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Performance curves for a conservation prioritization

Source: R/ps_performance.R
ps_performance.Rd

Compute performance curves describing how conservation value accumulates as sites are protected in the order given by a ps_prioritize() ranking.

Usage

ps_performance(ps, priority, target = 0.3)

# S3 method for class 'ps_performance'
plot(x, xvar = c("cost", "n_sites", "gain"), yvar = "value", ...)

Arguments

ps

The phylospatial object that was used to create priority.

priority

The result of ps_prioritize(). This must carry the "prioritization" attribute that ps_prioritize() attaches to its output; the attribute is lost if the result is written to file and read back in.

target

Numeric vector of one or more range protection targets, each between 0 and 1. For each target, the curve reports the fraction of the tree's total branch length belonging to lineages that have at least this fraction of their range protected. The default of 0.3 applies a 30% protection target to each lineage's range.

x

A ps_performance object.

xvar

Variable to plot on the x-axis: "cost" (the default), "n_sites", or "gain".

yvar

Variable to plot on the y-axis: "value" (the default) or one of the covX target columns.

...

Additional arguments passed to graphics::plot().

Value

A data frame of class ps_performance. For method = "optimal" prioritizations, and for method = "probable" prioritizations run with summarize = FALSE, it has one row per step per ranking, with columns:

ranking

Index of the ranking (1 for an optimal prioritization; the rep number for probabilistic prioritizations).

step

Step in the ranking, with 0 representing the starting state.

site

Index of the site added at this step, in the full set of sites (including unoccupied sites).

site_cost, site_gain, site_value

Cost of the site added at this step, the protection added (protection minus the site's init value), and the increase in network value.

n_sites, cost, gain, value

Cumulative number of sites added, cost, protection added, and network value.

covX

For each target, the fraction of total branch length belonging to lineages with at least X percent of their range protected.

For method = "probable" prioritizations run with summarize = TRUE, curves are summarized across reps at each step. The per-site columns are omitted, a stat column identifies the summary statistic ("mean" and percentiles "pctX"), and an n_reps column gives the number of reps that reached each step. Because these summaries are aligned by step, a summarized cost value represents the typical cost of reaching a given step, not a fixed budget.

Details

Curves are reconstructed from the settings, inputs, and raw rankings stored with the prioritization result, so init, cost, lambda, and protection are those used in the original call to ps_prioritize(). The curve begins at step 0, which reflects any existing protection supplied via init. At each subsequent step, the next site in the ranking is raised to the protection level. Curves stop at the last ranked site, so they are truncated if max_iter was used.

Network value is the conservation objective optimized by ps_prioritize(): the sum across all lineages of their benefit() (a function of the fraction of their range protected and the lambda parameter), weighted by their share of total tree length. It ranges from 0 (nothing protected) to 1 (every lineage's full range protected).

The function returns an error if priority lacks the prioritization attribute or if ps does not match the data set used for the prioritization, and gives a warning if the values in priority no longer match the stored rankings (e.g. because the object was modified after prioritization).

See also

ps_prioritize()

Examples

# \donttest{
set.seed(123)
ps <- ps_simulate()
cost <- terra::setValues(ps$spatial, rep(seq(100, 20, length.out = 20), 20))
p <- ps_prioritize(ps, cost = cost, progress = FALSE)

perf <- ps_performance(ps, p, target = c(.1, .3))
head(perf)
#>   ranking step site site_cost site_gain site_value n_sites      cost gain
#> 1       1    0   NA        NA        NA         NA       0   0.00000    0
#> 2       1    1  260  20.00000         1 0.03652507       1  20.00000    1
#> 3       1    2  130  62.10526         1 0.07891303       2  82.10526    2
#> 4       1    3  335  41.05263         1 0.02753456       3 123.15789    3
#> 5       1    4  129  66.31579         1 0.03813930       4 189.47368    4
#> 6       1    5  150  62.10526         1 0.02789538       5 251.57895    5
#>        value cov10 cov30
#> 1 0.00000000     0     0
#> 2 0.03652507     0     0
#> 3 0.11543810     0     0
#> 4 0.14297266     0     0
#> 5 0.18111196     0     0
#> 6 0.20900734     0     0
plot(perf)

plot(perf, xvar = "n_sites", yvar = "cov30")


# probabilistic prioritization, with curves summarized across reps
pp <- ps_prioritize(ps, cost = cost, method = "prob",
      n_reps = 25, max_iter = 50, progress = FALSE)
plot(ps_performance(ps, pp))

# }