# Optimal Project Prioritization

## Documentation for package ‘oppr’ version 1.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F G H I L M N O P R S T U V W misc

## -- A --

A | Optimization problem methods
A-method | Optimization problem methods
action_names | Action names
action_names-method | Action names
add_absolute_targets | Add absolute targets
add_absolute_targets-method | Add absolute targets
add_binary_decisions | Add binary decisions
add_default_solver | Add a default solver
add_feature_weights | Add feature weights
add_feature_weights-method | Add feature weights
add_gurobi_solver | Add a 'Gurobi' solver
add_heuristic_solver | Add a heuristic solver
add_locked_in_constraints | Add locked in constraints
add_locked_in_constraints-method | Add locked in constraints
add_locked_out_constraints | Add locked out constraints
add_locked_out_constraints-method | Add locked out constraints
add_lpsolveapi_solver | Add a lp_solve solver with 'lpSolveAPI'
add_lpsymphony_solver | Add a SYMPHONY solver with 'lpsymphony'
add_lsymphony_solver | Add a SYMPHONY solver with 'lpsymphony'
add_manual_locked_constraints | Add manually specified locked constraints
add_manual_locked_constraints-method | Add manually specified locked constraints
add_manual_targets | Add manual targets
add_manual_targets-method | Add manual targets
add_max_phylo_div_objective | Add maximum phylogenetic diversity objective
add_max_richness_objective | Add maximum richness objective
add_max_targets_met_objective | Add maximum targets met objective
add_min_set_objective | Add minimum set objective
add_random_solver | Add a random solver
add_relative_targets | Add relative targets
add_relative_targets-method | Add relative targets
add_rsymphony_solver | Add a SYMPHONY solver with 'Rsymphony'
ArrayParameter | Array parameter prototype
ArrayParameter-class | Array parameter prototype
array_parameters | Array parameters
as | Coerce object to another object
as.Id | Coerce object to another object
as.Id.character | Coerce object to another object
as.list-method | Manipulate tibbles
as.list.OptimizationProblem | Convert 'OptimizationProblem' to list
as.list.Parameters | Coerce object to another object

## -- B --

binary_matrix_parameter | Matrix parameters
binary_parameter | Scalar parameters
binary_parameter_array | Array parameters
branch_matrix | Branch matrix
branch_matrix.default | Branch matrix
branch_matrix.phylo | Branch matrix

## -- C --

Collection | Collection prototype
Collection-class | Collection prototype
col_ids | Optimization problem methods
col_ids-method | Optimization problem methods
compile | Compile a problem
compile.ProjectProblem | Compile a problem
Constraint | Constraint prototype
Constraint-class | Constraint prototype
constraints | Project prioritization problem constraints

## -- D --

Decision | Decision prototype
Decision-class | Decision prototype
decisions | Specify the type of decisions

## -- F --

feature_names | Feature names
feature_names-method | Feature names

## -- G --

get_data | Optimization problem methods
get_data-method | Optimization problem methods
GurobiSolver-class | Solver prototype

## -- H --

HeuristicSolver-class | Solver prototype

## -- I --

Id | Identifier
integer_parameter | Scalar parameters
integer_parameter_array | Array parameters
is | Is it?
is.Id | Is it?
is.Waiver | Is it?

## -- L --

lb | Optimization problem methods
lb-method | Optimization problem methods
LpsolveapiSolver-class | Solver prototype
LpsymphonySolver-class | Solver prototype

## -- M --

matrix_parameters | Matrix parameters
MiscParameter | Miscellaneous parameter prototype
MiscParameter-class | Miscellaneous parameter prototype
misc_parameter | Miscellaneous parameter
modelsense | Optimization problem methods
modelsense-method | Optimization problem methods

## -- N --

ncell | Optimization problem methods
ncell-method | Optimization problem methods
ncol | Optimization problem methods
ncol-method | Optimization problem methods
ncol-method | Manipulate tibbles
new_id | Identifier
new_optimization_problem | Optimization problem
new_waiver | Waiver
nrow | Optimization problem methods
nrow-method | Optimization problem methods
nrow-method | Manipulate tibbles
number_of_actions | Number of actions
number_of_actions-method | Number of actions
number_of_branches | Optimization problem methods
number_of_branches-method | Optimization problem methods
number_of_features | Number of features
number_of_features-method | Number of features
number_of_projects | Number of projects
number_of_projects-method | Number of projects
numeric_matrix_parameter | Matrix parameters
numeric_parameter | Scalar parameters
numeric_parameter_array | Array parameters

## -- O --

obj | Optimization problem methods
obj-method | Optimization problem methods
Objective | Objective prototype
Objective-class | Objective prototype
objectives | Problem objective
oppr | oppr: Optimal Project Prioritization
OptimizationProblem | Optimization problem class
OptimizationProblem-class | Optimization problem class
OptimizationProblem-methods | Optimization problem methods

## -- P --

Parameter | Parameter class
Parameter-class | Parameter class
Parameters | Parameters class
parameters | Parameters
Parameters-class | Parameters class
pipe | Pipe operator
plot.ProjectProblem | Plot a solution to a project prioritization problem
plot_feature_persistence | Plot a bar plot to visualize a project prioritization
plot_phylo_persistence | Plot a phylogram to visualize a project prioritization
pproto | Create a new 'pproto' object
print | Print
print-method | Print
print.ArrayParameter | Print
print.Id | Print
print.OptimizationProblem | Print
print.ProjectModifier | Print
print.ProjectProblem | Print
print.ScalarParameter | Print
print.Solver | Print
problem | Project prioritization problem
ProjectModifier | Conservation problem modifier prototype
ProjectModifier-class | Conservation problem modifier prototype
ProjectProblem | Project problem class
ProjectProblem-class | Project problem class
project_cost_effectiveness | Project cost effectiveness
project_names | Project names
project_names-method | Project names
proportion_parameter | Scalar parameters
proportion_parameter_array | Array parameters
pwlobj | Optimization problem methods
pwlobj-method | Optimization problem methods

## -- R --

RandomSolver-class | Solver prototype
replacement_costs | Replacement cost
rhs | Optimization problem methods
rhs-method | Optimization problem methods
row_ids | Optimization problem methods
row_ids-method | Optimization problem methods
RsymphonySolver-class | Solver prototype

## -- S --

ScalarParameter | Scalar parameter prototype
ScalarParameter-class | Scalar parameter prototype
scalar_parameters | Scalar parameters
sense | Optimization problem methods
sense-method | Optimization problem methods
show | Show
show-method | Show
simulate_ppp_data | Simulate data for the 'Project Prioritization Protocol'
simulate_ptm_data | Simulate data for 'Priority threat management'
sim_actions | Simulated data
sim_data | Simulated data
sim_features | Simulated data
sim_projects | Simulated data
sim_tree | Simulated data
solution_statistics | Solution statistics
solve | Solve
solve-method | Solve
Solver | Solver prototype
Solver-class | Solver prototype
solvers | Problem solvers

## -- T --

Target | Target prototype
Target-class | Target prototype
targets | Targets
tee | Tee operator
tibble-methods | Manipulate tibbles

## -- U --

ub | Optimization problem methods
ub-method | Optimization problem methods

## -- V --

vtype | Optimization problem methods
vtype-method | Optimization problem methods

## -- W --

Weight | Weight prototype
Weight-class | Weight prototype
weights | Weights

## -- misc --

%>% | Pipe operator
%T>% | Tee operator