‘raptr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D G I L M N P R S U

## -- A --

amount.held | Extract amount held for a solution
amount.held.RapSolved | Extract amount held for a solution
amount.target | Amount targets
amount.target.RapData | Amount targets
amount.target.RapUnsolOrSol | Amount targets
amount.target<- | Amount targets
amount.target<-.RapData | Amount targets
amount.target<-.RapUnsolOrSol | Amount targets
as.list | Convert object to list
as.list.GurobiOpts | 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 attribute spaces for different species.

## -- B --

blank.raster | Blank raster

## -- C --

calcBoundaryData | Calculate boundary data for planning units
calcBoundaryData.PolySet | Calculate boundary data for planning units
calcBoundaryData.sf | Calculate boundary data for planning units
calcBoundaryData.SpatialPolygons | Calculate boundary data for planning units
calcSpeciesAverageInPus | Calculate average value for species data in planning units
calcSpeciesAverageInPus.sf | Calculate average value for species data in planning units
calcSpeciesAverageInPus.SpatialPolygons | Calculate average value for species data in planning units
calcSpeciesAverageInPus.SpatialPolygonsDataFrame | Calculate average value for species data in planning units
casestudy_data | Case-study dataset for a conservation planning exercise
convert2PolySet | Convert object to PolySet data
convert2PolySet.sf | Convert object to PolySet data
convert2PolySet.SpatialPolygons | Convert object to PolySet data
convert2PolySet.SpatialPolygonsDataFrame | Convert object to PolySet data
cs_pus | Case-study dataset for a conservation planning exercise
cs_space | Case-study dataset for a conservation planning exercise
cs_spp | Case-study dataset for a conservation planning exercise

## -- D --

DemandPoints | Create new DemandPoints object
DemandPoints-class | DemandPoints: An S4 class to represent demand points
dp.subset | Subset demand points
dp.subset.RapData | Subset demand points
dp.subset.RapUnsolOrSol | Subset demand points

## -- G --

GurobiOpts | Create GurobiOpts object
GurobiOpts-class | GurobiOpts: An S4 class to represent Gurobi parameters

## -- I --

is.GurobiInstalled | Test if Gurobi is installed

## -- L --

logging.file | Log file
logging.file.RapResults | Log file
logging.file.RapSolved | Log file

## -- M --

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 specified solutions
maximum.targets | Maximum targets
maximum.targets.RapUnsolOrSol | Maximum targets

## -- N --

names | Names
names.RapData | Names
names.RapUnsolOrSol | Names
names<-.RapData | Names
names<-.RapUnsolOrSol | Names

## -- P --

PlanningUnitPoints | Create new PlanningUnitPoints object
PlanningUnitPoints-class | PlanningUnitPoints: An S4 class to represent planning units in an attribute space
plot | Plot object
plot-method | Plot object
PolySet | PolySet
PolySet-class | PolySet
print | Print objects
print.AttributeSpace | Print objects
print.AttributeSpaces | Print objects
print.GurobiOpts | Print objects
print.ManualOpts | Print objects
print.RapData | Print objects
print.RapReliableOpts | Print objects
print.RapResults | Print objects
print.RapSolved | Print objects
print.RapUnreliableOpts | Print objects
print.RapUnsolved | Print objects
prob.subset | Subset probabilities above a threshold
prob.subset.RapData | Subset probabilities above a threshold
prob.subset.RapUnsolOrSol | Subset probabilities above a threshold
pu.subset | Subset planning units
pu.subset.RapData | Subset planning units
pu.subset.RapUnsolOrSol | Subset planning units

## -- R --

randomPoints | Sample random points from a SpatRaster
rap | Generate prioritizations using RAP
RapData | Create new RapData object
RapData-class | RapData: An S4 class to represent RAP input data
RapOpts | RapOpts class
RapOpts-class | RapOpts class
RapReliableOpts | Create RapReliableOpts object
RapReliableOpts-class | RapReliableOpts: An S4 class to represent input parameters for the reliable formulation of RAP.
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 Prioritization Toolkit in R
raptr-deprecated | Deprecation notice
RapUnreliableOpts | Create RapUnreliableOpts object
RapUnreliableOpts-class | RapUnreliableOpts: An S4 class to represent parameters for the unreliable RAP problem
RapUnsolved | Create a new RapUnsolved object
RapUnsolved-class | RapUnsolved: An S4 class to represent RAP inputs
rrap.proportion.held | Proportion held using reliable RAP formulation.

## -- S --

score | Solution score
score.RapResults | Solution score
score.RapSolved | Solution score
selections | Extract solution selections
selections.RapResults | Extract solution selections
selections.RapSolved | Extract solution selections
show | Show objects
show-method | Show objects
sim.pus | Simulate planning units
sim.space | Simulate attribute space data for RAP
sim.space.sf | Simulate attribute space data for RAP
sim.space.SpatialPolygons | Simulate attribute space data for RAP
sim.space.SpatRaster | Simulate attribute space data for RAP
sim.species | Simulate species distribution data for RAP
sim.species.sf | Simulate species distribution data for RAP
sim.species.SpatialPolygons | Simulate species distribution data for RAP
sim.species.SpatRaster | Simulate species distribution data for RAP
simulated_data | Simulated dataset for a conservation planning exercise
sim_rs | Simulated dataset for a conservation planning exercise
sim_ru | Simulated dataset for a conservation planning exercise
solve | Solve RAP object
solve-method | Solve RAP object
SolverOpts | SolverOpts class
SolverOpts-class | SolverOpts class
space.held | Extract attribute space held for a solution
space.held.RapSolved | Extract attribute space held for a solution
space.plot | Plot space
space.plot.RapData | Plot space
space.plot.RapSolved | Plot space
space.plot.RapUnsolved | Plot space
space.target | Attribute space targets
space.target.RapData | Attribute space targets
space.target.RapUnsolOrSol | Attribute space targets
space.target<- | Attribute space targets
space.target<-.RapData | Attribute space targets
space.target<-.RapUnsolOrSol | Attribute space targets
SpatialPolygons2PolySet | Deprecation notice
spp.plot | Plot species
spp.plot.RapData | Plot species
spp.plot.RapSolved | Plot species
spp.plot.RapUnsolved | Plot species
spp.subset | Subset species
spp.subset.RapData | Subset species
spp.subset.RapUnsolOrSol | Subset species
summary | Summary of solutions

## -- U --

update | Update object
update.GurobiOpts | Update object
update.ManualOpts | Update object
update.RapData | Update object
update.RapReliableOpts | Update object
update.RapUnreliableOpts | Update object
update.RapUnsolOrSol | Update object
urap.proportion.held | Proportion held using unreliable RAP formulation.