Generate best guess of cover for each taxa*context

add_cover(
  df,
  context = "cell",
  env_prcomp,
  lucover,
  lucover_col = "cover_mid",
  small_cov = 0.009,
  remove_all_small = TRUE,
  fix_1to100 = TRUE,
  cov_func = median
)

Arguments

df: Dataframe with context, taxa and cover columns.
context: Character. Name of columns defining context.
env_prcomp: List. Result from call to envClean::env_pca()
lucover: Dataframe. Lookup from cover_code to numeric cover values
lucover_col: Character. Name of column in lucover containing cover values to use for any cover_code
small_cov: A small cover value assigned to any record for which there is no available site, pca or taxa cover value.
remove_all_small: Logical. If TRUE (default) context(s) where all taxa are assigned small_cov are removed.
fix_1to100: Logical. Any values found in cover field of df that are between above 1 and less than or equal to 100 are divided by 100.
cov_func: Function to summarise cover values for any context with more than one cover value.

Value

Dataframe with taxa, context and the following 'cover' columns: cover_adj a best guess proportion cover; use_cover_code the cover_code values from lucover that correspond to the best guess value; use_cover the lucover_col column that corresponds to the best guess value.