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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-format table or a set of pre-assembled tables. It returns aligned objects including:

  • site_df: site by x,y coordinates

  • env_df: site by environment numeric matrix

  • comm_res: site by resident abundance matrix

  • pa_res: site by resident presence-absence matrix

  • traits_res: resident by trait data frame (mixed types allowed)

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-format data frame with at least the columns site, x, y, species, and count.

site_df

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

env_df

Optional site by environment numeric data frame or matrix. Row names must correspond to site identifiers.

comm_res

Optional site by resident numeric matrix or data frame (wide), or a long-format table with columns site, species, and count.

traits_res

Optional resident by trait data frame with row names corresponding to species identifiers.

comm_long

Character string indicating how to interpret a separately supplied comm_res; one of "auto", "long", or "wide".

site_col, x_col, y_col, species_col, count_col

Column names used when building from long_df.

env_cols

Character vector of environment column names to extract.

env_prefix

Regular expression used to select environment columns.

trait_cols

Character vector of trait column names to extract.

trait_prefix

Regular expression used to select trait columns.

drop_empty_sites

Logical. If TRUE, drop sites with zero total abundance.

drop_empty_species

Logical. If TRUE, drop resident species with zero total abundance across all sites.

return_diversity

Logical. If TRUE, compute and return site-level diversity summaries.

make_plots

Logical. If TRUE, generate quick diagnostic plots.