# 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` 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` to report timings following the same methods
  as the other solvers.

# prioritizr 7.0.0.2

- Update `add_lpsymphony_solver` 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 that`gap = 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 R 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](https://www.ibm.com/products/ilog-cplex-optimization-studio)
  (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_ R 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_ R 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_ 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_solver` 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_ R 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 issue where _Rsymphony_ (and potentially _lpsymphony_) return 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_ (#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 version of _prioritizr_ (#38).
- Modify _lpsymphony_ examples and tests to skip on Linux operating systems.
- Add tests to unit tests that were being skipped in new version of _testthat_.

# 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. Address issue #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 `priortizr::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` from internal.R.
- 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.
