Man pages for weecology/portalPredictionsModels
Functions Used in Predicting Portal Rodent Dynamics

add_date_from_componentsAdd a date to a table that has the year month and day as...
add_moons_from_dateAdd a newmoon number to a table that has the date
add_to_cast_tabAdd the associated values to a cast tab
alternative_valuesReplace a value with an alternative if it is NULL or if it is...
append_csvSave data out to a csv, appending the file if it already...
argument_checkingCheck a function's arguments' values for validity
cast_covariatesCast the covariates
cast_windowDetermine the start and end calendar dates for a cast window
clear_tmpRemove files from the tmp subdirectory
combine_hist_and_castCombine a historical table and a cast table
covariate_modelsCreate a covariate model list
directory_configCreate, update, and read the directory configuration file
directory_creationCreate the structure of a forecasting directory
downloadDownload raw components of a portalcasting directory
download_climate_castsDownload and read covariate casts (presently only the NMME)
ensemble_castsCombine (ensemble) casts
error_if_deepError if a function's request is deeper than can be handled
file_extDetermine a file's extension or remove the extension from the...
files_controlCreate a control list for files
fill_directoryFill a forecasting directory with basic components.
foyCalculate the fraction of the year from a date
jags_ssRun a single-species JAGS model
lag_covariatesLag covariate data
last_censusDetermine the most recent data collection
list_depthDetermine the depth of a list
match.call.defaultsArgument matching with defaults
measure_cast_level_errorMeasure error/fit metrics for forecasts
messageqOptionally generate a message based on a logical input
messageq_breakProduce a horizontal break line for messaging
model_controlCreate a control list for a model
model_controlsProduce the control lists for models
models_to_castDetermine the paths to the scripts for models to cast with
most_abundant_speciesSelect the most abundant species from a data set
na_conformerConform NA entries to "NA" entries
named_null_listCreate a named empty list
name_from_urlAttempt to extract the record name from a URL
NMME_urlsProvide URLs for the Northwest Knowledge Network's North...
pathsDetermine the path for a specific level of a forecasting...
plot_cast_pointPlot predictions for a given point in time across multiple...
plot_casts_cov_RMSEPlot the forecast coverage and RMSE
plot_casts_err_leadPlot the forecast error as a function of lead time
plot_cast_tsVisualize a time series cast of a species
portalcastCast Portal rodents models
portalcastingFunctions for Portal -casting (Forecasting and Hindcasting)
portalcast_messagesSpecific message functions
prefab_data_setsProvide the names of the prefab data sets
prefab_model_functionsFunctions for the prefab portalcasting models
prefab_modelsProvide the names of the prefab models
prepare_historical_covariatesPrepare historical covariates data
prepare_moonsPrepare lunar data for the portalcasting repository
prepare_rodents_tablePrepare a rodents data tables for forecasting
prep_covariatesPrepare covariate data for casting
prep_metadataPrepare a model-running metadata list
prep_rodentsPrepare a list of rodents data tables for forecasting
read_cast_outputRead in cast output from a given cast
read_casts_metadataRead in the casts metadata file
read_dataRead in a data file and format it for specific class
remove_incompletesRemove any specific incomplete entries as noted by an NA
return_if_nullIf a value is NULL, trigger the parent function's return
rodents_controlCreate a control lists for generating a rodents data table
rodents_controlsCreate control lists for generating rodents data tables
rodent_speciesRodent species abbreviations
runjags_controlCreate a control list for a runjags JAGS model run
save_cast_outputSave cast output to files
select_castsFind casts that fit specifications
setup_dirCreate and fill a forecasting directory
species_in_tablesDetermine if columns in a table are species columns
summarize_daily_weather_by_moonSummarize a daily weather table by newmoons
target_moonsDetermine specific newmoon numbers
trim_moonsTrim a moons table based on target moons
update_listUpdate a list's elements
update_modelsUpdate models based on user input controls
verify_and_createVerify that folders exist and create folders
verify_modelsVerify that models requested to cast with exist
verify_raw_dataVerify that the raw data folder exists
write_dataSave data out to a file and return it
write_modelWrite the template for a model into model subdirectory
zenodo_downloadsCreate a downloads list for zenodo downloads
zenodo_urlObtain the URL for a Zenodo record to be downloaded
weecology/portalPredictionsModels documentation built on Nov. 6, 2019, 1:10 p.m.