getSpeciesTable: Get Table For Species

Description

Allows users to create a custom table for vector species. The invasive species count, trap nights, and abundance are calculated by chosen groupings or time intervals. The table has output options based on document format.

Usage

getSpeciesTable(
  token,
  interval,
  target_year,
  cumulative = FALSE,
  include_trap_nights = TRUE,
  include_abundance = FALSE,
  species = NULL,
  trap = NULL,
  sex = "female",
  separate_by = NULL,
  output_format = "auto",
  caption = NULL,
  agency_id = NULL
)

Value

A table displaying invasive species interval or/and cumulative counts over time

Arguments

token: Authentication token for API access, obtained from `getToken()`
interval: Time interval for aggregation. One of: "CollectionDate", "Week", "Biweek", "Month"
target_year: The focal year to highlight in the plot (integer)
cumulative: T/F Adds columns for the cumulative sum count Default to FALSE
include_trap_nights: T/F Adds column for the tally of trap nights
include_abundance: T/F Adds column for abundance (non-cumulative only)
species: Character vector for filtering species. View species in your data `unique(data$species_display_name)`. Defaults to all species if no selection
trap: Character vector for filtering trap type by acronym. View trap types in your data`unique(data$trap_acronym`. Defaults to all trap types
sex: Character vector for filtering sex type. View sex options `unique(data$sex_type`). Defaults to "female".
separate_by: Adds a column from the data as a grouping variable. Accepts 'site', 'city', 'county', 'agency', 'trap', 'spatial'
output_format: Format to output table display. Accepts 'html', 'pdf', 'word' or 'auto'. Default auto returns the console format dataframe.
caption: Caption for table
agency_id: Agency identifier to filter data if applicable