Skip to contents

Plot Benthic Cover Dynamics

plot_synthos.Rd

Generate Benthic Cover Trajectory or Heatmap Plots

Usage

plot_synthos(synthos_data, type = "")

Arguments

synthos_data

A data frame containing benthic survey observations. Required variables depend on data_type:

  • survey_depth – depth category

  • project_name – project identifier

  • site_name – site name (e.g., "Reef10 Site 1")

  • survey_start_date – survey timestamp

  • point_machine_classification – benthic class (HCC, SC, MA, etc.) used when data_type = "points"

  • cover – numeric benthic cover values used when data_type = "cover"

type

A character string specifying the type of plot to generate:

  • "trajectories" – time‐series plots (uses plot_group())

  • "heatmaps" – benthic cover heatmaps (uses plot_map())

data_type

A character string indicating the structure of input data:

  • "points" – raw point-based benthic classifications

  • "cover" – pre-aggregated benthic cover values

Value

A named list of ggplot objects, where each plot corresponds to a unique combination of depth and benthic classification group. The resulting list can be visualised directly or iterated over using purrr::walk().

Details

Produces a set of plots showing temporal patterns in benthic cover across survey depths and benthic classification groups. The function supports two data formats: point-level benthic classifications ("points") and aggregated benthic cover values ("cover"). Depending on the type argument, the output is either a series of time‐series trajectory plots or benthic‐cover heatmaps.

Based on data_type, the function:

  • aggregates point classifications into benthic cover proportions; or

  • averages numeric benthic cover values

Afterwards, it:

  • extracts year, reef, and site identifiers

  • splits the dataset by survey depth and classification

  • passes each subset to either plot_group() or plot_map()

  • returns all plots as a list

See also

plot_group(), plot_map()

Author

Julie