NEWS.md

In prioritizr/prioritizr: Systematic Conservation Prioritization in R

prioritizr 8.0.2.1

• Update problem() so that an error will be thrown if argument to features contains only missing (NA) values (e.g., an sf object is supplied that has NA values in all rows for a feature's column).
• Update publication record.

prioritizr 8.0.2

Notice

• The package has been updated to focus on using the sf and terra package for spatial vector and raster datasets. This is because the sf package is the successor to the sp package, and the terra package is the successor to the raster package. By leveraging these newer packages, the prioritizr package can provide better performance. Although sp and raster package classes (e.g., raster::stack() and sp::SpatialPolyonsDataFrame()) are still supported, the prioritizr package will now throw deprecation warnings. Since support for the sp and raster package classes will be fully deprecated and removed in a later version this year, we recommend updating code to use the sf and terra packages.

Breaking changes

• All proto classes have been migrated to R6 classes. This update reduces memory usage (#238), so problem() objects can now contain many more constraints and penalties. Note that any problem() objects that were produced using earlier versions of the package are no longer compatible.
• The proto, raster, sf, sp packages are no longer automatically loaded alongside prioritizr. As such, users will need to load them manually (e.g., using library(sf)).
• The built-in datasets have been removed and replaced with functions to import them as needed (i.e., get_sim_pu_raster(), get_sim_pu_polygons(), get_sim_pu_lines(), get_sim_pu_points(),, get_sim_locked_in_raster(), get_sim_locked_out_raster(), get_sim_zones_pu_raster(), get_sim_zones_pu_polygons(), get_sim_phylogeny(), get_sim_features(), get_sim_zones_features()). These functions now return sf::st_sf(), terra::rast(), ape::read.tree() and zones() objects. Note that these functions are provided because data(...) cannot be used with terra::rast() objects. See ?data for more information.
• The boundary_matrix() output format has been updated. This means that users will not be able to use boundary data generated using previous versions of the package.
• The add_lpsymphony_solver() now throws an error, instead of a warning, if an old version of the lpsymphony R package is installed that is known to produce incorrect results.
• The marxan_boundary_data_to_matrix() function is no longer compatible with boundary data for multiple zones.
• The distribute_load() function has been deprecated, because it is no longer used. For equivalent functionality, See parallel::splitIndices().
• The new_optimization_problem() and predefined_optimization_problem() functions have been superseded by the new optimization_problem() function.
• To simplify package documentation and functionality, the following functions are no longer exported: is.Waiver(), add_default_decisions() new_id(), is.Id(), print.Id(), pproto().

New features

• The print() function for problem(), optimization_problem(), and zones() objects has been updated to provide more information.
• New summary() function to provide extensive detail on problem() objects.
• Updates to improve the error messages and error message handling. Hopefully, users should no longer see "bad error message"!

Minor improvements and bug fixes

• Fix bug for add_feature_weights() when applied to problems with an add_max_phylo_div_objective() or add_max_phylo_end_objectve(). Specifically, the bug meant that weights weren't being applied to problems with these particular objectives.
• Fix instructions in add_gurobi_solver() documentation for opening vignette.
• Update solver functions to provide instructions for installing dependencies in error messages when their dependencies are not available.
• To ensure consistency among the portfolio functions, all of them (except for add_extra_portfolio()) default to generating 10 solutions.
• Update publication record.
• The solve() function will now output tibble::tibble() objects (instead of data.frame() objects), when the planning unit data are tibble::tibble() objects.
• The boundary_matrix() function now uses terra::sharedPaths() for calculations, providing greater performance (#257).
• The eval_ferrier_importance() function can now be used with any objective function that uses targets and a single zone.
• Fix CRAN note regarding C++ standards (#263).
• Remove doParallel and plyr packages as dependencies by simplifying the add_shuffle_portfolio() and eval_replacement_importance() functions.
• Assorted tweaks to improve writing in the vignettes and documentation. Many thanks to Marc Edwards (@edwardsmarc)!

prioritizr 8.0.1

• Assorted bug fixes.

prioritizr 8.0.0

• This version contains an incorrect version of the code, due to a mistake when preparing for CRAN release. We strongly recommend upgrading to version 8.0.1 to ensure correct results. We apologize any inconvenience this might have caused.

prioritizr 7.2.2.7

• Update README badges.
• Update publication record.

prioritizr 7.2.2.6

• Update publication record.

prioritizr 7.2.2.5

• Update publication record.

prioritizr 7.2.2.4

• Specify minimum version for Matrix package dependency (#255).

prioritizr 7.2.2.3

• New add_highs_solver() function for the HiGHS optimization software (#250).
• Update add_default_solver() to use the HiGHS solver if the Gurobi, IBM CPLEX, and CBC solvers aren't available.
• Fix add_default_solver() so that the add_lpsymphony_solver() is used instead of add_rsymphony_solver().

prioritizr 7.2.2.2

• Update problem() and eval_feature_representation_summary() to avoid needlessly converting sparse matrices to regular matrices (#252).
• Fix broken URLs in documentation.

prioritizr 7.2.2.1

• Fix mistake in NEWS.md.
• Update publication record.

prioritizr 7.2.2

• Release candidate for CRAN.
• Fix compiler warnings.
• Update tests to skip long-running tests on CRAN.
• Update examples to minimize overall package check timings for CRAN.

prioritizr 7.2.1

• Release candidate for CRAN (rejected due to package check timings).

prioritizr 7.2.0.9

• Fix compatibility with upcoming Matrix package version (version 1.5-0).
• Update package documentation to provide details for obtaining and installing the cplexAPI package since it has been archived on CRAN (#214).
• Fix bug that caused the add_cbc_solver() to throw a segfault when solving a problem wherein the rij_matrix(x) has a zero amount for the last feature in the last planning unit (#247).
• Update simulate_data(), simulate_cost() and simulate_species() functions to improve performance using the fields package.
• Update boundary_matrix() to use STR query trees by default.
• Remove maptools, PBSmapping, and rgeos packages as dependencies. This involved updating the unit tests to hard-code correct results, updating examples to use the sf package, and updating the boundary_matrix() to use the geos package (#218).
• Fix broken URLs in package documentation.

prioritizr 7.2.0.8

• Update simulate_cost() and simulate_species() so that they no longer depend on the RandomFields package.

prioritizr 7.2.0.7

• Update publication record.

prioritizr 7.2.0.6

• Update publication record.

prioritizr 7.2.0.5

• Update publication record.

prioritizr 7.2.0.4

• Fix broken URLs in documentation.

prioritizr 7.2.0.3

• Update the presolve_check() function to (i) reduce chances of it incorrectly throwing an error when the input data won't actually cause any issues, and (ii) provide recommendations for addressing issues.
• Update documentation for add_min_largest_shortfall_objective() so that examples complete in a shorter period of time.

prioritizr 7.2.0.2

• Fix bug in processing planning unit data when a problem is constructed using arguments to (i) x that are numeric or matrix format, (ii) x that contain missing (NA) values, and (iii) rij_matrix that are in dgCMatrix format. This bug only occurred when all three of these specific conditions were met. When it occurred, the bug caused planning units with NA cost values to receive very high cost values (e.g., 1e+300). This bug meant that when attempting to solve the problem, the presolve checks (per presolve_check()) would throw an error complaining about very high cost values (#236).

prioritizr 7.2.0.1

• Update publication record.

prioritizr 7.2.0.0

• Fix add_locked_in_constraints() and add_locked_out_constraints() to ensure that a meaningful error message is provided when no planing units are locked (#234).
• Fix presolve_check() so that it does not throw a meaningless warning when the mathematical objective function only contains zeros.
• Update presolve_check() to help reduce chances of mis-attributing high connectivity/boundary values due to planning unit costs.
• Update add_connectivity_penalties() function and documentation so that it is designed specifically for symmetric connectivity data.
• New add_asym_connectivity_penalties() function that is designed specifically for asymmetric connectivity data. This function has been created to help ensure that asymmetric connectivity data are handled correctly. For instance, using asymmetric connectivity data with add_connectivity_penalties() function in previous versions of the package sometimes resulted in the data being incorrectly treated as symmetric data. Additionally, this function uses an updated mathematical formulation for handling asymmetric connectivity so that it provides similar results to the Marxan software (#323).
• Update marxan_problem() function so that it can be used with asymmetric connectivity data. This is now possible because there are dedicated functions for symmetric and asymmetric connectivity.
• Update publication record.
• Update URLs in publication record so that they pass CRAN checks.

prioritizr 7.1.1.12

• Update publication record.

prioritizr 7.1.1.11

• Update publication record.

prioritizr 7.1.1.10

• Fix broken links in documentation.
• Update publication vignette.
• Improve documentation for the zones parameter of the add_connectivity_penalties() function.

prioritizr 7.1.1.9

• Update documentation for eval_ferrier_importance() (#220). Although this function is now recommended for general use, the documentation contained an outdated warning and so the warning has now been removed.

prioritizr 7.1.1.8

• Update publication record.
• Fix bug so that the eval_n_summary() function now returns a table with the column name "n" (instead of "cost") for the number of selected planning units (#219).
• Update reference index for package website.
• Fix minor typos in vignettes.

prioritizr 7.1.1.7

• Minimum version numbers are now provided for all R package dependencies (excepting base R packages) (#217).
• The data.table package is now listed as a suggested (optional) dependency. This is because it is only used by the marxan_problem() for importing Marxan data files.

prioritizr 7.1.1.6

• Update publication record.

prioritizr 7.1.1.5

• The Tasmania tutorial has been reworked into the Getting started tutorial. This tutorial now provides short introduction to using the package.
• The Salt Spring Island tutorial has been reworked into the Connectivity tutorial. This tutorial now explores different approaches for incorporating connectivity.
• The prioritizr vignette has been renamed to the Package overview vignette.
• New Calibrating trade-offs tutorial showcasing methods for running calibration analyses. It outlines blended and hierarchical approaches for generating a set of different prioritizations based on different parameters. It also covers different approaches for selecting a candidate prioritization based on different trade-offs.

prioritizr 7.1.1.4

• Update tests to reduce run time and pass given slightly different results with new Gurobi version (9.5.0).
• Update built-in sim_pu_sf and sim_pu_zones_sf data given class updates to the sf package (compatible with version 1.0.3+).
• Update example for write_problem() function.

prioritizr 7.1.1.3

• Update publication record.

prioritizr 7.1.1.2

• Update publication record.

prioritizr 7.1.1.1

• Fix URL in vignette.

prioritizr 7.1.1

• Release candidate for CRAN.

prioritizr 7.1.0.4

• Update eval_ferrier_importance() function with verified code.
• Update documentation with information about Ferrier importance scores.
• Brandon Edwards added to package author list.
• Update Gurobi Installation guide vignette.
• Update benchmark vignette.
• Update presolve_check() function to throw warning when really high values specified in add_neighbor_constraints().

prioritizr 7.1.0.3

Update add_cbc_solver() function so that it can use a starting solution to reduce run time (via the start_solution parameter).

prioritizr 7.1.0.2

• Fix examples that fail package checks.
• Remove xtable R package from Suggests because it is no longer used.

prioritizr 7.1.0.1

• Update publication vignette.

prioritizr 7.1.0.0

• New add_linear_constraint() function to add arbitrary constraints.
• Update add_min_shortfall_objective() and add_min_largest_shortfall_objective() functions to handle targets with a target threshold value of zero.
• Minor improvements to the documentation. These include moving mathematical details to dedicated sections, providing more links in the See also sections, fixing text formatting for the eval_connectivity_summary() function, and tweaking the header in the README.
• Update publication vignette.

prioritizr 7.0.1.5

• Update publication vignette.

prioritizr 7.0.1.4

• Update documentation and examples for problem() function.
• Update publication vignette.

prioritizr 7.0.1.3

• New solver benchmark vignette.

prioritizr 7.0.1.2

• Update add_gurobi_solver() function so that it doesn't print excess debugging information (accidentally introduced in previous version 7.0.1.1).

prioritizr 7.0.1.1

• Update add_gurobi_solver() function to support the node_file_start parameter for the Gurobi software. This functionality is useful solving large problems on systems with limited memory (#139).

prioritizr 7.0.1

• Release candidate for CRAN.
• Update DESCRIPTION with more information on the package usage.
• Update DESCRIPTION with details on rcbc R package installation.

prioritizr 7.0.0.8

• New write_problem() function to save the mixed integer programming representation of a conservation planning problem to a file. This function is useful for manually executing optimization solvers.

prioritizr 7.0.0.7

• Fix typo in rij_matrix() function documentation (#189).
• Update publication vignette.

prioritizr 7.0.0.6

• Update add_gurobi_solver() function to allow specification of a starting solution (#187). This functionality is useful for conducting a boundary penalty parameter calibration exercise. Specifically, users can specify the starting solution for a given penalty value based on the solution obtained using a smaller penalty value.
• Bug fix: solve now assigns layer names based on zone names for solutions in format.

prioritizr 7.0.0.5

• Update methods for calculating solver runtime.

prioritizr 7.0.0.4

• Update publication record.
• Bug fix: time_limit and verbose parameters for add_cbc_solver() now work as expected.

prioritizr 7.0.0.3

• Update add_gurobi_solver() function to report timings following the same methods as the other solvers.

prioritizr 7.0.0.2

• Update add_lpsymphony_solver() function to be more memory efficient (#183).
• Added slam R package to dependencies to enable more memory efficient usage of the lpsymphony R package (#183).

prioritizr 7.0.0.1

• Update unit tests to solve a greater proportion of them using continuous integration services (#181).
• Bug fix: add_cbc_solver() is now preferred over all other open source solvers.
• Bug fix: add_cbc_solver() would sometimes return incorrect solutions to problems with equality constraints.

prioritizr 7.0.0.0

• Remove unused shiny R package integration and dependencies (#141).

prioritizr 6.0.0.2

• New add_cbc_solver() function to generate solutions using the open source CBC solver via the rcbc R package (https://github.com/dirkschumacher/rcbc).
• Update add_rsymphony_solver() and add_lpsymphony_solver() functions to have a default time_limit argument set as the maximum machine integer for consistency.
• Update add_rsymphony_solver(), add_lpsymphony_solver(), and add_gurobi_solver() functions to require logical (TRUE/FALSE) arguments for the first_feasible parameter.
• Update documentation for solvers to provide more detailed information.
• Update publication record.
• Update add_default_solver() function so that it prefers add_lpsymphony_solver() over add_rsymphony_solver(), and add_cbc_solver() over all open source solvers.
• Bug fix: previous versions of the package reported that the gap parameter for the add_rsymphony_solver() and add_lpsymphony_solver() corresponded to the maximum absolute difference from the optimal objective value. This was an error due to misunderstanding the SYMPHONY documentation. Under previous versions of the package, the gap parameter actually corresponded to a relative optimality gap expressed as a percentage (such thatgap = 10 indicates that solutions must be at least 10% from optimality). We have now fixed this error and the documentation described for the gap parameter is correct. We apologize for any inconvenience this may have caused.

prioritizr 6.0.0.1

• Update Solution format section documentation for evaluation functions (i.e. all functions starting with eval_) to mention that the argument to solution should only contain columns that correspond to the solution (#176).
• Add examples using sf data to documentation for importance evaluation functions (#176).
• Add more helpful error messages when invalid solution arguments are supplied to the evaluation functions (#176).
• Add functionality to calculate importance scores using the Ferrier method with sf planning unit data.
• Fix broken link in add_manual_targets() documentation.
• Fix typo in equation for rarity weighted richness documentation.
• New add_min_largest_shortfall() objective function.

prioritizr 6.0.0.0

• New eval_cost() function to calculate the cost of a solution.
• New eval_boundary() function to calculate the exposed boundary length associated with a solution.
• New eval_connectivity() function to calculate the connectivity associated with a solution.
• Deprecated feature_representation() function. It is now superseded by the eval_feature_representation() function.
• New eval_feature_representation() function to assess how well each feature is represented by a solution. This function is similar to the deprecated eval_feature_representation() function, except that it follows conventions for other evaluation functions (e.g. eval_cost).
• New eval_target_representation() function to assess how well each target is met by a solution. This function is similar to the eval_feature_representation(), except that it corresponds to the targets in a conservation planning problem.
• Rename ferrier_score function as eval_ferrier_importance() function for consistency.
• Rename replacement_cost function as eval_replacement_importance() function for consistency.
• Rename rarity_weighted_richness function as eval_rare_richness_importance() function for consistency.
• Fix comparability issues with Matrix package (version 1.3-0) (#172).
• Add NEWS to build process (#173).
• Update publication vignette.

prioritizr 5.0.3.2

• Add Schuster et al. 2020 to documentation to provide information on solver benchmarks (#170).

prioritizr 5.0.3.1

• Fix add_locked_out_constraints() function to enable a single planning unit from being locked out of multiple zones (when data are specified in raster format).

prioritizr 5.0.3

• Release candidate for CRAN.

prioritizr 5.0.2.7

• Update publication record vignette.
• Fix URLs for CRAN checks.

prioritizr 5.0.2.6

• Implement GitHub Actions continuous integration (i.e. update tests and README).
• Update problem() function to reduce memory consumption for sparse matrix arguments (#164).
• Update Tasmania vignette to remove superfluous warnings (#168).
• Update publication record vignette.
• Fix compatibility issues between the testthat R package and the gurobi R package in package tests.

prioritizr 5.0.2.5

• New add_cplex_solver() function to generate solutions using IBM CPLEX (via the cplexAPI package).

prioritizr 5.0.2.4

• Update publication record vignette.
• Update add_gap_portfolio() documentation to note that it only works for problems with binary decisions (#159).
• Fix target calculations in add_loglinear_targets() and loglinear_interpolation() functions. Previously they used a natural logarithm for log-linear interpolation. To follow target setting approaches outlined by Rodrigues et al. (2004), they now use the decadic logarithm (i.e. log10()).

prioritizr 5.0.2.3

• Update publication record vignette.

prioritizr 5.0.2.2

• Update publication record vignette.

prioritizr 5.0.2.1

• Update documentation for ferrier_score() function. It no longer incorrectly states that these scores can be calculated using CLUZ and now states that this functionality is experimental until the formulation can be double checked.

prioritizr 5.0.2

• Release candidate for CRAN.

prioritizr 5.0.1.7

• Fix tests for updated datasets in the prioritizrdata R package.
• Fix small typos in documentation.
• Update citation for Scriven et al. (2020) in the Publication Record vignette.
• Update Salt Spring Island vignette with Ferrier method for calculating irreplaceability scores and adjust for changes in cost data.
• Update examples to run with CRAN checks (i.e. --run-donttest).

prioritizr 5.0.1.6

• Fix feature_representation() bug incorrectly throwing error with vector planning unit data (e.g. sf-class data).

prioritizr 5.0.1.5

• Fix typo causing rij_matrix() to throw an error for large raster data (#151).
• Fix "Non-file package-anchored link(s) in documentation object" warnings in R-devel checks.

prioritizr 5.0.1.4

• New add_linear_penalties() to add penalties that penalize planning units according to a linear metric.
• Update connectivity_matrix() documentation to provide an example of how to generate connectivity matrices that account for functional connectivity.
• Add more information to the documentation for the solve() function.
• Add links to the documentation for the solve() function to the Salt Spring Island and Tasmania vignettes.

prioritizr 5.0.1.3

• Update compile() to throw warning when compiling problems that include feature weights and an objective function that does not use feature weights.

prioritizr 5.0.1.2

• Add Schuster et al. (2020) to publication record.
• Update Hanson et al. (2020) in publication record.
• Update Flower et al. (2020) in publication record.

prioritizr 5.0.1.1

• Update add_gurobi_solver() function to provide more options for controlling the pre-solve step when solving a problem.

prioritizr 5.0.1

• Release candidate for CRAN.

prioritizr 5.0.0.1

• New ferrier_score() function to compute irreplaceability scores following Ferrier et al (2000).

prioritizr 5.0.0.0

• Add full support for sf package (#6).
• Add Flower et al. (2020), Hanson et al. (2020), and Visalli et al. (2020) to publication record (#131).
• New proximity_matrix() function to generate matrices indicating which planning units are within a certain distance of each other (#6).
• Rename connected_matrix() function to adjacency_matrix() function to follow the naming conventions of other spatial association functions (#6).
• New add_extra_portfolio(), add_top_portfolio(), add_gap_portfolio() functions to provide specific options for generating portfolios (#134).
• Enhance intersecting_units and fast_extract functions to use the exactextractr and fasterize packages to speed up raster data extraction (#130).
• Fix compatibility issues with upcoming version of tibble (3.0.0).
• Fix bug in boundary_matrix() function when handling SpatialPolygon planning unit data that contain multiple polygons (e.g. a single planning unit contains to two separate islands) (#132).
• Remove velox package dependency since it may be archived on CRAN (#130).
• Deprecate set_number_of_threads(), get_number_of_threads(), and is.parallel() functions since they are no longer used with new data extraction methods.
• Deprecate add_pool_portfolio() function because the new add_extra_portfolio() and add_top_portfolio() functions provide this functionality (#134).
• Built-in datasets are now saved with latest workspace version (i.e. version 3).

prioritizr 4.1.5.2

• Fix bug in add_rsymphony_solve()r and add_lpsymphony_solver() throwing an an infeasible error message for feasible problems containing continuous or semi-continuous variables.

prioritizr 4.1.5.1

• Add Lin et al. (in press) to publication record.

prioritizr 4.1.5

• Release candidate for CRAN.

prioritizr 4.1.4.4

• Fix warnings in R-devel CRAN checks related to documentation.

prioritizr 4.1.4.3

• Add Williams et al. (in press) to publication record.

prioritizr 4.1.4.2

• Add Rodewald et al. (2019) to publication record.
• Update in press version of Rodewald et al. (2019).
• Make error message for presolve_check() function more informative (#124).

prioritizr 4.1.4.1

• Add Scriven et al. (in press) to publication record.

prioritizr 4.1.4

• Release candidate for CRAN.

prioritizr 4.1.3.3

• Fix rij_matrix() so that amounts are calculated correctly for vector-based planning unit data.
• Fix documentation for fast_extract().

prioritizr 4.1.3.2

• Add Rodewald et al. (in press) to publication record.
• Update reference for Bombi et al. (2019) in publication record.

prioritizr 4.1.3.1

• Fix typo in README.

prioritizr 4.1.3

• Release candidate for CRAN.

prioritizr 4.1.2.8

• Update add_locked_in_constraints() and add_locked_out_constraints() functions so that they no longer throw an unnecessary warning when when they are added to multi-zone problems using raster data with NA values.
• Update documentation for add_locked_in_constraints() and add_locked_out_constraints() functions to provide recommended practices for raster data.
• Update documentation for constraints missing "See also" and "Value" sections.

prioritizr 4.1.2.7

• Fix issue with rarity_weighted_richness() returning incorrect scores when the feature data contains one feature that has zeros amounts in all planning units (e.g. the tas_features object in the prioritizrdata R package; #120).
• Fix issue with add_gurobi_solver() returning solution statuses that are slightly larger than one (e.g. 1+1.0e-10) when solving problems with proportion-type decisions (#118).

prioritizr 4.1.2.6

• Update replacement_cost() function to use parallel processing to speed up calculations (#119).
• New add_manual_bounded_constraints() function to apply lower and upper bounds on planning units statuses in a solution (#118).

prioritizr 4.1.2.5

• Update add_gurobi_solver(), add_lpsymphony_solver(), and add_rsymphony_solver() functions so that they will not return solutions with values less than zero or greater than one when solving problems with proportion-type decisions. This issue is the result of inconsistent precision when performing floating point arithmetic (#117).
• Update add_locked_in_constraints() and add_locked_out_constraints() functions to provide a more helpful error message the locked_in/locked_out argument refers to a column with data that are not logical (i.e. TRUE/FALSE; #118).

prioritizr 4.1.2.4

• Update solve() function to throw a more accurate and helpful error message when no solutions are found (e.g. due to problem infeasibility or solver time limits).
• Standardize error messages so that none of them end in a full stop.

prioritizr 4.1.2.3

• Rename add_max_phylo_objective() function to add_max_phylo_div_objective().
• New add_max_phylo_end_objective() function to maximize the phylogenetic endemism of species adequately represented in a prioritization (#113).
• Add add_max_phylo_end_objective(), replacement_cost(), and rarity_weighted_richness() functions to the Prioritizr vignette.
• Update simulated phylogeny dataset (sim_phylogeny).
• Update examples for add_max_phylo_div_objective() function.
• Prettify equations in the documentation for objective functions.

prioritizr 4.1.2.2

• New irreplaceability manual entry to document functions for calculating irreproducibility scores.
• New replacement_cost() function to calculate irreproducibility scores for each planning unit in a solution using the replacement cost method (#26).
• New rarity_weighted_richness() function to calculate irreproducibility scores for each planning unit in a solution using rarity weighted richness scores (#26).
• Updated Salt Spring Island vignette with a section on calculating and interpreting irreplaceability scores.

prioritizr 4.1.2.1

• Fix typo.
• Fix broken links to Gurobi academic licenses.
• Fix compiler warnings thrown during package installation.
• Skip tests on CRAN's Windows system to reduce CRAN check times.
• Skip plotting data in examples during testing to reduce CRAN check times.
• Throw warning message if both the prioritizr and _oppr_packages are loaded at the same time.

prioritizr 4.1.2

• Release candidate for CRAN (rejected).

prioritizr 4.1.1.2

• Fix example throwing an error during CRAN checks.

prioritizr 4.1.1.1

• Add Bombi et al. (in press) to publication record.

prioritizr 4.1.1.0

• Fix broken link in main vignette.

prioritizr 4.1.1

• Release candidate for CRAN.

prioritizr 4.1.0.1

• New add_min_shortfall_objective() function to find solutions that minimize target shortfalls.
• Add new add_min_shortfall_objective() function to main vignette.
• Fix problem() tests so that they work when no solvers are installed.

prioritizr 4.1.0.0

• The feature_representation() function now requires missing (NA) values for planning unit statuses in a solution for planning units that have missing (NA) cost data.

prioritizr 4.0.4.1

• New presolve_check() function to investigate potential sources of numerical instability before trying to solve a problem. The manual entry for this function discusses common sources of numerical instability and approaches for fixing them.
• The solve() function will now use the presolve_check() function to verify that problems do not have obvious sources of numerical instability before trying to solve them. If a problem is likely to have numerical instability issues then this function will now throw an error (unless the solve(x, force = TRUE)).
• The add_rsymphony_solver() function now uses sparse matrix formats so that attempts can be made to solve large problems with SYMPHONY---though it is unlikely that SYMPHONY will be able to solve such problems in a feasible period of time.
• Fix warnings thrown by the tibble R package when calling tibble::as.tibble() instead of tibble::as_tibble().
• Add example for calculating feature representation a solution in tabular format output by solve() (#110).
• Fix several typos in documentation.
• Thrown warnings are now immediately visible.
• Update references in the publication record vignette.
• Specify English (US) in the DESCRIPTION file.

prioritizr 4.0.4

• Release candidate for CRAN.

prioritizr 4.0.3.1

• Retain debugging symbols to conform with CRAN policies.

prioritizr 4.0.3

• Release candidate for CRAN.

prioritizr 4.0.2.16

• Add new citations.

prioritizr 4.0.2.15

• Fix typos in documentation for add_boundary_penalties() and add_connectivity_penalties() function (#106).

prioritizr 4.0.2.14

• Fix bug where use of add_rsymphony_solver() and add_lpsymphony_solver() sometimes returned infeasible solutions when subjected to a time limit (#105).

prioritizr 4.0.2.13

• Fix assorted bugs in the render, setter, and getter parameter functions for ConservationProblem-class objects. These methods were implemented to be used in future interactive applications and are not currently used in the package. As a consequence, these bugs do not affect the correctness of any results.

prioritizr 4.0.2.12

• Fix bad error message error being thrown when input rasters are not comparable (i.e. same coordinate reference system, extent, resolutions, and dimensionality) (#104).
• Add Domisch et al. (2019) to publication record vignette.

prioritizr 4.0.2.11

• Fix issue solve() printing annoying text about tbl_df (#75).

prioritizr 4.0.2.10

• Tweak add_max_features_objective() example code.

prioritizr 4.0.2.9

• Update publication record vignette.

prioritizr 4.0.2.8

• Fix bug where the add_neighbor_constraints() and add_contiguity_constraints() functions used more memory than they actually needed (#102). This is because the argument validation code converted sparse matrix objects (i.e. dgCMatrix) to base objects (i.e. matrix) class temporarily. This bug only meant inefficient utilization of computer resources---it did not affect the correctness of any results.

prioritizr 4.0.2.7

• New add_mandatory_allocation_constraints() function. This function can be used to ensure that every planning unit is allocated to a management zone in the solution. It is useful when developing land-use plans where every single parcel of land must be assigned to a specific land-use zone.
• Add the add_mandatory_allocation_constraints() to the Management Zones and Prioritizr vignettes.
• Fix bug in the $find(x) method for Collection prototypes that caused it to throw an error incorrectly. This method was not used in earlier versions of this package.

prioritizr 4.0.2.6

• Fix bug the feature_representation() function that caused the "amount_held" column to have NA values instead of the correct values. This bug only affected problems with multiple zones.

prioritizr 4.0.2.5

• Fix bug in argument validation code for the category_layer() function that it this function to incorrectly throw an error claiming that the input argument to x was invalid when it was in fact valid. This bug is encountered when different layers the argument to x have non-NA values in different cells.

prioritizr 4.0.2.4

• Update instructions for activating Gurobi licenses on remote machines (#98).

prioritizr 4.0.2.3

• The add_contiguity_constraints() function now uses sparse matrix formats internally for single-zone problems. This means that the constraints can be applied to single-zoned problem with many more planning units.

prioritizr 4.0.2.2

• The add_connectivity_penalties() function now uses sparse matrix formats internally for single-zone problems. This means that connectivity penalties can be applied to single-zoned problem with many more planning units.

prioritizr 4.0.2.1

• Update warning text when compiling problems that contain (i) objective functions that do not use targets and (ii) targets (#93).
• Update documentation for the add_max_utility_objective() and add_max_cover_objective() functions to make it clearer that they do not use targets (#94).

prioritizr 4.0.2

• Release candidate for CRAN.

prioritizr 4.0.1.6

• Fix bug in add_locked_in_constraints() and add_locked_out_constraints() that incorrectly threw an error when using logical locked data (i.e. TRUE/FALSE) because it incorrectly thought that valid inputs were invalid.
• Fix bug in add_locked_in_constraints(), add_locked_out_constraints(), and add_manual_locked_constraints() where solving the same problem object twice resulted in incorrect planning units being locked in or out of the solution (#92).
• Added unit tests for objectives, constraints, decisions, targets, and penalties to ensure that solving problems twice does not result in different solutions.

prioritizr 4.0.1.5

• Fix bug in feature_abundances() that caused the solve function to throw an error when attempting to solve problems with a single feature.
• Fix bug in add_cuts_portfolio() that caused the portfolio to return solutions that were not within the specified optimality gap when using the Gurobi solver.
• Add the ability to specify the search pool method and number of solutions to the add_pool_portfolio() function.

prioritizr 4.0.1.4

• The feature_representation() function now allows numeric solutions with attributes (e.g. when output by the solve() function) when calculating representation statistics for problems with numeric planning unit data (#91).
• The add_manual_targets() function threw a warning when some features had targets equal to zero. This resulted in an excessive amount of warnings. Now, warnings are thrown for targets that are less then zero.
• The problem() function sometimes incorrectly threw a warning that feature data had negative values when the data actually did not contain negative values. This has now been addressed.

prioritizr 4.0.1.3

• The problem function now allows negative values in the cost and feature data (and throws a warning if such data are detected).
• The add_absolute_targets() and add_manual_targets() functions now allow negative targets (but throw a warning if such targets are specified).
• The compile function throws an error if a problem is compiled using the expanded formulation with negative feature data.
• The add_absolute_targets() function now throws an warning---instead of an error---if the specified targets are greater than the feature abundances in planning units to accommodate negative values in feature data.

prioritizr 4.0.1.2

• Fix add_max_cover_objective() in prioritizr vignette (#90).

prioritizr 4.0.1.1

• The add_relative_targets() documentation now makes it clear that locked out planning units are included in the calculations for setting targets (#89).
• The add_loglinear_targets() function now includes a feature_abundances() parameter for specifying the total amount of each feature to use when calculating the targets (#89).

prioritizr 4.0.1

• Release candidate for CRAN.

prioritizr 4.0.0.12

• New feature_abundances() function to calculate the total amount of each feature in the planning units (#86).

prioritizr 4.0.0.11

• Fix some equations in the documentation (#83).

prioritizr 4.0.0.10

• Add version requirements for assertthat and tibble packages (#82).

prioritizr 4.0.0.9

• Fix minor typos in the Gurobi installation guide and update the Management zones tutorial.

prioritizr 4.0.0.8

• Add instructions for setting up the Gurobi Academic license on a computer that it is not connected to a university computer network using a computer that is on an academic network (#81). For example, these instructions could be used to set up Gurobi on a cloud-based system using a laptop computer that is connected a university's wireless network.

prioritizr 4.0.0.7

• The add_cuts_portfolio() function uses the Gurobi solution pool to generate unique solutions within a specified gap of optimality when tasked with solving problems with Gurobi (version 8.0.0+; #80).

prioritizr 4.0.0.6

• New add_pool_portfolio() function to generate a portfolio of solutions using the Gurobi solution pool (#77).

prioritizr 4.0.0.5

• The boundary_matrix() function now has the experimental functionality to use GEOS STR trees to speed up processing (#74).
• Solutions obtained from Gurobi that contain binary-type decisions are explicitly rounded to the nearest integer. This is because Gurobi can output solutions to binary problems that contain values which not exactly zero or one (e.g. 0.9999997 using default settings; #78).

prioritizr 4.0.0.4

• New feature_representation() function to how well features are represented in solutions (#73).

prioritizr 4.0.0.3

• The prioritizrdata package has been listed under Suggests.
• The vignettes in the prioritizrdata package have been moved to this package to make them easier to find.

prioritizr 4.0.0.2

• Fix issue with the solve() function printing superfluous text (#75).

prioritizr 4.0.0.1

• Minor improvements to the documentation for the problem() function.

prioritizr 4.0.0.0

• Added functionality to build and solve problems with multiple management zones (#14).
• New built-in datasets sim_pu_zones_stack, sim_pu_zones_polygons, and sim_features_zones for exploring conservation problems with multiple management zones.
• New zones function and Zones class to organize data with multiple zones.
• The problem() function now accepts Zone objects as arguments for feature to create problems with multiple zones.
• The add_relative_targets() and add_absolute_targets() functions for adding targets to problems can be used to specify targets for each feature in each zone.
• New add_manual_targets() function for creating targets that pertain to multiple management zones.
• The solve() function now returns a list of solutions when generating a portfolio of solutions.
• The add_locked_in_constraints() and add_locked_out_constraints() functions for specifying which planning units are locked in or out now accept matrix arguments for specifying which zones are locked in or out.
• New add_manual_locked_constraints() function to manually specify which planning units should or shouldn't be allocated to specific zones in solutions.
• All functions for adding constraints and penalties now have parameters that specify how they should treat planning units allocate to different zones (using the zones parameter) and specify how they they should be applied (using the data parameter. All of these functions have default arguments that mean that problems with a single zone should have the same optimal solution as problems created in the earlier version of the package.
• The add_feature_weights() function can be used to weight different the representation of each feature in each zone.
• The binary_stack(), category_layer(), and category_vector() functions have been provided to help work with data for multiple management zones.
• New Management zones vignette on building and solving problems with multiple management zones.
• Added mention of zones functionality to package DESCRIPTION, summary (in ?prioritizr), and README.
• The Quick Start Guide and Prioritizr Basics vignettes have been consolidated into the prioritizr vignette.
• The marxan_problem() has been updated with more comprehensive documentation and to provide more helpful error messages. For clarity, it will now only work with tabular data in the standard Marxan format.

prioritizr 3.0.3.6

• Fix typo in README and update documentation for add_boundary_penalties() (#62).

prioritizr 3.0.3.5

• Fix bug where add_locked_in_constraints() and add_locked_out_constraints() throw an exception when used with semi-continuous-type decisions (#59).
• Exception in compile() thrown when the same planning unit is locked in and locked out now prints the planning unit indices in a readable format.

prioritizr 3.0.3.4

• Fix bug where add_locked_in_constraints() and add_locked_out_constraints() are ignored when using proportion-type decisions (#58).

prioritizr 3.0.3.3

• Fix bug in predefined_optimization_problem() which incorrectly recognized some inputs as invalid when they were in fact valid.
• Addressed NOTE in R CMD check related to proto in Depends.

prioritizr 3.0.3.2

• Moved proto package from Imports to Depends in DESCRIPTION

prioritizr 3.0.3.1

• Depends on R version 3.4.0 (avoids 'patchlevel 0' NOTE/WARNING in checks)

prioritizr 3.0.3

• Release candidate for CRAN.

prioritizr 3.0.2.3

• Unit tests that fail when using lpsymphony due to a bug in lpsymphony are now skipped (partially addressing #40).

prioritizr 3.0.2.2

• add_lpsymphony_solver() now throws warnings to alert users to potentially incorrect solutions (partially addressing #40).

prioritizr 3.0.2.1

• Vignette sizes have been reduced.

prioritizr 3.0.2

• Release candidate for CRAN. Release postponed due issues on Travis CI.

prioritizr 3.0.1.1

• Unit tests for add_*_objectives now pass when executed with slow solvers (partially addressing #40).
• compile() now works when no solvers are installed (#41).
• Gap arguments in add_*_solvers are now unbounded and can accept values larger than 1 (#44).

prioritizr 3.0.1

• Release candidate for CRAN.

prioritizr 3.0.0.0

• The add_max_cover_objective() function has been renamed to the add_max_utility_objective(), because the formulation does not follow the historical formulation of the maximum coverage reserve selection problem (#38).
• The add_max_cover_objective() function now follows the historical maximum coverage objective. This fundamentally changes add_max_cover_objective() function and breaks compatibility with previous versions (#38).
• Update add_lpsymphony_solver() examples and tests to skip on Linux operating systems.
• Add tests to unit tests that were being skipped in new version of testthat package.

prioritizr 2.0.4.1

• Fix bug with add_lpsymphony_solver() causing error when attempting to solve problems.

prioritizr 2.0.4

• Release candidate for CRAN. Release postponed due to bug report.

prioritizr 2.0.3.1

• Fix bug when solving problems with numeric vector data that caused an error.
• Fix bug in compiling problems with numeric vector input with rij data containing NA values.
• Added unit tests for solving problems with various input formats.
• Updated package sizes reported in cran-comments.

prioritizr 2.0.3

• Initial release candidate for CRAN. Release postponed due to bug report.

prioritizr 2.0.2.9

• Added vignette to record publications that use prioritizr (#35).

prioritizr 2.0.2.8

• Unit tests now compatible with development version of testthat (#34).

prioritizr 2.0.2.7

• Fix bug in apply_boundary_penalties() and add_connectivity_penalties() causing the function to throw an error when the number of boundaries/edges is less than the number of planning units.

prioritizr 2.0.2.6

• Makevars now compatible with Mac OSX Sierra (#33).

prioritizr 2.0.2.5

• Fix bug in boundary_matrix() calculations (#30).

prioritizr 2.0.2.4

• Minor tweaks to vignettes.

prioritizr 2.0.2.3

• Add logo to README files and package website (#31).

prioritizr 2.0.2.2

• Broad-scale improvements to documentation.
• Fix documentation for add_max_phylo_objective() (#24).
• Update Gurobi Installation vignette.
• Remove prioritizrdata from package Suggests.
• Add shiny and xtable to Suggests for rendering parameters.
• Added code for ScalarParameter and ArrayParameter prototypes to check t that functions for generating widgets have their dependencies installed.
• URLs for lpsymphony on Bioconductor now use the package's DOI.
• Add more comprehensive tests to portfolios.
• Fix bug when numeric planning unit data and portfolios that caused the solve() to throw an error.
• Remove R-devel from AppVeyor testing because it fails for unknown reasons.

prioritizr 2.0.2.1

• Removed shiny functions for now to prep for CRAN release.
• Rebuilt website and documentation.

prioritizr 2.0.2.0

• Included vignette on Gurobi solver installation and testing.

prioritizr 2.0.1.0

• Fixed bug where Spatial*DataFrame input to marxan_problem() would always use the first column in the attribute table for the cost data. This bug is serious so analysis that used Spatial*DataFrame inputs in marxan_problem() should be rerun.
• Added functionality to use feature abundance/occurrence data stored as columns in the planning unit data when constructing problem() objects.

prioritizr 2.0.0.2

• Skip add_cuts_portfolio() on Travis.

prioritizr 2.0.0.1

• Skip add_cuts_portfolio() and add_shuffle_portfolio() tests on CRAN.

prioritizr 2.0.0.0

• This version breaks compatibility with previous releases because solutions in data.frame and Spatial*DataFrame objects are now stored in columns named "solution_*" (e.g. "solution_1") to store multiple solutions.
• Added support for multiple solutions (#23).
• Solutions now contain additional information in stored in the object's attributes (#24). See README.Rmd for examples on accessing this information.
• Tidy examples in add_gurobi_solver.R, add_lpsymphony_solver.R, add_rsymphony_solver.R, and solvers.R.
• Add logical verbose argument to all solvers. This replaces the verbosity argument in add_lpsymphony_solver() and add_rsymphony_solver().
• The verbosity of information presented when solving problems using add_lpsymphony_solver() and add_rsymphony_solver() is reduced.
• Assorted spelling mistakes have been fixed.

prioritizr 1.0.2.3

• ConservationProblem$print() now only prints the first three species names and a count of the total number of features. This update means that ConservationProblem objects with lots of features can now safely be printed without polluting the R console.
• Attempt to make equations in help files prettier.
• Fix bug where lpsymphony and Rsymphony solvers would return solutions containing NA values if they did not find a feasible solution within the argument to time_limit.

prioritizr 1.0.2.2

• Fix #19.

prioritizr 1.0.2.1

• Fix #20.

prioritizr 1.0.2.0

• Passes CRAN checks on Winbuilder.
• Added roxygen2 to Suggests for Travis CI.

prioritizr 1.0.1.6

• Simplify vignette workflow. Vignettes can now be compiled by using devtools::build_vignettes(). Earlier versions needed the vignettes to be compiled using the Makefile to copy files around to avoid tangled R code causing failures during R CMD CHECK. Although no longer needed, the vignettes can still be compiled using the shell command make vigns if desired.
• The README.Rmd now lives in the top-level directory following standard practices. It should now be complied using rmarkdown::render("README.Rmd") or using the shell command make readme. Note that the figures for README.md can be found in the directory man/figures.
• The example for prshiny will now only be run if executed during an interactive R session. Prior to this R CMD CHECK would hang.
• UTF-8 math characters in vignettes have been replaced with with MathJax compatible latex expressions.
• R code in the vignettes has been linted to follow the package's style guide.
• Fix example in vignette quick_start.Rmd showing how to run marxan_problem() using input data.frame() objects.
• Fix bug in vignette quick_start.Rmd counting number of selected planning units
• Make the data.table package automatically installed when prioritizr is installed (#18).
• Move shiny, shinydashboard, and leaflet packages to Imports to avoid polluting users environment.
• Update preliminary versions of the shiny apps to call functions from other packages explicitly.
• README.Rmd tweaks to make it look prettier on website
• Lint objective function definition files
• Remove "\text" latex sequences from objective function definition files because CRAN doesn't support amsmath extensions in equations.
• Update examples in objective function files to only show relevant objectives
• Added rmarkdown package to Suggests following recommended practices.

prioritizr 1.0.1.5

• Enable 64 bit Armadillo flag. This increases the maximum size of problems that can be solved.
• Disable bound-checks in Armadillo matrix operations. This should reduce processing time when running the compile() function.

prioritizr 1.0.1.4

• Fix bug in problem.data.frame that meant that it did not check for missing values in rij$pu.

prioritizr 1.0.1.3

• Fix bugs add_absolute_targets() and add_relative_targets` related to their standardGeneric being incorrectly defined
• Reduce installation size using Dirk Eddelbuettel's awesome advice: http://dirk.eddelbuettel.com/blog/2017/08/14#009_compact_shared_libraries
• Fix bug in add_corridor_targets() when argument connectivities is a list. The elements in the list are assumed to be dsCMatrix objects (aka symmetric sparse matrices in a compressed format) and are coerced to dgCMatrix objects to reduce computational burden. There was a typo, however, and so the objects were coerced to dgCmatrix and not dgCMatrix. This evidently was ok in earlier versions of the RcppArmadillo and/or Matrix packages but not in the most recent versions.

prioritizr 1.0.1.2

• Fix #21.

prioritizr 1.0.1.1

• Add roxygen2 to package SUGGESTS for building vignettes.

prioritizr 1.0.1.0

• Fix issue where parallel::detectCores() returns NA on some systems preventing users from using the Gurobi solver--even when one thread is specified.

prioritizr 1.0.0.5

• Fix building issue due to incorrect file order in DESCRIPTION.

prioritizr 1.0.0.4

• Compatibility with R 3.4.0.
• Replace structure(NULL, ...) with structure(list(), ...).
• Register compiled library files.
• Remove duplicate definition of new_waiver().
• Tests check if prioritizrdata package not installed and skip if it isn't.

prioritizr 1.0.0.3

• Fix missing links in documentation
• Fix typos in roxygen2 parameters
• Move add_default_decisions() and add_default_solver() to own help file
• Make add_default_objectives() and add_default_targets() private functions

prioritizr 1.0.0.2

• Fix #13

prioritizr 1.0.0.1

• Fix #8.
• Fix bug in add_corridor_constraints() that fails to actually add the constraints with argument to connectivity is a list.
• Fix bug in make install command so that it now actually installs the package.
• Fix link to Joe's website in the package's website.

prioritizr 1.0.0.0

• R interface fully functional.

prioritizr 0.1.2.9

• Package re-implementation.

prioritizr 0.1.2

• Prepare for CRAN submission.
• Add continuous integration.
• Fixed various bugs.
• Introduce maximum target coverage model.
• Add full vignette in addition to quickstart guide.

prioritizr 0.1.1

• Initial package version.

prioritizr/prioritizr documentation built on May 11, 2023, 2:30 p.m.