check_parameters: parameters checkings

In TAD: Realize the Trait Abundance Distribution

parameters checkings

Description

Checks all parameters of the TAD and raises errors if parameters' values are incoherent.

Usage

check_parameters(
  weights = NULL,
  weights_factor = NULL,
  trait_data = NULL,
  randomization_number = NULL,
  aggregation_factor_name = NULL,
  statistics_factor_name = NULL,
  seed = NULL,
  abundance_file = NULL,
  weighted_moments_file = NULL,
  stat_per_obs_file = NULL,
  stat_per_rand_file = NULL,
  stat_skr_param_file = NULL,
  regenerate_abundance_df = NULL,
  regenerate_weighted_moments_df = NULL,
  regenerate_stat_per_obs_df = NULL,
  regenerate_stat_per_rand_df = NULL,
  significativity_threshold = NULL,
  lin_mod = NULL,
  slope_distance = NULL,
  intercept_distance = NULL,
  csv_tsv_load_parameters = NULL
)

Arguments

weights	the dataframe of weights, one row correspond to a series of observation
weights_factor	the dataframe which contains the different factor linked to the weights
trait_data	a vector of the data linked to the different factor
randomization_number	the number of random abundance matrix to generate
aggregation_factor_name	vector of factor name for the generation of random matrix
statistics_factor_name	vector of factor name for the computation of statistics for each generated matrix
seed	the seed of the pseudo random number generator
abundance_file	the path and name of the RDS file to load/save the dataframe which contains the observed data and the generated matrix
weighted_moments_file	the path and name of the RDS file to load/save the dataframe which contains the calculated moments
stat_per_obs_file	the path and name of the RDS file to load/save the dataframe which contains the statistics for each observed row regarding the random ones
stat_per_rand_file	the path and name of the RDS file to load/save the dataframe which contains the statistics for each random matrix generated
stat_skr_param_file	default=NULL You can provide the output to write the SKR statistics results to.
regenerate_abundance_df	boolean to specify if the abundance dataframe is computed again
regenerate_weighted_moments_df	boolean to specify if the weighted moments dataframe is computed again
regenerate_stat_per_obs_df	boolean to specify if the statistics per observation dataframe is computed again
regenerate_stat_per_rand_df	boolean to specify if the statistics per random matrix dataframe is computed again
significativity_threshold	the significance threshold to consider that the observed value is in the randomized value
lin_mod	Indicates the type of linear model to use for (SKR): choose "lm" or "mblm"
slope_distance	slope of the theoretical distribution law (default: slope = 1 intercept = 1.86 skew-uniform distribution family)
intercept_distance	intercept of the theoretical distribution law (default: slope = 1 intercept = 1.86 skew-uniform distribution family)
csv_tsv_load_parameters	a list of parameters for each data structure we want to load. Each element must be named after the data structure we want to load.

TAD documentation built on April 4, 2025, 5:10 a.m.