plot.ProjectProblem: Plot a solution to a project prioritization problem

Description

Create a plot to visualize how well a solution to a project prioritization problem() will maintain biodiversity.

Usage

# S3 method for ProjectProblem
plot(x, solution, n = 1, symbol_hjust = 0.007, return_data = FALSE, ...)

Value

A ggplot() object.

Arguments

x: project prioritization problem().
solution: base::data.frame() or tibble::tibble() table containing the solutions. Here, rows correspond to different solutions and columns correspond to different actions. Each column in the argument to solution should be named according to a different action in x. Cell values indicate if an action is funded in a given solution or not, and should be either zero or one. Arguments to solution can contain additional columns, and they will be ignored.
n: integer solution number to visualize. Since each row in the argument to solutions corresponds to a different solution, this argument should correspond to a row in the argument to solutions. Defaults to 1.
symbol_hjust: numeric horizontal adjustment parameter to manually align the asterisks and dashes in the plot. Defaults to 0.007. Increasing this parameter will shift the symbols further right. Please note that this parameter may require some tweaking to produce visually appealing publication quality plots.
return_data: logical should the underlying data used to create the plot be returned instead of the plot? Defaults to FALSE.
...: not used.

Details

The type of plot that this function creates depends on the problem objective. If the problem objective contains phylogenetic data, then this function plots a phylogenetic tree where each branch is colored according to its probability of persistence. Otherwise, if the problem does not contain phylogenetic data, then this function creates a bar plot where each bar corresponds to a different feature. The height of the bars indicate each feature's probability of persistence, and the width of the bars indicate each feature's weight.

Features that directly benefit from at least a single completely funded project with a non-zero cost are depicted with an asterisk symbol. Additionally, features that indirectly benefit from funded projects---because they are associated with partially funded projects that have non-zero costs and share actions with at least one funded project---are depicted with an open circle symbol.

Examples

Run this code

# load data
data(sim_projects, sim_features, sim_actions)

# build problem without phylogenetic data
p1 <- problem(sim_projects, sim_actions, sim_features,
             "name", "success", "name", "cost", "name") %>%
      add_max_richness_objective(budget = 400) %>%
      add_feature_weights("weight") %>%
      add_binary_decisions()

if (FALSE) {
# solve problem without phylogenetic data
s1 <- solve(p1)

# visualize solution without phylogenetic data
plot(p1, s1)
}

# build problem with phylogenetic data
p2 <- problem(sim_projects, sim_actions, sim_features,
             "name", "success", "name", "cost", "name") %>%
      add_max_phylo_div_objective(budget = 400, sim_tree) %>%
      add_binary_decisions()

if (FALSE) {
# solve problem with phylogenetic data
s2 <- solve(p2)

# visualize solution with phylogenetic data
plot(p2, s2)
}