accepted_entries {fqacalc}

Return A Data Frame of Plant Species That Successfully Match to the Regional FQA Database of choice

Description

accepted_entries takes a data frame of user-entered plant species and returns a data frame of plant species that are successfully matched to the regional FQA database of choice. Regional databases are stored in the fqadata R package. accepted_entries is a utility function that is used in all other metric-calculating functions in this package.

Usage

accepted_entries(
  x,
  key = "name",
  db,
  native = c(TRUE, FALSE),
  wetland_warning = TRUE,
  cover_weighted = FALSE,
  cover_class = "percent_cover",
  allow_duplicates = FALSE,
  allow_no_c = FALSE,
  allow_non_veg = FALSE,
  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.

native

Boolean (TRUE or FALSE). If TRUE, calculate metrics using only native species.

wetland_warning

Boolean (TRUE or FALSE). If TRUE, show user messages regarding issues with wetness coefficients.

cover_weighted

Boolean (TRUE or FALSE). If TRUE, keep cover column in output. Note: if cover_weighted = TRUE, x must have a column named cover. This parameter is used to calculate cover-weighted metrics such as plot mean c, transect mean c, and cover-weighted FQI.

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_duplicates

Boolean (TRUE or FALSE). If TRUE, allow x to have duplicate observations for the same species. This is only recommended for calculating transect and relative frequency/abundance metrics. For non cover-weighted (inventory) assessments allow_duplicates is always FALSE. For cover-weighted functions, allow_duplicates can be set to TRUE for transect level metrics or FALSE for plot level metrics.

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 containing the key column–either acronym or name–as well as columns from the relevant FQA database. These columns include name_origin accepted_name, family, nativity, c (which represents the C Value), w (which represents wetness score), physiognomy, duration, and common_name

Examples

plant_list <- crooked_island

#with native and introduced species
accepted_entries(x = plant_list, key = "acronym", db = "michigan_2014", native = FALSE)

#with only native species
accepted_entries(x = plant_list, key = "acronym", db = "michigan_2014", native = TRUE)

#an example with duplicates allowed
duplicate_df <- data.frame(acronym  = c("ABEESC", "ABIBAL", "ABIBAL"),
cover = c(60, 50, 50))

accepted_entries(x = duplicate_df, key = "acronym",
db = "michigan_2014", native = FALSE, allow_duplicates = TRUE)

#an example of duplicates not allowed
accepted_entries(x = duplicate_df, key = "acronym",
db = "michigan_2014", native = FALSE, allow_duplicates = FALSE)

#an example of duplicates not allowed, adding cover values
accepted_entries(x = duplicate_df, key = "acronym",
db = "michigan_2014", native = FALSE, allow_duplicates = FALSE,
cover_weighted = TRUE)

#an example where some entries are synonyms shared by more than one species
same_syn <- data.frame(name = c("CAREX MURICATA", "POTENTILLA NANA", "ABIES BIFOLIA"),
cover = c(80, 60, 10))

#produces a warning saying CAREX MURICATA is a synonym to multiple species and will be omitted.
#To include this species, use the accepted scientific name.
accepted_entries(x = same_syn, key = "name",
db = "wyoming_2017", native = FALSE)

#an example where species is both a synonym and an accepted name
same_syn2 <- data.frame(name = c("CAREX FOENEA", "ABIES BIFOLIA"),
cover = c(80, 10))

#produces a warning saying CAREX FOENEA is an accepted scientific name and a synonym.
#It will default to accepted scientific name.
accepted_entries(x = same_syn2, key = "name",
db = "wyoming_2017", native = FALSE)