Package: raptr 1.0.1

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 (obtained from <https://www.gurobi.com/>). For more information on using this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.

Authors:Jeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]

raptr_1.0.1.tar.gz
raptr_1.0.1.zip(r-4.7-x86_64)raptr_1.0.1.zip(r-4.7-arm64)raptr_1.0.1.zip(r-4.6-x86_64)raptr_1.0.1.zip(r-4.6-arm64)raptr_1.0.1.zip(r-4.5-x86_64)
raptr_1.0.1.tgz(r-4.6-x86_64)raptr_1.0.1.tgz(r-4.6-arm64)raptr_1.0.1.tgz(r-4.5-x86_64)raptr_1.0.1.tgz(r-4.5-arm64)
raptr_1.0.1.tar.gz(r-4.7-arm64)raptr_1.0.1.tar.gz(r-4.7-x86_64)raptr_1.0.1.tar.gz(r-4.6-arm64)raptr_1.0.1.tar.gz(r-4.6-x86_64)
raptr_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
raptr/json (API)

# Install 'raptr' in R:

install.packages('raptr', repos = c('https://jeffreyhanson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jeffreyhanson/raptr/issues

Pkgdown/docs site:https://jeffrey-hanson.com

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

sim_rs - Simulated dataset for a conservation planning exercise
sim_ru - Simulated dataset for a conservation planning exercise

On CRAN:

cpp

5.56 score 8 stars 90 scripts 561 downloads 45 exports 120 dependencies

Last updated from:f67fa73b31. Checks:4 NOTE, 1 ERROR, 10 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	322
linux-devel-x86_64	NOTE	367
source / vignettes	ERROR	407
linux-release-arm64	OK	302
linux-release-x86_64	OK	380
macos-release-arm64	OK	363
macos-release-x86_64	OK	597
macos-oldrel-arm64	OK	294
macos-oldrel-x86_64	OK	547
windows-devel-arm64	NOTE	647
windows-devel-x86_64	NOTE	496
windows-release-arm64	OK	577
windows-release-x86_64	OK	424
windows-oldrel-x86_64	OK	362
wasm-release	OK	217

Exports:amount.held amount.target amount.target<-AttributeSpace AttributeSpaces blank.raster calcBoundaryData calcSpeciesAverageInPus convert2PolySet DemandPoints dp.subset GurobiOpts is.GurobiInstalled logging.file make.DemandPoints make.RapData ManualOpts maximum.targets PlanningUnitPoints prob.subset pu.subset randomPoints rap RapData RapReliableOpts RapResults RapSolved RapUnreliableOpts RapUnsolved rrap.proportion.held score selections sim.pus sim.space sim.species solve space.held space.plot space.target space.target<-SpatialPolygons2PolySet spp.plot spp.subset summary urap.proportion.held

Dependencies:abind ade4 adehabitatHR adehabitatLT adehabitatMA assertthat BH boot caret class classInt cli clock codetools cpp11 crayon data.table DBI diagram digest doParallel dplyr e1071 farver fastcluster FNN foreach future future.apply generics geometry ggplot2 globals glue gower gtable hardhat hitandrun hms hypervolume ipred isoband iterators kernlab KernSmooth ks labeling lattice lava lifecycle linprog listenv lpSolve lubridate magic magrittr maps MASS Matrix mclust mgcv ModelMetrics multicool mvtnorm nlme nnet numDeriv palmerpenguins parallelly pbapply PBSmapping pdist pillar pixmap pkgconfig plyr pracma prettyunits pROC prodlim progress progressr proxy purrr R6 raster rcdd RColorBrewer Rcpp RcppArmadillo RcppEigen RcppProgress recipes reshape2 rlang rpart s2 S7 scales sf shape sp sparsevctrs SQUAREM stringi stringr survival terra tibble tidyr tidyselect timechange timeDate tzdb units utf8 vctrs viridisLite withr wk

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

raptr: Representative and Adequate Prioritization Toolkit in R

Rendered fromraptr.Rmdusingknitr::rmarkdown_notangle

Last update: 2023-03-13
Started: 2016-07-19

Help page	Topics
Extract amount held for a solution	amount.held amount.held.RapSolved
Amount targets	amount.target amount.target.RapData amount.target.RapUnsolOrSol amount.target<- amount.target<-.RapData amount.target<-.RapUnsolOrSol
Convert object to list	as.list as.list.GurobiOpts
Create new AttributeSpace object	AttributeSpace
AttributeSpace: An S4 class to represent an attribute space.	AttributeSpace-class
Create new AttributeSpaces object	AttributeSpaces
AttributeSpaces: An S4 class to represent a collection of attribute spaces for different species.	AttributeSpaces-class
Blank raster	blank.raster
Calculate boundary data for planning units	calcBoundaryData calcBoundaryData.PolySet calcBoundaryData.sf calcBoundaryData.SpatialPolygons
Calculate average value for species data in planning units	calcSpeciesAverageInPus calcSpeciesAverageInPus.sf calcSpeciesAverageInPus.SpatialPolygons calcSpeciesAverageInPus.SpatialPolygonsDataFrame
Case-study dataset for a conservation planning exercise	casestudy_data cs_pus cs_space cs_spp
Convert object to PolySet data	convert2PolySet convert2PolySet.sf convert2PolySet.SpatialPolygons convert2PolySet.SpatialPolygonsDataFrame
Create new DemandPoints object	DemandPoints
DemandPoints: An S4 class to represent demand points	DemandPoints-class
Subset demand points	dp.subset dp.subset.RapData dp.subset.RapUnsolOrSol
Create GurobiOpts object	GurobiOpts
GurobiOpts: An S4 class to represent Gurobi parameters	GurobiOpts-class
Test if Gurobi is installed	is.GurobiInstalled
Log file	logging.file logging.file.RapResults logging.file.RapSolved
Generate demand points for RAP	make.DemandPoints
Make data for RAP using minimal inputs	make.RapData
Create ManualOpts object	ManualOpts
ManualOpts: An S4 class to represent parameters for manually specified solutions	ManualOpts-class
Maximum targets	maximum.targets maximum.targets.RapUnsolOrSol
Names	names names.RapData names.RapUnsolOrSol names<-.RapData names<-.RapUnsolOrSol
Create new PlanningUnitPoints object	PlanningUnitPoints
PlanningUnitPoints: An S4 class to represent planning units in an attribute space	PlanningUnitPoints-class
Plot object	plot plot,RapSolved,missing-method plot,RapSolved,numeric-method plot,RapSolved,RapSolved-method
PolySet	PolySet PolySet-class
Print objects	print print.AttributeSpace print.AttributeSpaces print.GurobiOpts print.ManualOpts print.RapData print.RapReliableOpts print.RapResults print.RapSolved print.RapUnreliableOpts print.RapUnsolved
Subset probabilities above a threshold	prob.subset prob.subset.RapData prob.subset.RapUnsolOrSol
Subset planning units	pu.subset pu.subset.RapData pu.subset.RapUnsolOrSol
Sample random points from a SpatRaster	randomPoints
Generate prioritizations using RAP	rap
Create new RapData object	RapData
RapData: An S4 class to represent RAP input data	RapData-class
RapOpts class	RapOpts RapOpts-class
Create RapReliableOpts object	RapReliableOpts
RapReliableOpts: An S4 class to represent input parameters for the reliable formulation of RAP.	RapReliableOpts-class
Create RapResults object	RapResults
RapResults: An S4 class to represent RAP results	RapResults-class
Create new RapSolved object	RapSolved
RapSolved: An S4 class to represent RAP inputs and outputs	RapSolved-class
raptr: Representative and Adequate Prioritization Toolkit in R	raptr-package raptr
Deprecation notice	raptr-deprecated SpatialPolygons2PolySet
Create RapUnreliableOpts object	RapUnreliableOpts
RapUnreliableOpts: An S4 class to represent parameters for the unreliable RAP problem	RapUnreliableOpts-class
Create a new RapUnsolved object	RapUnsolved
RapUnsolved: An S4 class to represent RAP inputs	RapUnsolved-class
Proportion held using reliable RAP formulation.	rrap.proportion.held
Solution score	score score.RapResults score.RapSolved
Extract solution selections	selections selections.RapResults selections.RapSolved
Show objects	show show,GurobiOpts-method show,ManualOpts-method show,RapData-method show,RapReliableOpts-method show,RapResults-method show,RapSolved-method show,RapUnreliableOpts-method show,RapUnsolved-method
Simulate planning units	sim.pus
Simulate attribute space data for RAP	sim.space sim.space.sf sim.space.SpatialPolygons sim.space.SpatRaster
Simulate species distribution data for RAP	sim.species sim.species.sf sim.species.SpatialPolygons sim.species.SpatRaster
Simulated dataset for a conservation planning exercise	simulated_data sim_rs sim_ru
Solve RAP object	solve solve,RapUnsolOrSol,GurobiOpts-method solve,RapUnsolOrSol,logical-method solve,RapUnsolOrSol,matrix-method solve,RapUnsolOrSol,missing-method solve,RapUnsolOrSol,numeric-method
SolverOpts class	SolverOpts SolverOpts-class
Extract attribute space held for a solution	space.held space.held.RapSolved
Plot space	space.plot space.plot.RapData space.plot.RapSolved space.plot.RapUnsolved
Attribute space targets	space.target space.target.RapData space.target.RapUnsolOrSol space.target<- space.target<-.RapData space.target<-.RapUnsolOrSol
Plot species	spp.plot spp.plot.RapData spp.plot.RapSolved spp.plot.RapUnsolved
Subset species	spp.subset spp.subset.RapData spp.subset.RapUnsolOrSol
Summary of solutions	summary
Update object	update update.GurobiOpts update.ManualOpts update.RapData update.RapReliableOpts update.RapUnreliableOpts update.RapUnsolOrSol
Proportion held using unreliable RAP formulation.	urap.proportion.held

Package: raptr 1.0.1

raptr: Representative and Adequate Prioritization Toolkit in R

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