check_parameters {TAD}R Documentation

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.


[Package TAD version 1.0.0 Index]