Skip to contents

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.
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_endpoint()
Construct a data.cdc.gov API endpoint from a dataset ID
data_cdc_gov_ids
Dataset IDs fordata.cdc.gov datasets of interest:
default_prism_bin_names
Names of PRISM bins
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 forecasts for scoring.
gather_hub_target_data()
Gather target truth data from a forecast hub.
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_to_scorable_quantiles()
Create a table for scoring hub model quantile forecasts from a local copy of a hub.
hubverse_std_colnames
Internal and user-exposed constants for forecasttools. 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()
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_nhsn()
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 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.