inst/doc/graph-outputs.R

In TAD: Realize the Trait Abundance Distribution

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 12,
  fig.height = 8,
  fig.asp = 0.8,
  out.width = "80%",
  dev.args = list(png = list(type = "cairo"))
)

## ----setup--------------------------------------------------------------------

weights <- TAD::AB[, 5:102]
weights_factor <- TAD::AB[, c("Year", "Plot", "Treatment", "Bloc")]
trait_data <- log(TAD::trait[["SLA"]][seq_len(ncol(weights))])
aggregation_factor_name <- c("Year", "Bloc")
statistics_factor_name <- c("Treatment")
regenerate_abundance_df <- TRUE
regenerate_weighted_moments_df <- TRUE
regenerate_stat_per_obs_df <- TRUE
regenerate_stat_per_rand_df <- TRUE
regenerate_stat_skr_df <- TRUE
randomization_number <- 100
seed <- 1312
significativity_threshold <- c(0.025, 0.975)
lin_mod <- "lm"
slope_distance <- TAD:::CONSTANTS$SKEW_UNIFORM_SLOPE_DISTANCE
intercept_distance <- TAD:::CONSTANTS$SKEW_UNIFORM_INTERCEPT_DISTANCE

future::plan(future::multisession)
results <- TAD::launch_analysis_tad(
  weights = weights,
  weights_factor = weights_factor,
  trait_data = trait_data,
  randomization_number = randomization_number,
  aggregation_factor_name = aggregation_factor_name,
  statistics_factor_name = statistics_factor_name,
  seed = seed,
  regenerate_abundance_df = TRUE,
  regenerate_weighted_moments_df = TRUE,
  regenerate_stat_per_obs_df = TRUE,
  regenerate_stat_per_rand_df = TRUE,
  regenerate_stat_skr_df = TRUE,
  significativity_threshold = significativity_threshold,
  lin_mod = lin_mod,
  slope_distance = slope_distance,
  intercept_distance = intercept_distance
)
future::plan(future::sequential)

## -----------------------------------------------------------------------------

str(results$weighted_moments)
str(results$statistics_per_observation)
moments_graph <- TAD::moments_graph(
  moments_df = results$weighted_moments,
  statistics_per_observation = results$statistics_per_observation,
  statistics_factor_name = statistics_factor_name,
  statistics_factor_name_breaks = c("Mown_Unfertilized", "Mown_NPK"),
  statistics_factor_name_col = c("#1A85FF", "#D41159")
)
moments_graph

## -----------------------------------------------------------------------------
str(results$weighted_moments)
skr_graph <- TAD::skr_graph(
  moments_df = results$weighted_moments,
  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
)
skr_graph

## -----------------------------------------------------------------------------
str(results$ses_skr)
skr_param_graph <- TAD::skr_param_graph(
  skr_param = results$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
)
skr_param_graph

## -----------------------------------------------------------------------------

results <- TAD::launch_analysis_tad(
  weights = weights,
  weights_factor = weights_factor,
  trait_data = trait_data,
  randomization_number = randomization_number,
  aggregation_factor_name = aggregation_factor_name,
  statistics_factor_name = statistics_factor_name,
  seed = seed,
  regenerate_abundance_df = TRUE,
  regenerate_weighted_moments_df = TRUE,
  regenerate_stat_per_obs_df = TRUE,
  regenerate_stat_per_rand_df = TRUE,
  regenerate_stat_skr_df = TRUE,
  significativity_threshold = significativity_threshold,
  lin_mod = lin_mod,
  slope_distance = slope_distance,
  intercept_distance = (intercept_distance <- 1.90)
)
str(results$ses_skr)
skr_param_graph <- TAD::skr_param_graph(
  skr_param = results$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 = 1,
  intercept_distance = intercept_distance
)
skr_param_graph