physiog_summary {fqacalc}

Create a cover-Weighted Summary of Physiognomic Groups

Description

physiog_summary produces a table summarizing physiognomic groups' frequency, total cover, relative frequency, relative cover, and relative importance. Physiognomic groups include shrub, tree, forb, sedge, grass, rush, fern, vine, and bryophyte. If the regional database does not have information on species physiognomy, the function will return a data frame with a single NA category.

Usage

physiog_summary(
  x,
  key = "name",
  db,
  cover_class = "percent_cover",
  allow_no_c = TRUE,
  allow_non_veg = 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.

allow_non_veg

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

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 where each row is a physiognomic group and each column is a metric about that species based on the input 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))

physiog_summary(transect, key = "acronym", db = "michigan_2014", plot_id = "plot_id")


#can also include bare ground and unvegetated water
transect_unveg <- data.frame(acronym  = c("GROUND", "ABEESC", "ABIBAL", "AMMBRE",
"ANTELE", "WATER", "GROUND", "ABEESC", "ABIBAL", "AMMBRE"),
cover = c(60, 50, 4, 20, 30, 20, 20, 40, 7, 60),
plot_id = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2))

physiog_summary(transect_unveg, key = "acronym", db = "michigan_2014",
plot_id = "plot_id")