Appendix A — Function Reference

A compact list of the functions coenosr exports, grouped by the stage of the workflow. Every reader returns the same coenos_rel table, so the analysis and display functions accept the output of any of them.

A.1 Reading data in

read_rel(path, encoding = "latin1")

Read a COENOS .REL file. path is the file; encoding is passed to readLines() (the bundled data is "latin1").

read_lists(path, present = "1", encoding = "latin1")

Read the ragged “site, then its species” form. present is the cover value given to a species listed without one (default "1", matching the 1 of a presence/absence table).

read_2way(path, absent = c("0", "", "NA"), transpose = FALSE, encoding = "latin1", ...)

Read a wide species-by-sites matrix. absent lists the cell values read as absence; set transpose = TRUE if your rows are sites and columns are species. Further arguments pass to read.csv().

A.2 Analysis

constancy(rel, sort = TRUE)

Count the relevés each species occupies. sort = TRUE (the default) returns them most-frequent first.

classify_species(rel)

Split the species by constancy into rare (fewer than 3 relevés), ubiquitous (two-thirds or more of the relevés), and the eligible middle — the candidates from which groups are formed.

form_groups(rel, x = 0.5, y = 0.2, min_species = 4, min_releves = 2)

Find the differential species groups among the eligible species. x is the inside threshold (a species’ minimum within-block density) and y the outside threshold (the most outside relevés a group species may occupy); the default 0.5/0.2 is the 50/20 level. min_species and min_releves set the smallest group reported.

coenos_table(x, cover = TRUE, reflect = FALSE)

Arrange the sorted two-way table from the groups. cover = TRUE fills cells with the recorded cover value, FALSE with "x" for presence; reflect flips the ordering left-to-right.

A.3 Display

differential_table(x, include = "core")

Pull the sorted table out as a plain data frame. include = "core" (the default) gives the grouped species and their relevés; "full" gives the whole sorted table.

coenos_gt(x, include = "core", shorten = TRUE, title = NULL, subtitle = NULL)

Render the table with gt, the groups drawn as labelled sections. shorten abbreviates the relevé headers; title and subtitle add optional header text.