species: Gather species attribute data

In smccord/terradactyl: Tools for Creating and Using TerrADat

Gather species attribute data

Description

Gather species attributes and join to species observations.

Quality control species attribute lists prior to running indicator calculations.

Usage

gather_species(
  species_file,
  species_growth_habit_code = "GrowthHabitSub",
  growth_habit_file = "",
  growth_habit_code = "Code"
)

generic_growth_habits(
  data,
  data_code = "code",
  species_list,
  species_code = "SpeciesCode",
  species_growth_habit_code = "GrowthHabitSub",
  species_duration = "Duration"
)

species_join(
  data,
  data_code = "code",
  species_file,
  species_code = "SpeciesCode",
  species_growth_habit_code = "GrowthHabitSub",
  species_duration = "Duration",
  growth_habit_file = "",
  growth_habit_code = "Code",
  overwrite_generic_species = FALSE,
  generic_species_file = "",
  by_species_key = TRUE
)

species_list_check(dsn_tall, species_list_file, ...)

species_list_compare(species_file, folder)

Arguments

species_file	Character string. The full file path (including file extension) to the file containing the species list OR the species list as a data frame.
species_growth_habit_code	Character. The field name for the growth habit codes in the species file. Defaults to "GrowthHabitSub"
growth_habit_file	Character string. The full file path (including file extension) to the file containing the growth habit list. If "" we assume the species list contains those values. Defaults to "".
growth_habit_code	Character. The field name for the growth habit codes in the growth habit file. Defaults to "Code"
data	Dataframe containing species data
data_code	Character. The field name with the species codes in the data.
species_list	Dataframe. Species list output from
species_code	Character. The field name for the species codes in the species file.
species_duration	Character. the field name for the Duration field in the species file.
generic_species_file	Character. The full file path (including file extension)to the file containing the species list.
by_species_key	Logical. If TRUE then the join will attempt to use the variable "SpeciesState" if it exists. Defaults to TRUE.
dsn_tall	The observed data data source
species_list_file	The file path to the species list. If the dsn contains the species list, then specify the layer within the dsn.

smccord/terradactyl documentation built on Dec. 1, 2023, 7:37 p.m.