
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.
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
)
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
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.
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
.
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.
Boolean (TRUE or FALSE). If TRUE, calculate metrics using only native species.
Boolean (TRUE or FALSE). If TRUE, show user messages regarding issues with wetness coefficients.
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.
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.
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.
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.
Boolean (TRUE or FALSE). If TRUE, allow input to contain un-vegetated ground and un-vegetated water.
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.
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)
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