NEWS

raptr 1.0.1 (2024-01-28)

The package has been overhauled to support modern spatial data structures. Specifically, sf package objects (sf::st_sf()) are now use for vector data and terra package objects (terra::rast()) for raster data. These updates impact many of the user-facing functions (e.g., calcBoundaryData(), sim.species(), sim.space(), calcSpeciesAverageInPus(), rap()), so users will likely need to update their code.
The cs_pus, cs_spp, and cs_spaces built-in datasets have been removed. This is because terra::rast() objects cannot be distributed as built-in datasets for packages. These datasets can now be manually imported from external files distributed with the package (see ?cs_pus for more details).
Remove rgdal and rgeos packages as dependencies (#13).
Support for the raster package has been deprecated.
The SpatialPolygons2PolySet function has been renamed to convert2PolySet.
Update citation format.
Update package startup message.
Update C++ specification to C++14.
Update examples and unit tests.

The data simulation function has been updated such that the RandomFields package is no longer a dependency.
The sim.space and sim.species functions no longer accept RandomFileds objects as arguments. To simulate spatially auto-correlated data using random fields, a numeric value should be supplied to the model parameter.
Small tweaks to case study in vignette.

The RandomFields and RgoogleMaps R packages are now optional dependencies.
Minimum supported versions are now specified for most dependencies.
The verbose parameter of solve() can now be used to suppress output from the Gurobi solver.
Fix compatibility issues with updates to the ggplot2 package.
Fix note during package checks related to the rgdal package.

Update example datasets and make.RapData function to improve compatibility with updates to coordinate reference system (sp::CRS) objects. These updates simply mean that warning messages will no longer be displayed. The compatibility issues that resulted in warnings did not affect the correctness of any results.

Fix compatibility issues between the testthat R package and the gurobi R package in package tests.

Fix "Non-file package-anchored link(s) in documentation object" warnings in R-devel checks.

Fix errors in R-devel CRAN checks due changes in is.finite behaviour for character class objects.
Fix WorldClim URLs.

Fix bug that caused the R session to crash when none of the planning units associated with an attribute space were selected in a manually specified solution. Now the space-held calculations will return a negative infinity value in such cases.
Permit attribute spaces to have a single demand point.

Fix compatibility issues with demand point examples and hypervolume R package (version 2.0.10).
Update package citation.
Removed rgurobi R package dependency because the gurobi R package (version 8.0.0+) provides the functionality to access solutions from the solution pool.
Multiple solutions can now be generated using the three different search pool methods provided Gurobi.
Permit a zero MIPGAP in argument to GurobiOpts.
The print.RapResults function now prints information in a prettier manner.
The raptr::solve function now throws a warning if some species are poorly represented in the solution.

Unit tests now compatible with testthat R package (version 1.0.2.9000).
The assertthat R package is now used for validating function arguments.
Vignette now uses knitr::rmarkdown_notangle engine to avoid running the code during package checks, and placeholder vignette file has been removed.
Code has been linted.
Functions from other packages are now called explicitly using pkg::function.
Messages are now displayed using message following best practices.
Updated readme.
Added citation for Methods in Ecology and Evolution paper.
Strip debugging symbols from compiled files to reduce installation size.
The is.GurobiInstalled now does not run gurobi to avoid spurious notes during CRAN checks on academic license.