Package index • forecasttools

All functions

GeomPathPoint GeomLinePoint: Geometric object showing a path of connected points.

assert_date_in_epiweek(): assert that a date corresponds to a given epidemiological week and year, according to the given epiweek standard.

assert_hubverse_output_types(): Assert that a vector consists only of valid hubverse output types

bottom_up_aggregation(): Bottom up aggregation of base forecasts

categorize_prism(): Categorize a vector of values into PRISM activity level bins.

categorize_vector(): Categorize entries in a numeric vector according to a list of breakpoints and labels.

cdc_hub_additional_colnames: Names of additional standard columns for the CDC FluSight and COVID-19 Forecast Hubs beyond those in hubverse_std_colnames.

cdc_hub_std_colnames covidhub_std_colnames flusight_std_colnames: Names of standard columns for the the CDC FluSight and COVID-19 Forecast Hubs, with convenient aliases.

copula2tbl(): Convert Copula Samples to a Tibble

count_trajectories(): Count the number of trajectories per location

daily_to_epiweekly(): Aggregate a daily timeseries to epiweekly

data_cdc_gov_base_query(): Construct a base SOQL query pointing at at data.cdc.gov endpoint.

data_cdc_gov_dataset_id(): Retrieve the dataset IDs for supported data.cdc.gov datasets

data_cdc_gov_dataset_lookup(): Look up rows of the data.cdc.gov dataset table corresponding to the entries of a given vector.

data_cdc_gov_dataset_table: Dataset IDs and metadata for data.cdc.gov datasets

data_cdc_gov_endpoint(): Construct data.cdc.gov API endpoints from dataset IDs

data_cdc_gov_soda_query(): Helper function for common Socrata open data API (SODA) queries targeted at data.cdc.gov datasets.

default_prism_bin_names: Names of PRISM bins

do_soda_query(): Perform an abitrary SOQL query against an arbitrary dataset, and return the results as a tibble.

download_hub(): Download a forecast hub from hub_url to directory hub_path.

draw_key_path_point(): Legend key glyph for GeomPathPoint and subclasses of it.

epiweek_fn(): Get a date-to-epiweek function from an epiweek standard.

epiweek_start() epiweek_end(): Get the start or end day of an epiweek.

epiweek_to_date(): Get a date from an epiweek and epiyear

epiyear_first_date(): Get the first date of an epidemiological year ("epiyear")

epiyear_fn(): Get a date-to-epiyear function from an epiweek standard.

epiyear_n_days(): Get the number of days in a given epidemiological year.

epiyear_n_weeks(): Get the number of epidemiological weeks in a given epidemiological year.

ex_inferencedata_dataframe: Example InferenceData DataFrame

example_daily_forecast_flu: An example daily-resolution set of forecast trajectories for influenza.

filter_to_shared_forecasts(): Filter a table of forecasts to include only those present for all values of a given column.

filter_to_subset_forecasts(): Filter a table of forecasts to include only those present for a value of a given column.

floor_epiweek() ceiling_epiweek() floor_isoweek() floor_mmwr_epiweek() ceiling_isoweek() ceiling_mmwr_epiweek(): Get the first date in an epidemiological week.

gather_hub_location_data(): Gather location data from a forecast hub.

gather_hub_quantile_forecasts(): Collect and reformat hub quantile forecasts for scoring.

geom_path_point() geom_line_point(): Plot a path of connected points

get_available_qi_widths(): Get a table of quantile interval widths that can be computed from a given set of absolute quantile levels.

get_hubverse_quantile_table() get_epiweekly_hubverse_table() get_flusight_hub_table() get_covid_hub_table(): Format quantile forecasts for a hubverse submission

get_prism_cutpoints(): Get PRISM activity level cutpoints for given diseases and locations

get_shared_forecasts(): Compute the set of forecasts present for all values of a given column.

get_subset_forecasts(): Compute the set of forecasts present for a given value of a given column.

horizons_from_target_end_dates(): Compute Horizon from Target End Dates

hub_quantiles_to_median_qi(): Convert a hubverse-format table of quantiles into a ggdist-format table of quantile intervals.

hub_target_data_as_of(): Filter to a given vintage of hub target data and drop the as_of column.

hub_to_scorable_quantiles(): Create a table for scoring hub model quantile forecasts from a local copy of a hub.

hubverse_output_types: Internal and user-exposed constants for forecasttools. Names of the valid output_type values for hubverse tables.

hubverse_std_colnames: Names of the standard columns for hubverse tables. Alias for hubUtils::std_colnames.

hubverse_table_with_obs(): Join hubverse forecasts to observed data

idata_names_to_tidy_names(): Convert InferenceData column names to tidy column names

inferencedata_to_tidy_draws(): Convert InferenceData DataFrame to nested tibble of tidy_draws

modify_reference_date(): Modify Reference Date

nhsn_soda_query() deprecated: Construct a Socrata open data API (SODA) query for the NHSN Hospital Respiratory Data set.

nullable_comparison(): Compare two quantities a and b with a given comparison operator, returning a single TRUE if b is NULL.

pivot_hubverse_quantiles_wider(): Pivot a hubverse quantile table wider with columns representing individual quantile levels.

plot_coverage_by_date(): Plot of empirical forecast coverage by reference date.

plot_hubverse_file_quantiles(): Plot hubverse formatted forecasts for all or a subset of forecasted locations.

plot_hubverse_loc_quant_ts(): Plot a hubverse formatted quantile forecast timeseries for a single location.

plot_hubverse_pointintervals(): Plot a table of hubverse-formatted forecasts as pointintervals

plot_pred_obs_by_forecast_date(): Plot median predictions and prediction intervals against observed data by forecast date.

plot_pred_obs_pointintervals(): Plot median predictions and prediction intervals as pointintervals against observed data

plot_quantile_timeseries(): Plot a timeseries of quantiles.

plots_to_pdf(): Save a list of ggplot plots as a PDF, with a grid of nrow by ncol plots per page

prism_thresholds: PRISM respiratory virus activity level thresholds

pull_data_cdc_gov_dataset(): Pull a dataset from data.cdc.gov with standard selection and filtering options.

pull_nhsn() deprecated: Pull NHSN data from data.cdc.gov

quantile_table_to_median_qi(): Convert a tidy table of quantiles into a ggdist-format table of quantile intervals.

quantile_table_to_scorable(): Create a scoringutils-ready quantile table from a hubverse table

rank_sampled_trajectories(): Rank sampled trajectories

read_tabular() write_tabular() write_tabular_file() read_tabular_file(): Read from or write to tabular files, with file format inferred from the file extension.

sample_aggregated_trajectories(): Generate sample trajectories based on ranked base forecasts

prism_colors prism_levels scale_fill_prism() scale_color_prism() scale_colour_prism(): Prism color scale

soql_nullable_is_in(): Add an "is in" statement to a SOQL query, or return the original query if match_values is NULL.

soql_nullable_select(): Add a soql::soql_select() statement to a query to select a set of columns columns, or return the original query if columns is NULL.

soql_nullable_where(): Add a soql::soql_where() statement to a SOQL query, or return the original query if where_value is NULL.

summarise_scores_with_baseline() summarize_scores_with_baseline(): Summarize a scoring table with scores relative to a baseline model.

sym_limits(): Get limits spanning a set of values that are symmetric about a central value

target_end_dates_from_horizons(): Get a correctly-formatted set of hubverse target_end_date values for the given reference date and set of horizons.

theme_forecasttools(): forecasttools ggplot2 theme.

to_us_location_table_column() to_location_table_column(): Map location format strings to corresponding us location lookup table column names.

trajectories_to_quantiles(): Aggregate individual trajectory timeseries or forecasts to quantile timeseries or forecasts

update_hub(): Update the forecast hub located at the path hub_path.

us_loc_abbr_to_code(): Convert a two-letter USA location abbreviation to a two-character USA location code

us_loc_code_to_abbr(): Convert a 2-character USA location code to a 2-letter USA location abbreviation.

us_location_lookup() location_lookup(): Look up rows of the USA location table corresponding to the entries of a given vector.

us_location_recode(): Recode a vector of US locations from one format to another

us_location_table: Table of US location names and codes

validate_base_forecasts(): Validate the base forecasts

widths_to_qi_table(): Get a table of quantile intervals ("qi") corresponding to a vector of interval widths.

with_epidate(): Annotate a dataframe with epiweek and epiyear columns with an epidate column.

with_hubverse_oracle_output(): Join hubverse oracle output to a hubverse forecast table for scoring.