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Assemble community matrices for invasion-fitness workflows

Source: R/assemble_matrices.R
assemble_matrices.Rd

assemble_matrices() creates the standard inputs used throughout the invasion-fitness pipeline from either a single “long” table or a set of already-formed tables. It returns aligned objects:

  • site_df (site × x,y),

  • env_df (site × environment; numeric matrix),

  • comm_res (site × resident abundances; numeric matrix),

  • pa_res (site × resident presence/absence; integer matrix),

  • traits_res (resident × traits; data frame, keeps mixed types).

Usage

assemble_matrices(
  long_df = NULL,
  site_df = NULL,
  env_df = NULL,
  comm_res = NULL,
  traits_res = NULL,
  comm_long = c("auto", "long", "wide"),
  site_col = "site",
  x_col = "x",
  y_col = "y",
  species_col = "species",
  count_col = "count",
  env_cols = NULL,
  env_prefix = "^env",
  trait_cols = NULL,
  trait_prefix = "^trait",
  drop_empty_sites = TRUE,
  drop_empty_species = TRUE,
  return_diversity = TRUE,
  make_plots = FALSE
)

Arguments

long_df

Optional long data frame with at least site, x, y, species, count.

site_df

Optional data frame with columns site, x, y (used when long_df is NULL).

env_df

Optional site × environment numeric data frame/matrix (row names must be site IDs; used when long_df is NULL).

comm_res

Optional site × resident numeric matrix/data frame (wide) or a long table with site, species, count (see comm_long).

traits_res

Optional resident × traits data frame (row names = species).

comm_long

How to interpret a separately supplied comm_res: one of c("auto","long","wide"); "auto" detects a long table and pivots.

site_col, x_col, y_col, species_col, count_col

Column names to use when building from long_df. Defaults: "site", "x", "y", "species", "count".

env_cols, env_prefix, trait_cols, trait_prefix, drop_empty_sites,

drop_empty_species,return_diversity,make_plots See details in original docs.