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