- Update
presolve_check()to throw warning if a problem has a single feature (#309). Thanks to Sandra Neubert (@sandra-neubert) for code contribution. - Update
print()andsummary()forproblem()objects so that all text is printed at once (rather than sequentially). - Fix
write_problem()so that it works as expected (#312). - Update
problem(),add_linear_constraints(),add_linear_penalties(),add_locked_in_constraints(),add_locked_out_constraints(),adjacency_matrix(),binary_stack(),category_layer(),connectivity_matrix(),fast_extract(),intersecting_units(),proximity_matrix(),rij_matrix(),simulate_data(),simulate_species(),simulate_cost(), andzones()and other functions so that they will throw an error if a categoricalterra::rast()object is provided as an argument (#313). This is because categorical rasters are not supported. Thanks to Martin Jung (@Martin-Jung) for bug report. - Fix NAMESPACE issues related to registration of internal S3 methods.
- Fix bug with
problem()not throwing multiple warnings with unusual data (e.g., given cost and feature data with negative values, previously only a single warning about negative costs would be thrown). Thanks to Sandra Neubert (@sandra-neubert) for bug report.
- Update publication record.
- Update package-level manual entry.
- Update URLs.
- Update
problem()to be more memory efficient when using a sparse matrix (dgCMatrix) argument for therij_matrixparameter. - Update error messages for checking that objects have the same coordinate reference system and overlapping spatial extents to format argument names correctly.
- Update error messages for nested expressions to refer to expressions using
Caused by errorinstead ofCaused by NULL.
- Update publication record.
- Fix
add_locked_in_constraints()andadd_locked_in_constraints()error messages when supplyinglocked_inandlocked_outobjects that do not spatially intersect with the planning units. - Update error message for checking if objects spatially overlap to improve clarity.
- Update publication record.
- Update URLs.
- Fix aliasing for package manual entry (#301).
- Update publication record.
- CRAN release.
- We have developed a better approach for rescaling boundary data to
avoid numerical issues during optimization (#297). Earlier versions of the
package recommended the use of the
scales::rescale()to rescale such data. However, we now realize that this approach can produce inconsistencies for boundary length data (e.g., the total perimeter of a planning unit might not necessarily equal the sum of the edge lengths). In some cases, these inconsistencies can cause solutions generated with high boundary penalties (i.e., usingadd_boundary_penalties()with a highpenaltyvalue) to contain a large reserve (i.e., a spatial cluster of selected of planning units) with a single unselected planning unit in the middle of the reserve. In the the worst case, these inconsistencies produce a situation where increasing boundary penalties (i.e., generating multiple solutions withadd_boundary_penalties()and increasingpenaltyvalues) does not alter the spatial configuration of solutions. Although use ofscales::rescale()did not produce such behavior prior to version 8.0.0, changes to the output format forboundary_matrix()in subsequent versions now mean thatscales::rescale()can cause these issues. We now recommend using the newrescale_matrix()function to rescale boundary length data to avoid numerical issues, whilst also avoid such inconsistencies.
- New
rescale_matrix()function to help with rescaling boundary length (e.g., generated usingboundary_matrix()) and connectivity (e.g., generated usingconnectivity_matrix()) data so avoid numerical issues during optimization (#297). Thanks to Jason Flower (@jflowernet) and Joan Giménez Verdugo for bug reports.
- Update the
print()andsummary()methods forproblem()objects so that they will now better describe situations when the planning cost data all contain a constant value (e.g., all costs equal to 1).
- Update examples and vignettes to use the
rescale_matrix()function instead of thescales::rescale()function for rescaling boundary length and connectivity data (#297). - Update publication record.
- Update
add_neighbors_constraints()so that it has an additionalclampargument so the minimum number of neighbors permitted for each planning unit in the solution is clamped to the number of neighbors that each planning unit has. For example, if a planning unit has 2 neighbors,k = 3, andclamp = FALSE, then the planning unit could not ever be selected in the solution. However, ifclamp = TRUE, then the planning unit could potentially be selected in the solution if both of its 2 neighbors were also selected.
- Fix issue with
problem()that preventsfeaturesbeing supplied as adata.framethat contains feature names stored as afactor(#295). Thanks to Carl Boetigger (@cboettig) for bug report.
- Fix URLs.
- Update
problem()so that it will throw a meaningful error message if the user accidentally specifies the geometry column forsfplanning unit data as a feature.
- Fix compatibility with updates to terra package.
- Fix
rij_matrix()so that it works when none of the raster layers being processed fit into memory (#290). Thanks to Edwards Marc (@edwardsmarc) for bug report. - Fix spatial extent of built-in raster datasets so that extents are between
0 and 1 (i.e.,
get_sim_pu_raster(),get_sim_locked_in_raster(),get_sim_locked_out_raster(),get_sim_zones_pu_raster(),get_sim_features(),get_sim_zones_features()). - Update
add_manual_locked_constraints()andadd_manual_bounded_constraints()so that the indices in the specified in the argumentdata$pushould consistently refer to the total units. In other words, the indices indata$pushould refer to the row numbers (for planning units insfordata.frameformat) or cell numbers (for planning units inRasterorSpatRasterformat) of the planning units that should be locked. - Fix warnings thrown due to package version comparisons.
- Update publication record.
- Export
solve.ConservationProblem()so that it can be called directly (#283). Thanks to Tin Buenafe (@SnBuenafe) for bug report.
- Update publication record.
- Fix compatibility with highs package (version 0.1-10) (#281).
- Update publication record.
- Update
problem()so that an error will be thrown if argument tofeaturescontains only missing (NA) values (e.g., an sf object is supplied that hasNAvalues in all rows for a feature's column).
- Update publication record.
- 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()andsp::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.
- 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 anyproblem()objects that were produced using earlier versions of the package are no longer compatible. Thanks to Jason Flower (@jflowernet) for bug report on memory issues. - 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 returnsf::st_sf(),terra::rast(),ape::read.tree()andzones()objects. Note that these functions are provided becausedata(...)cannot be used withterra::rast()objects. See?datafor 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 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, Seeparallel::splitIndices(). - The
new_optimization_problem()andpredefined_optimization_problem()functions have been superseded by the newoptimization_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(). - Updates to improve the error messages and error message handling.
Hopefully, users should no longer see
"bad error message"!
- The
print()function forproblem(),optimization_problem(), andzones()objects has been updated to provide more information. - New
summary()function to provide extensive detail onproblem()objects.
- Fix bug for
add_feature_weights()when applied to problems with anadd_max_phylo_div_objective()oradd_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. - The
solve()function will now outputtibble::tibble()objects (instead ofdata.frame()objects), when the planning unit data aretibble::tibble()objects. - The
boundary_matrix()function now usesterra::sharedPaths()for calculations, providing greater performance (#257). Thanks to Jason Flower (@jflowernet) for bug report. - 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()andeval_replacement_importance()functions.
- Assorted tweaks to improve writing in the vignettes and documentation. Many thanks to Marc Edwards (@edwardsmarc) for code contribution!
- Update publication record.
- Assorted bug fixes.
- 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.
- Update README badges.
- Update publication record.
- Update publication record.
- Update publication record.
- Specify minimum version for Matrix package dependency (#255). Thanks to Bruno Carturan (@BrunoCartu) for bug report.
- 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 theadd_lpsymphony_solver()is used instead ofadd_rsymphony_solver().
- Update
problem()andeval_feature_representation_summary()to avoid needlessly converting sparse matrices to regular matrices (#252).
- Fix URLs.
- Fix mistake in
NEWS.md. - Update publication record.
- 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.
- Release candidate for CRAN (rejected due to package check timings).
- Update
boundary_matrix()to use STR query trees by default. - Update
simulate_data(),simulate_cost()andsimulate_species()functions to improve performance using the fields package.
- 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 therij_matrix(x)has a zero amount for the last feature in the last planning unit (#247). Thanks to Jason Everett (@jaseeverett) for bug report. - 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 URLs.
- Update
simulate_cost()andsimulate_species()so that they no longer depend on the RandomFields package. Note that these functions will now produce different outputs from previous versions (even when controlling for the random number generator state).
- Update publication record.
- Update publication record.
- Update publication record.
- Fix URLs.
- 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.
- Fix bug in processing planning unit data when a problem is constructed
using arguments to (i)
xthat arenumericormatrixformat, (ii)xthat contain missing (NA) values, and (iii)rij_matrixthat are indgCMatrixformat. This bug only occurred when all three of these specific conditions were met. When it occurred, the bug caused planning units withNAcost values to receive very high cost values (e.g., 1e+300). This bug meant that when attempting to solve the problem, the presolve checks (perpresolve_check()) would throw an error complaining about very high cost values (#236). Thanks to @lmathon for bug report.
- Update publication record.
- 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 withadd_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 (#223). Thanks to Nina Faure Beaulieu (@ninzyfb) for bug report.
- Fix
add_locked_in_constraints()andadd_locked_out_constraints()to ensure that a meaningful error message is provided when no planing units are locked (#234). Thanks to Alec Nelson (@AlecNelson) for bug report. - 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
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.
- Update publication record.
- Update publication record.
- Update publication vignette.
- Fix URLs.
- Improve documentation for the
zonesparameter of theadd_connectivity_penalties()function.
- 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.
- 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 publication record.
- Update reference index for package website.
- Fix minor typos in vignettes.
- 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.
- Update publication record.
- 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.
- Update tests to reduce run time and pass given slightly different results with new Gurobi version (9.5.0).
- Update built-in
sim_pu_sfandsim_pu_zones_sfdata given class updates to the sf package (compatible with version 1.0.3+).
- Update example for
write_problem()function.
- Update publication record.
- Update publication record.
- Fix URL in vignette.
- Release candidate for CRAN.
- Brandon Edwards added to package author list.
- Update
eval_ferrier_importance()function with verified code.
- Update
presolve_check()function to throw warning when really high values specified inadd_neighbor_constraints().
- Update documentation with information about Ferrier importance scores.
- Update Gurobi Installation guide vignette.
- Update benchmark vignette.
Update add_cbc_solver() function so that it can use a starting solution to reduce run time (via the start_solution parameter).
- Remove xtable package from Suggests because it is no longer used.
- Fix examples that fail package checks.
- Update publication vignette.
- New
add_linear_constraint()function to add arbitrary constraints.
- Update
add_min_shortfall_objective()andadd_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.
- Update publication vignette.
- Update documentation and examples for
problem()function. - Update publication vignette.
- New solver benchmark vignette.
- Update
add_gurobi_solver()function so that it doesn't print excess debugging information (accidentally introduced in previous version 7.0.1.1).
- Update
add_gurobi_solver()function to support thenode_file_startparameter for the Gurobi software. This functionality is useful solving large problems on systems with limited memory (#192). Thanks to @negira and Alec Nelson (@AlecNelson) for bug reports and suggestions.
- Release candidate for CRAN.
- Update DESCRIPTION with more information on the package usage.
- Update DESCRIPTION with details on rcbc package installation.
- 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.
- Fix typo in
rij_matrix()function documentation (#189). - Update publication vignette.
- 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. - Fix
solve()so it assigns layer names based on zone names for solutions in raster format.
- Update methods for calculating solver runtime.
- Fix
add_cbc_solver()so thattime_limitandverboseparameters work as expected.
- Update publication record.
- Update
add_gurobi_solver()function to report timings following the same methods as the other solvers.
- Update
add_lpsymphony_solver()function to be more memory efficient (#183). - Added slam package to dependencies to enable more memory efficient usage of the lpsymphony package (#183).
- Update unit tests to solve a greater proportion of them using continuous integration services (#181).
- Update
add_default_solver()so thatadd_cbc_solver()is now preferred over all other open source solvers. - Fix bug in
add_cbc_solver()that resulted in incorrect solutions to problems with equality constraints.
- Remove unused shiny package integration and dependencies (#141).
- New
add_cbc_solver()function to generate solutions using the open source CBC solver via the rcbc package (https://github.com/dirkschumacher/rcbc).
- Update
add_rsymphony_solver()andadd_lpsymphony_solver()functions to have a defaulttime_limitargument set as the maximum machine integer for consistency. - Update
add_rsymphony_solver(),add_lpsymphony_solver(), andadd_gurobi_solver()functions to requirelogical(TRUE/FALSE) arguments for thefirst_feasibleparameter. - Update
add_default_solver()function so that it prefersadd_lpsymphony_solver()overadd_rsymphony_solver(), andadd_cbc_solver()over all open source solvers.
- Previous versions of the package reported that the
gapparameter for theadd_rsymphony_solver()andadd_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, thegapparameter actually corresponded to a relative optimality gap expressed as a percentage (such thatgap = 10indicates that solutions must be at least 10% from optimality). We have now fixed this error and the documentation described for thegapparameter is correct. We apologize for any inconvenience this may have caused. - Update documentation for solvers to provide more detailed information.
- Update publication record.
- New
add_min_largest_shortfall()objective function.
- Add more helpful error messages when invalid
solutionarguments are supplied to the evaluation functions (#176). Thanks to Phil Dyer (@PhDyellow) for bug report. - Add functionality to calculate importance scores using the Ferrier method
with
sfplanning unit data.
- Update Solution format section documentation for evaluation functions
(i.e. all functions starting with
eval_) to mention that the argument tosolutionshould only contain columns that correspond to the solution (#176). Thanks to Phil Dyer (@PhDyellow) for bug report. - Add examples using
sfdata to documentation for importance evaluation functions (#176). - Fix broken link in
add_manual_targets()documentation. - Fix typo in equation for rarity weighted richness documentation.
- 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. - New
eval_feature_representation()function to assess how well each feature is represented by a solution. This function is similar to the deprecatedeval_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 theeval_feature_representation(), except that it corresponds to the targets in a conservation planning problem.
- Rename
ferrier_scorefunction aseval_ferrier_importance()function for consistency. - Rename
replacement_costfunction aseval_replacement_importance()function for consistency. - Rename
rarity_weighted_richnessfunction aseval_rare_richness_importance()function for consistency. - Deprecated
feature_representation()function. It is now superseded by theeval_feature_representation()function.
- Fix comparability issues with Matrix package (version 1.3-0) (#172).
- Add NEWS to build process (#173).
- Update publication vignette.
- Add Schuster et al. (2020) to documentation to provide information on solver benchmarks (#170). Thanks to Stefan Blumentrath (@ninsbl) for suggestion.
- 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).
- Release candidate for CRAN.
- Update publication record vignette.
- Fix URLs for CRAN checks.
- Implement GitHub Actions continuous integration (i.e. update tests and README).
- Update
problem()function to reduce memory consumption for sparse matrix arguments (#164). - Fix compatibility issues between the testthat package and the gurobi package in package tests.
- Update Tasmania vignette to remove superfluous warnings (#168). Thanks to Jason Flower (@jflowernet) for bug report.
- Update publication record vignette.
- New
add_cplex_solver()function to generate solutions using IBM CPLEX (via the cplexAPI package).
- Fix target calculations in
add_loglinear_targets()andloglinear_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()).
- Update publication record vignette.
- Update
add_gap_portfolio()documentation to note that it only works for problems with binary decisions (#159). Thanks to @kkemink for report.
- Update publication record vignette.
- Update publication record vignette.
- 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.
- Release candidate for CRAN.
- Fix tests for updated datasets in the prioritizrdata 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).
- Fix
feature_representation()bug incorrectly throwing error with vector planning unit data (e.g.sf-class data).
- 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.
- 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.
- Update
compile()to throw warning when compiling problems that include feature weights and an objective function that does not use feature weights.
- Add Schuster et al. (2020) to publication record.
- Update Hanson et al. (2020) in publication record.
- Update Flower et al. (2020) in publication record.
- Update
add_gurobi_solver()function to provide more options for controlling the pre-solve step when solving a problem.
- Release candidate for CRAN.
- New
ferrier_score()function to compute irreplaceability scores following Ferrier et al (2000).
- Add full support for sf package (#6).
- New
proximity_matrix()function to generate matrices indicating which planning units are within a certain distance of each other (#6). - New
add_extra_portfolio(),add_top_portfolio(),add_gap_portfolio()functions to provide specific options for generating portfolios (#134).
- Rename
connected_matrix()function toadjacency_matrix()function to follow the naming conventions of other spatial association functions (#6). - Deprecate
set_number_of_threads(),get_number_of_threads(), andis.parallel()functions since they are no longer used with new data extraction methods. - Deprecate
add_pool_portfolio()function because the newadd_extra_portfolio()andadd_top_portfolio()functions provide this functionality (#134).
- Enhance
intersecting_unitsandfast_extractfunctions 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 handlingSpatialPolygonplanning 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). Thanks to Jeffrey Evans (@jeffreyevans) for report.
- Built-in datasets are now saved with latest workspace version (i.e. version 3).
- Add Flower et al. (2020), Hanson et al. (2020), and Visalli et al. (2020) to publication record (#131). Thanks to Jason Flower (@jflowernet) for report.
- Fix bug in
add_rsymphony_solver()andadd_lpsymphony_solver()throwing an an infeasible error message for feasible problems containing continuous or semi-continuous variables.
- Add Lin et al. (in press) to publication record.
- Release candidate for CRAN.
- Fix warnings in R-devel CRAN checks related to documentation.
- Add Williams et al. (in press) to publication record.
- Make error message for
presolve_check()function more informative (#124). Thanks to Amanda Liczner (@aliczner) for bug report.
- Add Rodewald et al. (2019) to publication record.
- Update in press version of Rodewald et al. (2019).
- Add Scriven et al. (in press) to publication record.
- Release candidate for CRAN.
- Fix
rij_matrix()so that amounts are calculated correctly for vector-based planning unit data.
- Fix documentation for
fast_extract().
- Add Rodewald et al. (in press) to publication record.
- Update reference for Bombi et al. (2019) in publication record.
- Fix typo in README.
- Release candidate for CRAN.
- Update
add_locked_in_constraints()andadd_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 withNAvalues.
- Update documentation for
add_locked_in_constraints()andadd_locked_out_constraints()functions to provide recommended practices for raster data. - Update documentation for constraints missing "See also" and "Value" sections.
- 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. thetas_featuresobject in the prioritizrdata 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). Thanks to Martin Jung (@Martin-Jung) for bug report.
- New
add_manual_bounded_constraints()function to apply lower and upper bounds on planning units statuses in a solution (#118). Thanks to Martin Jung (@Martin-Jung) for suggestion.
- Update
replacement_cost()function to use parallel processing to speed up calculations (#119).
- Update
add_gurobi_solver(),add_lpsymphony_solver(), andadd_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). Thanks to Martin Jung (@Martin-Jung) for bug report. - Update
add_locked_in_constraints()andadd_locked_out_constraints()functions to provide a more helpful error message thelocked_in/locked_outargument refers to a column with data that are not logical (i.e.TRUE/FALSE; #118). Thanks to Martin Jung (@Martin-Jung) for bug report.
- 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.
- Rename
add_max_phylo_objective()function toadd_max_phylo_div_objective().
- New
add_max_phylo_end_objective()function to maximize the phylogenetic endemism of species adequately represented in a prioritization (#113). Thanks to @FerreiraPSM for suggestion.
- Update simulated phylogeny dataset (
sim_phylogeny).
- Add
add_max_phylo_end_objective(),replacement_cost(), andrarity_weighted_richness()functions to the Prioritizr vignette. - Update examples for
add_max_phylo_div_objective()function. - Prettify equations in the documentation for objective functions.
- 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).
- New
irreplaceabilitymanual entry to document functions for calculating irreproducibility scores. - Updated Salt Spring Island vignette with a section on calculating and interpreting irreplaceability scores.
- 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.
- Fix typo.
- Fix broken links to Gurobi academic licenses.
- Release candidate for CRAN (rejected).
- Fix example throwing an error during CRAN checks.
- Add Bombi et al. (in press) to publication record.
- Fix broken link in main vignette.
- Release candidate for CRAN.
- New
add_min_shortfall_objective()function to find solutions that minimize target shortfalls.
- Fix
problem()tests so that they work when no solvers are installed.
- Add new
add_min_shortfall_objective()function to main vignette.
- 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.
- 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 thepresolve_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 thesolve(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 package when calling
tibble::as.tibble()instead oftibble::as_tibble().
- Add example for calculating feature representation a solution in tabular
format output by
solve()(#110). Thanks to Martin Jung (@Martin-Jung) for suggestion. - 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.
- Release candidate for CRAN.
- Retain debugging symbols to conform with CRAN policies.
- Release candidate for CRAN.
- Add new citations.
- Fix typos in documentation for
add_boundary_penalties()andadd_connectivity_penalties()function (#106).
- Fix bug where use of
add_rsymphony_solver()andadd_lpsymphony_solver()sometimes returned infeasible solutions when subjected to a time limit (#105). Thanks to @magalicombes for bug report.
- Fix assorted bugs in the render, setter, and getter parameter functions for
ConservationProblem-classobjects. 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.
- Fix
bad error messageerror being thrown when input rasters are not comparable (i.e. same coordinate reference system, extent, resolutions, and dimensionality) (#104). Thanks to @faengl for bug report.
- Add Domisch et al. (2019) to publication record vignette.
- Fix issue
solve()printing annoying text abouttbl_df(#75). Thanks to Javier Fajardo (@javierfajnolla) for bug report.
- Tweak
add_max_features_objective()example code.
- Update publication record vignette.
- Fix bug where the
add_neighbor_constraints()andadd_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.
- 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.
- Fix bug in the
$find(x)method forCollectionprototypes that caused it to throw an error incorrectly. This method was not used in earlier versions of this package.
- Add the
add_mandatory_allocation_constraints()to the Management Zones and Prioritizr vignettes.
- 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.
- 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 toxwas invalid when it was in fact valid. This bug is encountered when different layers the argument toxhave non-NA values in different cells.
- Update instructions for activating Gurobi licenses on remote machines (#98).
- 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.
- 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.
- 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()andadd_max_cover_objective()functions to make it clearer that they do not use targets (#94).
- Release candidate for CRAN.
- Fix bug in
add_locked_in_constraints()andadd_locked_out_constraints()that incorrectly threw an error when usinglogicallocked 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(), andadd_manual_locked_constraints()where solving the same problem object twice resulted in incorrect planning units being locked in or out of the solution (#92). Thanks to Javier Fajardo (@javierfajnolla) for bug report. - Added unit tests for objectives, constraints, decisions, targets, and penalties to ensure that solving problems twice does not result in different solutions.
- 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.
- The
feature_representation()function now allowsnumericsolutions with attributes (e.g. when output by thesolve()function) when calculating representation statistics for problems withnumericplanning unit data (#91). Thanks to Javier Fajardo (@javierfajnolla) for bug report. - 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.
- The
problemfunction now allows negative values in the cost and feature data (and throws a warning if such data are detected). - The
add_absolute_targets()andadd_manual_targets()functions now allow negative targets (but throw a warning if such targets are specified). - The
compilefunction 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.
- Fix
add_max_cover_objective()in prioritizr vignette (#90).
- The
add_loglinear_targets()function now includes afeature_abundances()parameter for specifying the total amount of each feature to use when calculating the targets (#89). Thanks to Liz Law (@lizlaw) for suggestion.
- The
add_relative_targets()documentation now makes it clear that locked out planning units are included in the calculations for setting targets (#89).
- Release candidate for CRAN.
- New
feature_abundances()function to calculate the total amount of each feature in the planning units (#86). Thanks to Javier Fajardo (@javierfajnolla) for suggestion.
- Fix some equations in the documentation (#83).
- Add version requirements for assertthat and tibble packages (#82).
- Fix minor typos in the Gurobi installation guide.
- Update the Management zones tutorial.
- 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.
- 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).
- New
add_pool_portfolio()function to generate a portfolio of solutions using the Gurobi solution pool (#77).
- 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).
- New
feature_representation()function to how well features are represented in solutions (#73).
- 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.
- Fix issue with the
solve()function printing superfluous text (#75).
- Minor improvements to the documentation for the
problem()function.
- Added functionality to build and solve problems with multiple management zones (#14).
- New built-in datasets
sim_pu_zones_stack,sim_pu_zones_polygons, andsim_features_zonesfor exploring conservation problems with multiple management zones. - New
zonesfunction andZonesclass to organize data with multiple zones. - New
add_manual_targets()function for creating targets that pertain to multiple management zones. - New
add_manual_locked_constraints()function to manually specify which planning units should or shouldn't be allocated to specific zones in solutions. - New
binary_stack(),category_layer(), andcategory_vector()functions have been provided to help work with data for multiple management zones.
- The
problem()function now acceptsZoneobjects as arguments forfeatureto create problems with multiple zones. - The
add_relative_targets()andadd_absolute_targets()functions for adding targets to problems can be used to specify targets for each feature in each zone. - The
solve()function now returns alistof solutions when generating a portfolio of 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
zonesparameter) and specify how they they should be applied (using thedataparameter. 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_locked_in_constraints()andadd_locked_out_constraints()functions for specifying which planning units are locked in or out now acceptmatrixarguments for specifying which zones are locked in or out. - The
add_feature_weights()function can be used to weight different the representation of each feature in each zone.
- New Management zones vignette on building and solving problems with multiple management zones.
- Added mention of zones functionality to package DESCRIPTION, summary (i.e.,
?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.
- Fix typo in README.
- Update documentation for
add_boundary_penalties()(#62). Thanks to Liz Law (@lizlaw) for report.
- Fix bug where
add_locked_in_constraints()andadd_locked_out_constraints()throw an exception when used with semi-continuous-type decisions (#59). - Error message in
compile()thrown when the same planning unit is locked in and locked out now prints the planning unit indices in a readable format.
- Fix bug where
add_locked_in_constraints()andadd_locked_out_constraints()are ignored when using proportion-type decisions (#58).
- Fix bug in
predefined_optimization_problem()which incorrectly recognized some inputs as invalid when they were in fact valid. - Addressed NOTE in
R CMD checkrelated to proto package in Depends.
- Moved proto package from Imports to Depends in DESCRIPTION
- Depends on R version 3.4.0 (avoids 'patchlevel 0' NOTE/WARNING in checks)
- Release candidate for CRAN.
- Unit tests that fail when using lpsymphony due to a bug in lpsymphony are now skipped (partially addressing #40).
- Update
add_lpsymphony_solver()to throw warnings to alert users to potentially incorrect solutions (partially addressing #40).
- Vignette sizes have been reduced.
- Release candidate for CRAN. Release postponed due issues on Travis CI.
- Unit tests for
add_*_objectivesnow pass when executed with slow solvers (partially addressing #40). - Update
compile()to work when no solvers are installed (#41). - Gap arguments in
add_*_solversare now unbounded and can accept values larger than 1 (#44).
- Release candidate for CRAN.
- The
add_max_cover_objective()function has been renamed to theadd_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 changesadd_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.
- Fix bug with
add_lpsymphony_solver()causing error when attempting to solve problems.
- Release candidate for CRAN. Release postponed due to bug report.
- Fix bug when solving problems with
numericvector data that caused an error. - Fix bug in compiling problems with
numericvector input with rij data containing NA values. - Added unit tests for solving problems with various input formats.
- Updated package sizes reported in
cran-comments.mdfile.
- Initial release candidate for CRAN. Release postponed due to bug report.
- Added vignette to record publications that use prioritizr (#35).
- Unit tests now compatible with development version of testthat (#34).
- Fix bug in
apply_boundary_penalties()andadd_connectivity_penalties()causing the function to throw an error when the number of boundaries/edges is less than the number of planning units.
- Makevars now compatible with Mac OSX Sierra (#33).
- Fix bug in
boundary_matrix()calculations (#30).
- Minor tweaks to vignettes.
- Add logo to README files and package website (#31).
- Remove prioritizrdata from package Suggests.
- Add shiny and xtable to Suggests for rendering parameters.
- Added code for
ScalarParameterandArrayParameterprototypes to check that functions for generating widgets have their dependencies installed. - Fix bug when
numericplanning unit data and portfolios that caused thesolve()to throw an error. - Remove R-devel from AppVeyor testing because it fails for unknown reasons.
- Broad-scale improvements to documentation.
- Fix documentation for
add_max_phylo_objective()(#24). - Update Gurobi Installation vignette.
- URLs for lpsymphony on Bioconductor now use the package's DOI.
- Add more comprehensive tests to portfolios.
- Removed shiny functions for now to prepare for CRAN release.
- Rebuilt website and documentation.
- Included vignette on Gurobi solver installation and testing.
- Fixed bug where
Spatial*DataFrameinput tomarxan_problem()would always use the first column in the attribute table for the cost data. This bug is serious so analysis that usedSpatial*DataFrameinputs inmarxan_problem()should be rerun.
- Added functionality to use feature abundance/occurrence data stored as
columns in the planning unit data when constructing
problem()objects.
- Skip
add_cuts_portfolio()on Travis.
- Skip
add_cuts_portfolio()andadd_shuffle_portfolio()tests on CRAN.
- This version breaks compatibility with previous releases because
solutions in
data.frameandSpatial*DataFrameobjects are now stored in columns named "solution_*" (e.g. "solution_1") to store multiple solutions. - Solutions now contain additional information in stored in the object's
attributes (#24). See
README.Rmdfor examples on accessing this information.
- Added support for multiple solutions (#23).
- Add logical
verboseargument to all solvers. This replaces theverbosity - The verbosity of information presented when solving problems using
add_lpsymphony_solver()andadd_rsymphony_solver()is reduced.
- Tidy examples in
add_gurobi_solver.R,add_lpsymphony_solver.R,add_rsymphony_solver.R, andsolvers.R. argument inadd_lpsymphony_solver()andadd_rsymphony_solver(). - Assorted spelling mistakes have been fixed.
ConservationProblem$print()now only prints the first three species names and a count of the total number of features. This update means thatConservationProblemobjects with lots of features can now safely be printed without polluting the R console.- 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.
- Attempt to make equations in help files prettier.
- Update
marxan_problem()to work with absolute file paths and theINPUTDIRin Marxan input files (#19). Thanks to Dan Rosauer (@DanRosauer) for bug report.
- Fix bug in
solve()when the rij data does not contain the highest planning unit identifier specified when building theproblem()(#20).
- Passes CRAN checks on Winbuilder.
- Added roxygen2 to Suggests for Travis CI.
- 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 commandmake vignsif desired. - 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.
- Lint objective function definition files.
- Added rmarkdown package to Suggests following recommended practices.
- The
README.Rmdnow lives in the top-level directory following standard practices. It should now be complied usingrmarkdown::render("README.Rmd")or using the shell commandmake readme. Note that the figures forREADME.mdcan be found in the directoryman/figures. - The example for
prshinywill 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.Rmdshowing how to runmarxan_problem()using inputdata.frame()objects. - Fix bug in vignette
quick_start.Rmdcounting number of selected planning units README.Rmdtweaks to make it look prettier on website.- 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
- 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.
- Fix bug in
problem.data.framethat meant that it did not check for missing values inrij$pu.
- 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 argumentconnectivitiesis alist. The elements in the list are assumed to bedsCMatrixobjects (aka symmetric sparse matrices in a compressed format) and are coerced todgCMatrixobjects to reduce computational burden. There was a typo, however, and so the objects were coerced todgCmatrixand notdgCMatrix. This evidently was ok in earlier versions of the RcppArmadillo and/or Matrix packages but not in the most recent versions.
- Fix bug in
problem()causing node stack overflows (#21). Thanks to Dan Rosauer (\DanRosauer) for bug report.
- Add roxygen2 to package SUGGESTS for building vignettes.
- Fix issue where
parallel::detectCores()returnsNAon some systems preventing users from using the Gurobi solver--even when one thread is specified.
- Fix building issue due to incorrect file order in DESCRIPTION.
- Compatibility with R 3.4.0.
- Replace
structure(NULL, ...)withstructure(list(), ...). - Register compiled library files.
- Remove duplicate definition of
new_waiver(). - Update tests to skip if prioritizrdata package not installed.
- Make
add_default_objectives()andadd_default_targets()private functions.
- Fix missing links in documentation.
- Fix typos in roxygen2 parameters.
- Move
add_default_decisions()andadd_default_solver()to own help file.
- Fix bug in
rij_matrix()duplicating feature data (#13).
- Fix velox package dependency (#8).
- Fix bug in
add_corridor_constraints()that fails to actually add the constraints with argument toconnectivityis a list. - Fix bug in
make installcommand so that it now actually installs the package.
- Fix link to Joe's website in the package's website.
- R interface fully functional.
- Package re-implementation.
- Prepare for CRAN submission.
- Introduce maximum target coverage model.
- Add continuous integration.
- Fixed various bugs.
- Add full vignette in addition to quickstart guide.
- Initial package version.