assemble_data_to_fit()

assemble_data_to_fit

R Documentation

Assemble Final Data List for Model Fitting

Description

Validates that the community matrix, scaled abiotic data, and coordinate data all share the same sample rows in the same order, then bundles them into the named list expected by ‘fit_jsdm_model()’.

Usage

assemble_data_to_fit(
  data_community_filtered = NULL,
  data_abiotic_scaled_list = NULL,
  data_coords_to_fit = NULL
)

Arguments

data_community_filtered

A numeric matrix with row names ’"<dataset_name>__<age>"’ and taxon columns, as returned by ‘filter_constant_taxa()’.

data_abiotic_scaled_list

A named list with elements ‘data_abiotic_scaled’ and ‘scale_attributes’, as returned by ‘scale_abiotic_for_fit()’. ‘data_abiotic_scaled’ must have row names matching those of the community matrix.

data_coords_to_fit

A data frame with row names ’"<dataset_name>__<age>"’ and columns ‘coord_long’ and ‘coord_lat’, as returned by ‘prepare_coords_for_fit()’.

Details

This function performs only validation and assembly; all data transformations are handled by the preceding pipeline targets. An error is raised if any two inputs differ in row count or row name ordering.

Value

A named list with four elements:

‘data_community_to_fit’: The (filtered) community matrix.
‘data_abiotic_to_fit’: The scaled abiotic data frame.
‘data_coords_to_fit’: The per-sample coordinate data frame.
‘scale_attributes’: Scaling attributes for back-transformation.