colony_presence_absence {portalr}

Ant Colony Presence Absence

Description

Get ant species presence/absence by year/plot/stake from colony census data

Anomalies in ant colony census protocol over the years means that it can be difficult to discern true absences of all species in all years. This function uses information from Portal_ant_species.csv and Portal_ant_dataflags.csv to predict true presence/absence of species per plot per year. If a more conservative estimate is desired, setting the argument 'rare_sp = T' will only include species we are confident were censused regularly. Setting 'rare_sp = F' may include some false absences, since it is unknown if some rare species were censused in all years. Unknowns may also be excluded from output if desired.

Usage

colony_presence_absence(
  path = get_default_data_path(),
  level = "Site",
  rare_sp = FALSE,
  unknowns = FALSE,
  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

level

level at which to summarize data: 'Site', 'Plot', or 'Stake'

rare_sp

include rare species (T) or not (F). Rare species may or may not have been censused in all years. Setting 'rare_sp = FALSE' gives a more conservative estimate of presence/absence

unknowns

include unknown species (TRUE) or not (FALSE). Unknowns include those only identified to genus.

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

data frame with year, species, (plot if applicable), and presence [1, 0, NA]