shrub_cover {portalr}

Generate percent cover from Portal plant transect data

Description

This function calculates percent cover from transect data. It handles the pre-2015 data differently from the current transects, becase they are collected differently. But it returns a single time-series with all years of transect data available. It also returns mean height beginning in 2015.

Usage

shrub_cover(
  path = get_default_data_path(),
  type = "Shrubs",
  plots = "all",
  unknowns = FALSE,
  correct_sp = TRUE,
  download_if_missing = TRUE,
  quiet = FALSE
)

Arguments

path

either the file path that contains the PortalData folder or "repo", which then pulls data from the PortalData GitHub repository

type

specify subset of species; If type=Annuals, removes all non-annual species. If type=Summer Annuals, returns all annual species that can be found in the summer If type=Winter Annuals, returns all annual species that can be found in the winter If type=Non-woody, removes shrub and subshrub species If type=Perennials, returns all perennial species (includes shrubs and subshrubs) If type=Shrubs, returns only shrubs and subshrubs

plots

specify subset of plots; can be a vector of plots, or specific sets: "all" plots or "Longterm" plots (plots that have had the same treatment for the entire time series)

unknowns

either removes all individuals not identified to species (unknowns = FALSE) or sums them in an additional column (unknowns = TRUE)

correct_sp

correct species names suspected to be incorrect in early data (T/F)

download_if_missing

if the specified file path doesn't have the PortalData folder, then download it

quiet

logical, whether to run without version messages

Value

a data.frame of percent cover and mean height