rank_based_rsq_contribs: Calculates contributions to variance for Rfit regression...

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Calculates contributions to variance for Rfit regression models

Description

Calculates contributions to variance for Rfit regression models

Usage

rank_based_rsq_contribs(
  species_cmps,
  mets_melt,
  config_table,
  cmp_mods = NULL,
  adj_rsq = F,
  nperm_start = 0,
  nperm_taxa = 5,
  signif_threshold = 0.1,
  return_perm = F,
  add_residual = F,
  nperm_max = 300
)

Arguments

species_cmps	Table of species contributions (without residuals)
mets_melt	Table of metabolite concentrations
config_table	Configuration table including model-fitting settings
cmp_mods	Output of fit_cmp_mods
adj_rsq	Whether to decompose standard disp rsq or adjusted
signif_threshold	Will only analyze models with a p-value below this threshold
return_perm	Whether to return full table of permutation results
add_residual	Whether to add the residual as an additional contributor at the end
nperm_max	Maximum # of random orderings to do, regardless of the # of taxa (default 1500)
nperm	Number of permutations per decomposition

Value

Data table of variance shares by each species in the original table for each metabolite

Examples

rank_based_rsq_contribs(species_cmps, mets_melt, config_table)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.