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Summarise invasiveness and invasibility (tables, maps, rankings)

Source: R/summarise_results.R
summarise_results.Rd

Thin wrapper around summarise_invasiveness_invasibility that extracts inputs from a new_invasimapr_fit container, forwards optional arguments, and optionally overlays a boundary layer on the site map. This function is intended as a reporting step after computing invasion fitness and/or establishment probabilities.

Usage

summarise_results(
  fit,
  boundary_sf = NULL,
  boundary_params = list(inherit.aes = FALSE, fill = NA, color = "black", size = 0.3),
  traits_inv = NULL,
  ...
)

Arguments

fit

An object produced by the invasimapr workflow, containing fitness and/or prob components created by upstream steps.

boundary_sf

Optional object of class sf providing a boundary layer to overlay on the site map.

boundary_params

Named list of aesthetics passed to ggplot2::geom_sf(). Defaults to list(inherit.aes = FALSE, fill = NA, color = "black", size = 0.3).

traits_inv

Optional override of the invader trait table used for invader-ranked summaries. If NULL, traits are taken from the container.

...

Additional arguments forwarded to summarise_invasiveness_invasibility.

Value

The input fit object with an added or updated fit$summary list. Invisibly returns fit to support piping.

Details

Inputs used from the container

  • fit$fitness$lambda_is: site-by-invader invasion fitness matrix (optional).

  • fit$prob$p_is: site-by-invader establishment probability matrix (optional).

  • fit$inputs$site_df: site metadata with coordinates x and y (optional).

  • fit$inputs$comm_res: resident community matrix for context summaries (optional).

  • invader trait tables stored in the container, used for invader rankings.

At least one of lambda_is or p_is must be present; otherwise an error is thrown.

Behaviour

  1. Extract invasion fitness and/or establishment probability matrices from the container.

  2. Select site metadata and an effective invader trait table when available.

  3. Call summarise_invasiveness_invasibility to construct tidy summary tables and plots (site maps, rankings, heatmaps).

  4. If a boundary layer is supplied and plots are available, overlay it on the site map using geom_sf().

Output layout The returned container gains a summary element mirroring the structure returned by summarise_invasiveness_invasibility, typically containing summary tables, plots, and the arguments used.

See also

compute_invasion_fitness, compute_establishment_probability, summarise_invasiveness_invasibility, assemble_matrices

Examples

if (FALSE) { # \dontrun{
fit <- prepare_inputs(
  sites = site_df,
  residents = resident_df,
  invaders = invader_df,
  traits = trait_df
)

fit <- learn_sensitivities(fit)
fit <- predict_invaders(fit, traits_inv = invader_traits)

fit <- summarise_results(fit)
fit$summary$plots$site_map
} # }