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Prepare inputs (assemble and align core tables)

Source: R/prepare_inputs.R
prepare_inputs.Rd

Thin wrapper around assemble_matrices that standardises and stores assembled inputs in a new_invasimapr_fit object for downstream modelling. Use this function to run the input-assembly step once and pass a single structured container through subsequent pipelines.

Usage

prepare_inputs(..., make_plots = FALSE)

Arguments

...

Arguments passed on to assemble_matrices

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, propagate make_plots to assemble_matrices so that diagnostic plots are produced during assembly. Defaults to FALSE.

Value

An object of class invasimapr_fit with components:

inputs

The full list returned by assemble_matrices.

meta

A list with elements n_sites, n_residents, and n_traits.

Details

What this does

  1. Calls assemble_matrices to build core site-by-species and site-by-trait matrices, perform consistency checks, and harmonise keys and factor levels.

  2. Wraps the returned list into a lightweight S3 container of class invasimapr_fit, with a dedicated inputs slot and a small meta block containing basic counts used by later steps.

Object layout


invasimapr_fit
  inputs : list   (output from assemble_matrices)
  meta   : list   (n_sites, n_residents, n_traits)

Notes

  • No mutation of the assembled inputs occurs here; the function only packages and annotates them.

  • To inspect the assembled data, use fit$inputs on the returned object.

See also

assemble_matrices, new_invasimapr_fit

Examples

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

str(fit, 1)
str(fit$inputs, 1)
fit$meta
} # }