oppr 1.0.2 (released)
oppr 1.0.1.1
- Replace
tibble::as.tibble with tibble::as_tibble to avoid warnings.
oppr 1.0.1 (released)
oppr 1.0.0.1
- Fix compatibility issues with upcoming tibble (3.0.0) R package.
oppr 1.0.0 (released)
oppr 0.0.4.1
- Fix warnings in R-devel CRAN checks related to documentation.
- Add citation for the research article that accompanies this package.
oppr 0.0.4 (released)
oppr 0.0.3.1
- Fix typo.
- Fix broken links to Gurobi academic licenses.
oppr 0.0.3 (released)
oppr 0.0.2.1
- Retain debugging symbols to conform with CRAN policies.
oppr 0.0.2 (released)
oppr 0.0.1.1
- Fix address sanitizer issues causing CRAN checks to fail.
- Tests successfully complete when the shiny R package is not installed.
oppr 0.0.1 (released)
oppr 0.0.0.19
- Add argument to
add_heuristic_solver to skip initial step for removing projects and actions that exceed the budget. While this initial step improves solution quality, it is not conventionally used in project prioritization algorithms and so should be omitted to provide accurate benchmarks.
oppr 0.0.0.18
- Reduce precision of extinction probability calculations when formulating a problem with a maximum expected phylogenetic diversity objective (i.e.
add_max_phylo_div_objective). Specifically, 1’000 points instead of 10’000 points are now used for piece-wise linear components. It appears that reducing the precision in this manner does not affect the correctness of results, but substantially reduces the time needed to solve problems to optimality in certain situations.
oppr 0.0.0.17
- Update
add_heuristic_solver algorithm so that cost-effectiveness values are calculated with projects sharing costs (e.g. if two projects share an action that costs $100, then this action contributes $50 to the cost of each project). This update makes the algorithm similar to backwards heuristics conventionally used in prioritizing species recovery projects (i.e. https://github.com/p-robot/ppp; #14).
oppr 0.0.0.16
- Fix bug in
add_heuristic_solver function introduced in version 0.0.0.15.
oppr 0.0.0.15
- Update
add_heuristic_solver algorithm so that it removes projects, and not actions, in an iterative fashion. This update (i) makes the algorithm comparable to the backwards heuristics conventionally used in prioritizing species recovery projects (i.e. https://github.com/p-robot/ppp) and (ii) substantially reduces run time (#14).
oppr 0.0.0.14
- Fix bugs in
add_heuristic_solver and add_random_solver arising from floating point comparison issue. These were causing infeasible solutions to be returned in R version 3.4.4.
oppr 0.0.0.13
- Fix bug in
project_cost_effectiveness reporting incorrect costs, and cost-effectiveness values.
oppr 0.0.0.12
- Assorted documentation tweaks.
oppr 0.0.0.11
- Update
add_heuristic_solver algorithm so that all actions and projects which exceed the budget are automatically removed prior to the iterative action removal.
- Update
add_random_solver algorithms so that projects are selected instead of individual actions. This means that solutions from this solver are (i) similar to those in previous project prioritization studies and (ii) more likely to deliver better solutions (#13).
oppr 0.0.0.10
- Rename package to oppr since ppr is already on CRAN.
- Fix issue with
replacement_costs yielding incorrect results for baseline projects when used with SYMPHONY solvers.
oppr 0.0.0.9
- Add new
project_cost_effectiveness function to calculate the cost-effectiveness for each conservation project in a problem.
oppr 0.0.0.8
- Fix typos in documentation (#8).
- The
solution_statistics function outputs which projects are completely funded in each solution (#9).
- Add example for saving tabular data to vignette (#10).
- Add examples to vignette for working with the solution output (#11).
oppr 0.0.0.7
- Fix annoying “
Found more than one class "tbl_df" in cache; using the first, from namespace 'tibble'” text.
oppr 0.0.0.6
- Actually fix bug when solving problems with a phylogenetic objective and branches that have a constant probability of persistence (#6).
- Fix bug in
add_max_phylo_div_objective yielding incorrect solutions when features are ordered differently in the phylogenetic and tabular input data.
- Fix bug in
solution_statistics yielding objective values for phylogenetic problems when features are ordered differently in the phylogenetic and tabular input data.
- Fix bug when handling phylogenetic data when a species is associated with two tip branches. Although such data probably indicate errors in the phylogenetic data, this functionality could be useful when combining multiple datasets.
oppr 0.0.0.5
- Add
return_data argument to plot_feature_persistence and plot_phylo_persistence so that plotting data can be obtained for creating custom plots.
oppr 0.0.0.4
- Fix bug in
add_relative_targets and add_manual_targets (when relative targets supplied) calculations. This result in incorrect calculations.
- Fix issue with expected persistence probabilities not accounting for the “do nothing” scenario (#7).
oppr 0.0.0.3
- The gurobi solver (i.e.
add_gurobi_solver function) now uses NumericFocus=3 to help avoid numerical issues.
- The
compile function now throws a warning if problems are likely to have numerical issues.
oppr 0.0.0.2
- Fix bug when solving problems with a phylogenetic objective and branches that have a constant probability of persistence (#6). Hindsight shows this attempt did not cover all edge cases.
- Add additional data sanity checks to
problem. It will now throw descriptive error messages if features are missing baseline probabilities, or are associated with baseline probabilities below 1e-11.
- Fix unit test for
simulate_ptm_data that had a very small chance of failing due to simulating a data set where an action is not associated with any project.
- Feature columns in simulated data produced using
simulate_ppp_data and simulate_ptm_data are now sorted.
oppr 0.0.0.1