fqacalc (version 1.1.1)

plot_summary: Calculate Plot-level Summary Statistics

Description

Input a transect with one or more plots (designated with a unique plot ID) as a single data frame and the output will be a data frame with plot-level species richness, native species richness, mean c, native mean c, FQI, native FQI, adjusted FQI, cover-weighted FQI, and native cover-weighted FQI.

Usage

plot_summary(
  x,
  key = "name",
  db,
  cover_class = "percent_cover",
  plot_id,
  allow_no_c = TRUE,
  allow_non_veg = TRUE
)

Value

A data frame where each row is a plot and columns contain FQI and cover-weighted FQI statistics.

Arguments

x

A data frame containing a list of plant species. This data frame must have one of the following columns: name or acronym. For cover-weighted or relative functions, this data frame must also have a column called cover containing cover values and ideally a column containing plot IDs.

key

A character string representing the column that will be used to join the input data frame x with the regional FQA database. If a value is not specified, the default is "name". "name" and "acronym" are the only acceptable values for key.

db

A character string representing the regional FQA database to use. See db_names for a list of potential values and the fqadata R package where the databases are hosted.

cover_class

a character string representing the cover classification used. Acceptable cover classes are: "percent_cover", "carolina_veg_survey", "braun-blanquet", "daubenmire", and "usfs_ecodata". "percent_cover" is the default.

plot_id

A character string representing the column in x that contains plot identification values. plot_id is a required argument in plot_summary, where it acts as a grouping variable. plot_id is optional but highly recommended for cover-weighted functions and relative functions. If plot_id is set in a cover-weighted function or a relative function, it only prevents duplicates from occurring in the same plot. It does not act as a grouping variable.

allow_no_c

Boolean (TRUE or FALSE). If TRUE, allow species that are found in the regional FQA database but have not been assigned a C Values. If FALSE, omit species that have not been assigned C Values.

allow_non_veg

Boolean (TRUE or FALSE). If TRUE, allow input to contain un-vegetated ground and un-vegetated water.

Examples

transect <- transect <- data.frame(
acronym  = c("ABEESC", "ABIBAL", "AMMBRE", "ANTELE", "ABEESC", "ABIBAL", "AMMBRE"),
cover = c(50, 4, 20, 30, 40, 7, 60),
plot_id = c(1, 1, 1, 1, 2, 2, 2))

plot_summary(transect, key = "acronym", db = "michigan_2014",
cover_class = "percent_cover", plot_id = "plot_id")