Tidy Data and Workflow Layer for Epidemic Nowcasting

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Documentation for package ‘tbl.now’ version 1.0.0

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A C D E F G H I L M N P R S T U V W Z misc

-- A --

add Set, change and remove the attributes of a 'tbl_now'
add_covariates Set, change and remove the attributes of a 'tbl_now'
add_is_censored_report Set, change and remove the attributes of a 'tbl_now'
add_is_censored_revision Set, change and remove the attributes of a 'tbl_now'
add_revision_date Set, change and remove the attributes of a 'tbl_now'
add_strata Set, change and remove the attributes of a 'tbl_now'
add_temporal_effects Attach calendar effects to a 'tbl_now', and turn them into columns
add_temporal_effects.data.frame Attach calendar effects to a 'tbl_now', and turn them into columns
add_temporal_effects.tbl_now Attach calendar effects to a 'tbl_now', and turn them into columns
aggregate_time_units Coarsen a 'tbl_now' onto a bigger time unit
align_weeks Put weekly data on a common weekday
align_weeks.data.frame Put weekly data on a common weekday
align_weeks.tbl_now Put weekly data on a common weekday
as.data.frame.grouped_tbl_now Coerce a 'tbl_now' to a tibble or a data frame
as.data.frame.tbl_now Coerce a 'tbl_now' to a tibble or a data frame
as.data.table.tbl_now Coerce a 'tbl_now' with another package's generic
assign_tbl Base R operations on a 'tbl_now'
as_epidist_aggregate_data.tbl_now Coerce a 'tbl_now' with another package's generic
as_epidist_linelist_data.tbl_now Coerce a 'tbl_now' with another package's generic
as_forecast_point.nowcast_backtest Score a nowcast against observed data
as_forecast_quantile.nowcast_backtest Score a nowcast against observed data
as_forecast_sample.nowcast_backtest Score a nowcast against observed data
as_reporting_triangle.tbl_now Coerce a 'tbl_now' with another package's generic
as_tbl_now Transform an object into a 'tbl_now'
as_tbl_now.data.frame Transform an object into a 'tbl_now'
as_tbl_now.data.table Transform an object into a 'tbl_now'
as_tbl_now.enw_preprocess_data Transform an object into a 'tbl_now'
as_tbl_now.epidist_aggregate_data Transform an object into a 'tbl_now'
as_tbl_now.epidist_linelist_data Transform an object into a 'tbl_now'
as_tbl_now.reporting_triangle Transform an object into a 'tbl_now'
as_tbl_now.tbl_now Transform an object into a 'tbl_now'
as_tbl_now.tbl_now_epinow2_snapshots Transform an object into a 'tbl_now'
as_tbl_now.tbl_now_surveillance_list Transform an object into a 'tbl_now'
as_tbl_now.tbl_now_triangle_list Transform an object into a 'tbl_now'
as_tbl_now.tbl_ts Transform an object into a 'tbl_now'
as_tibble.grouped_tbl_now Coerce a 'tbl_now' to a tibble or a data frame
as_tibble.tbl_now Coerce a 'tbl_now' to a tibble or a data frame
as_tibble.tbl_nowcast Coerce a 'tbl_nowcast' into a 'tibble'
as_tsibble.tbl_now Coerce a 'tbl_now' with another package's generic
autoplot.tbl_now Diagnostic 'autoplot' for a 'tbl_now'
autoplot.tbl_nowcast Plot a nowcast

-- C --

calendar_effect_plots Calendar effects on the case counts or on the reporting delay
cases_per_date Individual blocks of a 'tbl_now' summary
censoring Record a report or a delay as a bound rather than a fact
censor_reporting_delays Record a report or a delay as a bound rather than a fact
censor_reporting_delays_above Record a report or a delay as a bound rather than a fact
censor_reports Record a report or a delay as a bound rather than a fact
censor_revisions Record a report or a delay as a bound rather than a fact
censor_revision_delays Record a report or a delay as a bound rather than a fact
censor_revision_delays_above Record a report or a delay as a bound rather than a fact
change Set, change and remove the attributes of a 'tbl_now'
change_case_count Set, change and remove the attributes of a 'tbl_now'
change_covariates Set, change and remove the attributes of a 'tbl_now'
change_event_date Set, change and remove the attributes of a 'tbl_now'
change_is_censored_report Set, change and remove the attributes of a 'tbl_now'
change_is_censored_revision Set, change and remove the attributes of a 'tbl_now'
change_now Set, change and remove the attributes of a 'tbl_now'
change_report_date Set, change and remove the attributes of a 'tbl_now'
change_revision_date Set, change and remove the attributes of a 'tbl_now'
change_strata Set, change and remove the attributes of a 'tbl_now'
complete_zeroes Fill in the days when nothing was reported
compute_temporal_effects Attach calendar effects to a 'tbl_now', and turn them into columns
covid_colombia COVID-19 Notifications - Colombia 2020-2023
covid_us covid_us: CDC COVID-19 Case Surveillance Public Use Data (2020)
cumulative_growth Individual blocks of a 'tbl_now' summary

-- D --

date_ranges Individual blocks of a 'tbl_now' summary
delay_summary Individual blocks of a 'tbl_now' summary
denguedat denguedat: Dengue fever individual-level reporting data from Puerto Rico
diagnose Diagnose a 'tbl_now'
diagnose.default Diagnose a 'tbl_now'
diagnose.tbl_now Diagnose a 'tbl_now'
diagnose_batches Screen the report axis for batched reporting
diagnose_batches2 Test whether one report date drew from unusually old event dates
diagnose_changepoint Detect an abrupt change point in the reporting-delay distribution
diagnose_declarations Individual blocks of a 'tbl_now' diagnosis
diagnose_drift Test whether the reporting-delay distribution drifts over time
diagnose_duplicates Individual blocks of a 'tbl_now' diagnosis
diagnose_missing Individual blocks of a 'tbl_now' diagnosis
diagnose_negatives Individual blocks of a 'tbl_now' diagnosis
diagnose_now Individual blocks of a 'tbl_now' diagnosis
diagnose_ordering Individual blocks of a 'tbl_now' diagnosis
diagnose_revision_delay Compare revision delays between confirmed and retracted cases
diagnose_strata Individual blocks of a 'tbl_now' diagnosis
diagnose_truncation Individual blocks of a 'tbl_now' diagnosis
diagnose_units Individual blocks of a 'tbl_now' diagnosis
diagnostic_plot Diagnostic plots of the reporting process

-- E --

engine Specify a nowcasting model and its arguments
engine_baselinenowcast Engines for the built-in nowcasting packages
engine_diseasenowcasting Engines for the built-in nowcasting packages
engine_epinow2 Engines for the built-in nowcasting packages
engine_epinowcast Engines for the built-in nowcasting packages
engine_nobbs Engines for the built-in nowcasting packages
engine_surveillance Engines for the built-in nowcasting packages
example_engine A toy engine for examples

-- F --

flusight flusight: NHSN Weekly Hospital Respiratory Data from FluSight

-- G --

get_case_count Read what a 'tbl_now' was told about itself
get_covariates Read what a 'tbl_now' was told about itself
get_data_type Read what a 'tbl_now' was told about itself
get_event_date Read what a 'tbl_now' was told about itself
get_event_units Read what a 'tbl_now' was told about itself
get_initial_reported_cases Cases at a chosen point in the reporting process
get_initial_revised_cases Cases at a chosen point in the revision process
get_is_censored_report Read what a 'tbl_now' was told about itself
get_is_censored_revision Read what a 'tbl_now' was told about itself
get_latest_first Cases at a chosen point in the reporting process
get_latest_reported_cases Cases at a chosen point in the reporting process
get_latest_revised_cases Cases at a chosen point in the revision process
get_now Read what a 'tbl_now' was told about itself
get_nth_reported_cases Cases at a chosen point in the reporting process
get_nth_revised_cases Cases at a chosen point in the revision process
get_num_covariates Read what a 'tbl_now' was told about itself
get_num_strata Read what a 'tbl_now' was told about itself
get_report_date Read what a 'tbl_now' was told about itself
get_report_units Read what a 'tbl_now' was told about itself
get_revision_date Read what a 'tbl_now' was told about itself
get_revision_levels Read what a 'tbl_now' was told about itself
get_revision_type Read what a 'tbl_now' was told about itself
get_revision_units Read what a 'tbl_now' was told about itself
get_strata Read what a 'tbl_now' was told about itself
get_surveillance_range The date grids 'surveillance::nowcast()' needs
get_surveillance_when The date grids 'surveillance::nowcast()' needs
get_temporal_effects Read what a 'tbl_now' was told about itself
get_temporal_effect_cols Read what a 'tbl_now' was told about itself

-- H --

hai_bucaramanga Healthcare-Associated Infections - Bucaramanga, Colombia 2020-2023
has_revision Read what a 'tbl_now' was told about itself

-- I --

is_nowcast_engine Is this an engine?
is_tbl_now Check that an object is a valid 'tbl_now'
is_tbl_nowcast Is this object a 'tbl_nowcast'?
is_weekday Is a date a weekday or a weekend?

-- L --

list_nowcast_methods List the available nowcasting methods

-- M --

money_tbl_now Base R operations on a 'tbl_now'
mpoxdat mpoxdat: Mpox reporting data from the 2022 New York City outbreak

-- N --

names<-.grouped_tbl_now Base R operations on a 'tbl_now'
names<-.tbl_now Base R operations on a 'tbl_now'
names_tbl_now Base R operations on a 'tbl_now'
nowcast_backtest Refit several methods at past 'now' dates and score them
nowcast_data_getters Read what a 'tbl_now' was told about itself
nowcast_diagnose_components Individual blocks of a 'tbl_now' diagnosis
nowcast_engines Engines for the built-in nowcasting packages
nowcast_ensemble Combine several nowcasts into an ensemble
nowcast_fit Fit a nowcast with one modelling package
nowcast_fit.baselinenowcast Fit a nowcast with one modelling package
nowcast_fit.default Fit a nowcast with one modelling package
nowcast_fit.diseasenowcasting Fit a nowcast with one modelling package
nowcast_fit.EpiNow2 Fit a nowcast with one modelling package
nowcast_fit.epinowcast Fit a nowcast with one modelling package
nowcast_fit.example A toy engine for examples
nowcast_fit.NobBS Fit a nowcast with one modelling package
nowcast_fit.surveillance Fit a nowcast with one modelling package
nowcast_quantile_levels Default quantile levels for a nowcast
nowcast_summary_components Individual blocks of a 'tbl_now' summary
nowcast_tidy Standardise a fitted nowcast
nowcast_tidy.baselinenowcast Standardise a fitted nowcast
nowcast_tidy.default Standardise a fitted nowcast
nowcast_tidy.diseasenowcasting Standardise a fitted nowcast
nowcast_tidy.EpiNow2 Standardise a fitted nowcast
nowcast_tidy.epinowcast Standardise a fitted nowcast
nowcast_tidy.example A toy engine for examples
nowcast_tidy.NobBS Standardise a fitted nowcast
nowcast_tidy.surveillance Standardise a fitted nowcast
nowcast_weights Ensemble weights from a backtest

-- P --

plot_cycles Periodogram of the case counts or of the reporting delay
plot_day_of_week_effects Calendar effects on the case counts or on the reporting delay
plot_delay_distribution Empirical distribution of the reporting or revision delay
plot_delay_drift Visualise whether the reporting-delay distribution drifts over time
plot_delay_profiles Plot the per-date delay profiles
plot_epidemic_process The epidemic process and the reporting process
plot_holiday_effects Calendar effects on the case counts or on the reporting delay
plot_holiday_lag_effects Calendar effects on the case counts or on the reporting delay
plot_month_of_year_effects Calendar effects on the case counts or on the reporting delay
plot_observed_cases Observed epidemic process with the incompleteness line
plot_reporting_hexamap Plot the reporting triangle as an age-period-cohort hexamap
plot_reporting_process The epidemic process and the reporting process
plot_reporting_triangle Plot the reporting triangle
plot_revision_status How much of each day has been resolved
plot_transport_discriminant Plot the transport-discriminant plane
plot_weekend_effects Calendar effects on the case counts or on the reporting delay
plot_week_of_year_effects Calendar effects on the case counts or on the reporting delay
print.tbl_now_diagnosis Print a 'tbl_now' diagnosis
print.tbl_now_epinow2_snapshots Snapshots of one series, as 'EpiNow2' estimates truncation from
print.tbl_now_summary_table Print a 'tbl_now' summary
print.tbl_now_surveillance_list One 'surveillance' line list per stratum
print.tbl_now_triangle_list One reporting triangle per stratum
prop_censored Individual blocks of a 'tbl_now' summary
prop_covariate_levels Individual blocks of a 'tbl_now' summary
prop_revision_type Individual blocks of a 'tbl_now' summary
prop_strata Individual blocks of a 'tbl_now' summary

-- R --

remove Set, change and remove the attributes of a 'tbl_now'
remove_all_covariates Set, change and remove the attributes of a 'tbl_now'
remove_all_strata Set, change and remove the attributes of a 'tbl_now'
remove_covariates Set, change and remove the attributes of a 'tbl_now'
remove_is_censored_report Set, change and remove the attributes of a 'tbl_now'
remove_is_censored_revision Set, change and remove the attributes of a 'tbl_now'
remove_revision_date Set, change and remove the attributes of a 'tbl_now'
remove_strata Set, change and remove the attributes of a 'tbl_now'
remove_temporal_effects Set, change and remove the attributes of a 'tbl_now'
replace_temporal_effects Set, change and remove the attributes of a 'tbl_now'
revised_cases Cases at a chosen point in the revision process
revision_delay Compare revision delays between confirmed and retracted cases
run_nowcast Nowcast a 'tbl_now' with any supported modelling package

-- S --

sari_bh sari_bh: Severe Acute Respiratory Illness data from Belo Horizonte (Brazil), 2020-2022
score_nowcast Score a nowcast against observed data
simulate_batch Inject a batch into a 'tbl_now' by withholding and then releasing reports
summary.tbl_now Summarise a 'tbl_now'
surveillance_grids The date grids 'surveillance::nowcast()' needs

-- T --

tbl_now Create a 'tbl_now' object
tbl_nowcast A nowcast produced by 'run_nowcast()'
tbl_now_attributes List what a 'tbl_now' was told about itself
tbl_now_baselinenowcast Convert between 'tbl_now' and 'baselinenowcast'
tbl_now_coercion_methods Coerce a 'tbl_now' with another package's generic
tbl_now_data_table Convert between 'tbl_now' and 'data.table'
tbl_now_epidist Convert between 'tbl_now' and 'epidist'
tbl_now_EpiNow2 Convert between 'tbl_now' and 'EpiNow2'
tbl_now_epinow2_snapshots Snapshots of one series, as 'EpiNow2' estimates truncation from
tbl_now_epinowcast Convert between 'tbl_now' and 'epinowcast'
tbl_now_from_baselinenowcast Convert between 'tbl_now' and 'baselinenowcast'
tbl_now_from_data_table Convert between 'tbl_now' and 'data.table'
tbl_now_from_epidist Convert between 'tbl_now' and 'epidist'
tbl_now_from_EpiNow2 Convert between 'tbl_now' and 'EpiNow2'
tbl_now_from_epinowcast Convert between 'tbl_now' and 'epinowcast'
tbl_now_from_tsibble Convert between 'tbl_now' and 'tsibble'
tbl_now_nobbs Convert a 'tbl_now' into the line list 'NobBS' nowcasts from
tbl_now_palette The 'tbl.now' colour palette
tbl_now_summary Summarise a 'tbl_now'
tbl_now_surveillance Convert a 'tbl_now' into the line list 'surveillance' nowcasts from
tbl_now_surveillance_list One 'surveillance' line list per stratum
tbl_now_to_baselinenowcast Convert between 'tbl_now' and 'baselinenowcast'
tbl_now_to_data_table Convert between 'tbl_now' and 'data.table'
tbl_now_to_epidist Convert between 'tbl_now' and 'epidist'
tbl_now_to_EpiNow2 Convert between 'tbl_now' and 'EpiNow2'
tbl_now_to_epinowcast Convert between 'tbl_now' and 'epinowcast'
tbl_now_to_nobbs Convert a 'tbl_now' into the line list 'NobBS' nowcasts from
tbl_now_to_surveillance Convert a 'tbl_now' into the line list 'surveillance' nowcasts from
tbl_now_to_tsibble Convert between 'tbl_now' and 'tsibble'
tbl_now_triangle_list One reporting triangle per stratum
tbl_now_tsibble Convert between 'tbl_now' and 'tsibble'
temporal_effects Calendar effects to include in a nowcast
tidy Tidy a fitted nowcast into one standard table
tidy.baselinenowcast_df Tidy a fitted nowcast into one standard table
tidy.delay_distribution Tidy a fitted delay distribution
tidy.epidist_fit Tidy a fitted delay distribution
tidy.epinow Tidy a fitted nowcast into one standard table
tidy.epinowcast Tidy a fitted nowcast into one standard table
tidy.estimate_dist Tidy a fitted delay distribution
tidy.estimate_infections Tidy a fitted nowcast into one standard table
tidy.estimate_truncation Tidy a fitted nowcast into one standard table
tidy.list Tidy a fitted nowcast into one standard table
tidy.nowcast Tidy a fitted nowcast into one standard table
tidy.nowcast_backtest Tidy the predictions and scores of a 'nowcast_backtest()'
tidy.stsNC Tidy a fitted nowcast into one standard table
tidy.tbl_nowcast Tidy a nowcast produced by 'run_nowcast()' or 'nowcast_ensemble()'
to_count Convert between linelist and aggregated count data
to_count.tbl_now Convert between linelist and aggregated count data
transport_discriminant The transport discriminant of a reporting series
triangle_occupancy Individual blocks of a 'tbl_now' summary

-- U --

update.tbl_now Append newly arrived data to a 'tbl_now'
update_now Set, change and remove the attributes of a 'tbl_now'

-- V --

validate_tbl_now Check that an object is a valid 'tbl_now'

-- W --

week_2_date Put weekly data on a common weekday

-- Z --

zero_run_summary Individual blocks of a 'tbl_now' summary

-- misc --

$<-.grouped_tbl_now Base R operations on a 'tbl_now'
$<-.tbl_now Base R operations on a 'tbl_now'
[.grouped_tbl_now Base R operations on a 'tbl_now'
[.tbl_now Base R operations on a 'tbl_now'