Make a description for an ecosystem

make_eco_desc(
  bio_df,
  bio_wide,
  clust_df,
  ind_val_df = NULL,
  context,
  clust_col = "cluster",
  taxa_col = "taxa",
  cov_col = "cover_adj",
  ind_abu_col = "use_cover",
  str_col = "lifeform",
  lustr,
  taxonomy,
  use_prop_thresh = 0.8,
  use_p_val = 0.05,
  n_ind_max = 3,
  ind_val_iter = 3000,
  wt_ht_quant = 0.5,
  sites_sf_quant = 0.75,
  ht_sf_quant = 0.5,
  sites_sf_taxa_quant = 0.95
)

Arguments

bio_df: Dataframe containing the site and taxa data in long format.
bio_wide: Wide version of bio_df.
clust_df: Dataframe with context column(s) and a column with cluster membership for that context. Optional if clust_col appears in bio_df.
ind_val_df: Result from envCluster::make_ind_val_df(). If not provided it will be made from the other provided dfs (which is slow).
context: Character. Name(s) of column(s) that define the context.
clust_col: Character. Name of column containing cluster membership.
taxa_col: Character. Name of column containing the taxa names.
cov_col: Character. Name of column containing numeric abundance data ( usually 'cover' for plants).
ind_abu_col: Character. Name of column containing numeric abundance data for use in indicator analysis (labdsv::indval()). This can be the same as cov_col but at times a different measure of abundance is helpful here.
str_col: Character name of column in bio_df containing lifeform (or structural) information.
lustr: Dataframe containing lifeform (structural) information.
taxonomy: Dataframe containing indigenous status of taxa in bio_df
use_prop_thresh: Numeric. Threshold (proportion) for taxa to include in description. Taxa that occur in more than use_prop_thresh proportion of sites in the cluster will be included in the description.
use_p_val: Numeric 0 to 1. The p-value to use to accept a taxa as an indicator for an ecosystem.
n_ind_max: Maximum number of taxa to list as indicators.
ind_val_iter: Passed to the ... argument of envCluster::make_ind_val_df(), and then into the numitr argument of labdsv::indval().
wt_ht_quant: Numeric. Threshold (quantile) of weighted heights per site that are allowed through to further definition analysis.
sites_sf_quant: Numeric. Threshold (quantile) of counts above which to select structural features for the description.
ht_sf_quant: Numeric. Threshold (quantile) of heights above which to select structural features for the description.
sites_sf_taxa_quant: Numeric. Threshold (quantile) of counts above which a taxa will be used as an example of a structural feature.