Generate a Pie Chart of Observations by Species or Complex

Creates an interactive pie chart showing the distribution of observations by species or species complexes, based on a specified observation variable from a pre-processed dataset. Optionally groups species with a small proportion of observations into an "Other" category, and can save the plot as an HTML file for sharing or embedding.

Usage

obs_complex_species_pie(data, threshold_prop_other = 0.05, plot_dir = NULL)

Arguments

data

A list containing the following elements: - `data.req`: A data frame with observation data. Must contain a column named with the pattern `<varname>.den` (e.g., `"parous_rate.den"`). - `varname`: A character string indicating the base name of the observation variable. - `nice_varname`: A character string used for naming the saved output file.

threshold_prop_other

A numeric value between 0 and 1 indicating the minimum proportion of total observations required for a species or complex to appear as its own slice in the pie chart. Species below this threshold are grouped under "Other". Default is 0.05 (5 percent).

plot_dir

Optional. A character string giving the directory path where the HTML version of the pie chart should be saved. If `NULL`, the chart is not saved. Default is a specific folder on the user's system.

Value

A list containing: - `plotly`: An interactive pie chart showing the distribution of observations. - `HTML file`: If `plot_dir` is provided, the chart is also saved as an HTML file.

Details

- Species names starting with `"unlabel_"` are treated as complexes and labeled accordingly. - The observation variable used in the calculation must match the pattern `<varname>.den`. - The pie chart uses **plotly** for interactive visualization and **htmlwidgets** to export.