skr_param_graph: skr_param_graph

In TAD: Realize the Trait Abundance Distribution

skr_param_graph

Description

Graph of the parameters computed from the SKR, compared to null model

Usage

skr_param_graph(
  skr_param,
  statistics_factor_name,
  statistics_factor_name_breaks = NULL,
  statistics_factor_name_col = NULL,
  slope_distance = CONSTANTS$SKEW_UNIFORM_SLOPE_DISTANCE,
  intercept_distance = CONSTANTS$SKEW_UNIFORM_INTERCEPT_DISTANCE,
  save_skr_param_graph = NULL,
  dpi = 600
)

Arguments

skr_param	SES of SKR parameters data frame (SES and Significance)
statistics_factor_name	column of data use for colors discrimination
statistics_factor_name_breaks	vector of factor levels of the statistics_factor_name, same dimension than statistics_factor_name_col
statistics_factor_name_col	vector of colors, same dimension than statistics_factor_name_breaks
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)
save_skr_param_graph	The path to save the graph
dpi	The dpi number to use when we generate png/jpg graph

Value

A graph instance

Examples

  results <- TAD::launch_analysis_tad(
    weights = TAD::AB[, 5:102],
    weights_factor = TAD::AB[, c("Year", "Plot", "Treatment", "Bloc")],
    trait_data = log(TAD::trait[["SLA"]]),
    aggregation_factor_name = c("Year", "Bloc"),
    statistics_factor_name = (statistics_factor_name <- c("Treatment")),
    randomization_number = 100,
    slope_distance = (
      slope_distance <- TAD::CONSTANTS$SKEW_UNIFORM_SLOPE_DISTANCE
    ),
    intercept_distance = (
      intercept_distance <- TAD::CONSTANTS$SKEW_UNIFORM_INTERCEPT_DISTANCE
    )
  )

  # if you want to display the graph
  graph <- TAD::skr_param_graph(
    skr_param = results$ses_skr,
    statistics_factor_name = statistics_factor_name,
    statistics_factor_name_breaks = c("Mown_Unfertilized", "Mown_NPK"),
    statistics_factor_name_col = c("#1A85FF", "#D41159"),
    slope_distance = slope_distance,
    intercept_distance = intercept_distance
  )

  plot(graph)

  output_path <- file.path(tempdir(), "outputs")
  dir.create(output_path)

  # if you want to save the graph as a file
  # either jpg, jpeg, png or svg are
  TAD::skr_param_graph(
    skr_param = results$ses_skr,
    statistics_factor_name = statistics_factor_name,
    statistics_factor_name_breaks = c("Mown_Unfertilized", "Mown_NPK"),
    statistics_factor_name_col = c("#1A85FF", "#D41159"),
    slope_distance = slope_distance,
    intercept_distance = intercept_distance,
    save_skr_param_graph = file.path(output_path, "skr_param_graph.jpeg"),
    dpi = 300
  )

  unlink(output_path, recursive = TRUE, force = TRUE)

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