Create a Directory Settings List

Compose parts of and complete directory settings controls lists.

Most users will not want or need to change the directory folders and file names, but it is helpful to have them be flexible for certain circumstances, and directory_files, directory_subdirectories, and directory_settings gather them into a set of lists for pipeline functionality.
directory_resources dictates the source and version (and any other specialized arguments) for each of the raw resources collected for the directory.
time_settings collates the temporal aspects of the data, and can be used to set up alternate forecast timelines for specialized projects and sandboxing.

Usage

directory_settings(
  files = directory_files(),
  subdirectories = directory_subdirectories(),
  resources = directory_resources(),
  time = time_settings(),
  confidence_level = 0.95,
  nsamples = 10000,
  save = TRUE,
  overwrite = TRUE,
  force = FALSE,
  unzip_pause = 30,
  download_timeout = getOption("timeout")
)

time_settings(
  timeseries_start = as.Date("1995-01-01"),
  origin = Sys.Date(),
  forecast_date = Sys.Date(),
  lead_time = 365,
  max_lag = 365,
  lag_buffer = 60,
  lead_time_buffer = 30
)

directory_files(
  directory_configuration = "directory_configuration.yaml",
  app = "app.R",
  newmoons = "newmoons.csv",
  covariates = "covariates.csv",
  datasets_controls = "datasets_controls.yaml",
  models_controls = "models_controls.yaml",
  forecasts_evaluations = "forecasts_evaluations.csv",
  forecasts_results = "forecasts_results.csv",
  forecasts_metadata = "forecasts_metadata.csv",
  metadata = "metadata.yaml",
  about_md = "about.md",
  models_html = "models.html",
  models_rmd = "models.Rmd",
  rodents_profiles_html = "rodents_profiles.html",
  rodents_profiles_csv = "rodents_profiles.csv",
  species_names = "species_names.csv"
)

directory_subdirectories(
  forecasts = "forecasts",
  fits = "fits",
  models = "models",
  resources = "resources",
  data = "data",
  www = "www"
)

directory_resources(
  PortalData = list(source = "github", version = "latest"),
  portalPredictions = list(source = "github", version = NULL),
  climate_forecasts = list(source = "NMME", version = as.character(Sys.Date()), data =
    list(mintemp = "tasmin", meantemp = "tasmean", maxtemp = "tasmax", precipitation =
    "pr"))
)

production_settings(download_timeout = max(getOption("timeout"), 600))

sandbox_settings()

Arguments

files: list of character names of standard files, see directory_files.
subdirectories: list of character names of standard subdirectories, see directory_subdirectories.
resources: character name for the resources subdirectory.
time: list of time settings, see time_settings.
confidence_level: numeric confidence level used in summarizing model output. Must be between 0 and 1.
nsamples: integer (or integer numeric) number of samples used to summarizing model output of sample-based estimates.
save: logical indicator controlling if the output should be saved out.
overwrite: logical indicator of whether or not file writing should occur even if a local copy already exists.
force: logical indicator of whether or not existing files or folders (such as the archive) should be over-written if an up-to-date copy exists (most users should leave as FALSE).
unzip_pause: Positive integer or integer numeric seconds for pausing during steps around unzipping that require time delay.
download_timeout: Positive integer or integer numeric seconds for timeout on downloads. Temporarily overrides the "timeout" option in base::options.
timeseries_start: Date after which historic samples are included in the timeseries fit. Default value is 1995-01-01, corresponding to moon 217.
origin: Date forecast origin. Default is today's date (set using Sys.Date).
forecast_date: Date of when the forecasts are occurring. Default is today's date (set using Sys.Date).
lead_time: integer (or integer numeric) value for the number of calendar days forward a forecast will cover.
As of version 0.51.0, default is now 365, which when divided by 29.5 (duration of a lunar month), gives 13. The previous value was previously 12. We are now using 13 to align with the timestep being a lunar month, and 13 lunar months covers a full calendar year.
max_lag: integer (or integer numeric) maximum number of calendar days that any covariate is lagged for prediction in a model.
Default is 365 for the logistic covariate models.
lag_buffer: integer (or integer numeric) additional number of calendar days back in time to add to the maximum lag.
Default value of 60 corresponds to two additional lunar months.
lead_time_buffer: integer (or integer numeric) additional number of calendar days forward in time to forecast.
Default value of 30 corresponds to one additional lunar month.
directory_configuration: character name for the directory configuration YAML.
app: character name for the application R file.
newmoons: character name for the lunar data csv.
covariates: character name for the combined historical and forecast covariates csv.
datasets_controls: character name for the YAML of datasets control list(s).
models_controls: character name for the YAML of models controls list(s).
forecasts_evaluations: character name for the forecast evaluations csv.
forecasts_results: character name for the forecast combination results csv.
forecasts_metadata: character name for the forecast metadata csv.
metadata: character name for the Forecast metadata YAML.
about_md: character name for the md file for the about page of the app.
models_html: character name for the html file where the models page will be saved for the app.
models_rmd: character name for the Rmd file for the models page of the app.
rodents_profiles_html: character name for the html file where the rodents profiles page will be saved for the app.
rodents_profiles_csv: character name for the csv file containing content for the rodents profiles table for the app.
species_names: character name for the csv file containing the output from portalr::rodent_species, with set = "forecasting", type = "table", and total = TRUE.
forecasts: character name for the forecasts subdirectory.
fits: character name for the fits subdirectory.
models: character name for the models subdirectory.
data: character name for the data subdirectory.
www: character name for the application www helpers subdirectory.
PortalData: list of source and version elements of character values for the Portal Data download. Default values retrieve the latest data from github
portalPredictions: list of source and version elements of character values for the archive download. Default values point to github, but verison = NULL indicates no download.
climate_forecasts: list of source, version, and data elements of character values for the climate forecasts download. Default values retrieve the current day's forecast of min, mean, and max temperature and precipitation from the Northwest Knowledge Network's North American Multi-Model Ensemble (NMME) climate forecasts.

Value

Named list of settings for the directory (for directory_settings) or list of settings components (for directory_files, directory_subdirectories, and directory_resources).

Examples

   directory_settings( )
   directory_files( )
   directory_subdirectories( )
   directory_resources( )
   time_settings( )

Usage

Arguments

Value

See also

Examples