make_clusters_explore: Explore clusters
In Acanthiza/envCluster: Create Clusters From Records of Taxa

make_clusters_explore

R Documentation

Explore clusters

Description

Deprecated. Use individual make_ functions.

Usage

make_clusters_explore(
  clusters_df,
  n_sample = 10,
  cores = 1,
  save_results = TRUE,
  do_env = TRUE,
  do_ind = TRUE,
  out_exp = tempdir(),
  exp_type = "cluster",
  do_gc = FALSE,
  obj_list
)

Arguments

`clusters_df`	Dataframe with column 'clusters'.
`n_sample`	Number of samples to use to calculate gap statistic.
`cores`	How many cores to use in `multidplyr::new_cluster()`?
`save_results`	Logical. If true, results will be saved along the way. If the file already exists, that result will not be recreated.
`do_env`	Logical. Run make env silhouette, wss and gap.
`do_ind`	Logical. Make
`out_exp`	Directory into which results are saved.
`exp_type`	Name to prefix files with and appended to `out_exp`.
`do_gc`	Run `gc()` after each output to save memory across `cores`.
`obj_list`	List of objects required: dist_bio `dist(bio_wide)`. dist_env `dist(env_wide)`. bio_wide Wide version of bio_tidy. bio_tidy Cleaned data set of taxa observations. visit_cols context. p_thresh usually 0.05. n_sites How many unique contexts in `bio_tidy`. most_freq_prop_thresh Threshold for proportion of sites in a cluster that must all contain at least one taxa in common.

Details

Explore clusters using silhouette width, within-group sum-of-squares, indicators and widespread taxa.

Value

Each output saved along the way to out_exp. Outputs are not made if they have already been saved. Created outputs returned in list with elements:

clusters_sil: biota result from make_sil_df().
clusters_wss: biota result from calc_wss().
clusters_sil_env: env result from make_sil_df().
clusters_wss_env: env result from calc_wss().
clusters_ind_val: indicator values for biota from make_ind_val_df(), clusters_with_indicator() and sites_with_indicator().
clusters_freq: biota results from clusters_with_freq_taxa() and sites_with_freq_taxa()