Distribution of credible values for taxa richness.

Model the effect of between 0 and 2 categorical variables on taxa richness within a context. Highlight, based on thresholds, contexts where taxa richness is 'excessively' high or low.

make_effort_mod(
  df,
  context = "cell",
  cat_cols = NULL,
  threshold_lo = 0.05/2,
  threshold_hi = 0.05/2,
  use_family = rstanarm::neg_binomial_2(),
  ...
)

Arguments

df: Dataframe. Cleaned data specifying context.
context: Character. Column names that define context, usually a 'visit' to a 'cell'.
cat_cols: Character. Name of column(s) (0 to 2) specifying the categorical variables to model. Usually a taxonomic level (say, class) and a geographic level (say, IBRA Region). If NULL (default), model is y ~ 1.
threshold_lo, threshold_hi: Numeric between 0 and 1 specifying the threshold above/below which richness is excessively above or below 'normal' and should be filtered.
use_family: Passed to rstanarm::stan_glm family argument.
...: Other arguments passed to rstanarm::stan_glm (e.g. chains, iter).

Value

List of model outputs:

dat_exp: dataframe of data used in pre-model data exploration
mod: model object
mod_pred: dataframe resulting from rstanarm::posterior_predict
mod_resid: dataframe of residuals
mod_resid_plot: plot of residuals (ggplot object)
mod_res: dataframe of summarised mod_pred results
mod_plot: plot of distribution of credible values, faceted by any variables in the model
mod_cell_result: dataframe of all contexts with column keep indicating whether the context is outside acceptable taxa richness
mod_cell_tab: dataframe tabulating how many contexts were above and below the acceptable richness quantile thresholds