Data Retrieval

Functions to download and update data

download_observations()

Download the PortalData repo

check_for_newer_data()

Check for latest version of data files

get_data_versions()

get version and download info for PortalData

check_default_data_path() get_default_data_path() use_default_data_path()

Manage the default path for downloading Portal Data into

Data Summaries

Functions to return data summaries

summarize_rodent_data() abundance() biomass() energy() summarise_rodent_data()

Generate summaries of Portal rodent data

summarize_plant_data() plant_abundance() summarise_plant_data()

Generate summaries of Portal plant data

summarize_individual_rodents() summarise_individual_rodents()

Return cleaned Portal rodent individual data

make_timeseries()

Makes a standardized monthly time series for Portal rodents

ndvi()

NDVI by calendar month or lunar month

weather()

Weather by day, calendar month, or lunar month

bait_presence_absence()

Ant Bait Presence Absence

colony_presence_absence()

Ant Colony Presence Absence

shrub_cover()

Generate percent cover from Portal plant transect data

fcast_ndvi()

Forecast ndvi using a seasonal auto ARIMA

get_future_moons()

Get future moon dates

Unprocessed Data

Functions to load in raw or otherwise unprocessed data

load_datafile()

read in a raw datafile from the downloaded data or the GitHub repo

load_rodent_data() load_plant_data() load_ant_data() load_trapping_data()

Read in the Portal data files

Data Processing

Functions to do various data processing steps

add_seasons() yearly()

Add Seasons

clean_plant_data()

Do basic cleaning of Portal plant data

clean_rodent_data()

Do basic cleaning of Portal rodent data

fill_missing_ndvi()

Fill in historic ndvi data to the complete timeseries being fit

find_incomplete_censuses()

Period code for incomplete censuses