Cluster points into sites based on geographical attributes and additional extracted point values.

From a dataframe of points and point data, this function clusters points into sites (within each habitat type), using a user defined clustering method that considers both geographical data and additional extracted data (such as depth).

Usage

cluster_reef_points(
  points,
  habitat_col = "habitat",
  x_col = "X",
  y_col = "Y",
  additional_variable_cols = c("depth"),
  reef_id_col = "UNIQUE_ID",
  habitat_clustering_function = reef_skater_fast,
  clustering_function_args = list()
)

Arguments

points

data.frame. Contains a row for each point and values for each variable to be input into habitat_clustering_function.

habitat_col

character or integer. Column containing the categorical habitat allocations of points. Default = "habitat".

x_col

character or integer. Column containing the continuous geographical X values for points. Default = "X".

y_col

character or integer. Column containing the continuous geographical Y values for points. Default = "Y".

additional_variable_cols

character vector. Vector containing column names for columns with additional clustering variable values. This vector can have length > 1. Values will be standardised and output as *variable*_standard. Default = c("Depth").

reef_id_col

character or integer. Column containing the single unique reef ID to be assigned as an identifier before outputting cluster allocations. Default = "UNIQUE_ID".

habitat_clustering_function

function. A function that takes a dataframe of points for a single habitat type as the first argument and additional arguments, and returns a dataframe of input points with an additional column containing assigned site_id values. Additional arguments must include px_per_cluster, habitat_col, x_col, y_col and additional_variable_cols. Default options available include reef_skater and constrained_hclust.

clustering_function_args

named list. A named list where elements of the list are arguments that will be passed on to habitat_clustering_function. Defaults to an empty list default arguments of habitat_clustering_function are used.

Value

data.frame containing points that have a site ID allocated in site_id column. Output data includes clustering execution time.