transect_summary {fqacalc}

Print a Summary of Cover-Weighted FQA Metrics

Description

transect_summary calculates and prints a summary of both inventory metrics and cover-weighted metrics, including Species Richness, Native Species Richness, Introduced Species Richness, % of species within C value ranges, Mean C, Native Mean C, Cover-weighted Mean C, Native Cover-Weighted Mean C, Total FQI, Native FQI, Cover-Weighted FQI, Native Cover-weighted FQI, Adjusted FQI, Mean Wetness, Native Mean Wetness and % Hydrophytes. Cover-weighted metrics allow duplicate entries for transect level summary metrics.

Usage

transect_summary(
  x,
  key = "name",
  db,
  cover_class = "percent_cover",
  allow_no_c = TRUE,
  plot_id = NULL
)

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.

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.

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.

Value

A data frame

Examples

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))

transect_summary(x = transect, key = "acronym", db = "michigan_2014",
plot_id = "plot_id")