Baseline Nowcasting for Right-Truncated Epidemiological Data

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Documentation for package ‘baselinenowcast’ version 0.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

allocate_reference_times	Allocate training volume based on combination of defaults and user-specified values for training volume for delay and uncertainty estimation.
apply_delay	Apply the delay to generate a point nowcast
apply_reporting_structure	Apply reporting structure to generate a single retrospective reporting triangle
apply_reporting_structures	Apply reporting structures to generate retrospective reporting triangles
as.data.frame.reporting_triangle	Convert reporting_triangle to data.frame
as.matrix.reporting_triangle	Convert reporting_triangle to plain matrix
assert_baselinenowcast_df	Assert validity of 'baselinenowcast_df' objects
assert_reporting_triangle	Assert validity of 'reporting_triangle' objects
as_ChainLadder_triangle	Convert reporting_triangle to ChainLadder triangle format
as_reporting_triangle	Create a 'reporting_triangle' object
as_reporting_triangle.data.frame	Create a 'reporting_triangle' object from a data.frame
as_reporting_triangle.matrix	Create a 'reporting_triangle' from a matrix
as_reporting_triangle.triangle	Convert ChainLadder triangle to reporting_triangle format
baselinenowcast	Generate a nowcast
baselinenowcast.data.frame	Create a dataframe of nowcast results from a dataframe of cases indexed by reference date and report date
baselinenowcast.reporting_triangle	Create a dataframe of nowcast results from a single reporting triangle
baselinenowcast_df	Nowcast Data.frame Object
baselinenowcast_df-class	Nowcast Data.frame Object
combine_obs_with_pred	Combine observed data with a single prediction draw
estimate_and_apply_delay	Estimate and apply delay from a reporting triangle
estimate_and_apply_delays	Estimate and apply delays to generate retrospective nowcasts
estimate_and_apply_uncertainty	Estimate and apply uncertainty to a point nowcast matrix
estimate_delay	Estimate a delay distribution from a reporting triangle
estimate_uncertainty	Estimate uncertainty parameters
estimate_uncertainty_retro	Estimate uncertainty parameters using retrospective nowcasts
example_downward_corr_rt	Example reporting triangle with downward corrections
example_reporting_triangle	Simple example reporting triangle for demonstrations
fit_by_horizon	Helper function that fits its each column of the matrix (horizon) to an observation model.
fit_nb	Fit a negative binomial to a vector of observations and expectations
germany_covid19_hosp	Incident COVID-19 hospitalisations indexed by the date of positive test (reference date) and report date from Germany in 2021 and 2022.
get_delays_from_dates	Compute delays between report dates and reference dates
get_delays_unit	Get delays unit from a reporting triangle
get_max_delay	Get maximum delay from reporting_triangle
get_mean_delay	Get mean delay for each row of reporting_triangle
get_quantile_delay	Get quantile delay for each row of reporting_triangle
get_reference_dates	Get reference dates from reporting_triangle
get_reporting_structure	Get reporting structure from a reporting triangle
get_report_dates	Compute report dates from reference dates and delays
head.reporting_triangle	Get first rows of a reporting_triangle
is_reporting_triangle	Check if an object is a reporting_triangle
new_baselinenowcast_df	Combine data from a nowcast dataframe, strata, and reference dates
new_reporting_triangle	Class constructor for 'reporting_triangle' objects
preprocess_negative_values	Preprocess negative values in the reporting triangle
print.reporting_triangle	Print a reporting_triangle object
reporting_triangle	Reporting Triangle Object
reporting_triangle-class	Reporting Triangle Object
sample_nb	Sample from negative binomial model given a set of predictions
sample_nowcast	Generate a single draw of a nowcast combining observed and predicted values
sample_nowcasts	Generate multiple draws of a nowcast combining observed and predicted values
sample_prediction	Get a draw of only the predicted elements of the nowcast vector
sample_predictions	Get a dataframe of multiple draws of only the predicted elements of the nowcast vector
summary.reporting_triangle	Summarize a reporting_triangle object
syn_nssp_df	A synthetic dataset containing the number of incident cases indexed by reference date and report date. While data of this form could be from any source, this data is meant to represent the output of pre-processing the syn_nssp_line_list dataset, which is a synthetic patient-level line list data from the United State's National Syndromic Surveillance System (NSSP).
syn_nssp_line_list	A synthetic dataset resembling line-list (each row is a patient) data from the United States' National Syndromic Surveillance System (NSSP) accessed via the Essence platform. All entries are synthetic, formatted to look as close to the real raw data as possible.
tail.reporting_triangle	Get last rows of a reporting_triangle
truncate_to_delay	Truncate reporting triangle to a specific maximum delay
truncate_to_quantile	Truncate reporting_triangle to quantile-based maximum delay
truncate_to_row	Truncate reporting triangle by removing a specified number of the last rows
truncate_to_rows	Truncate reporting triangle by removing bottom rows
validate_reporting_triangle	Validate a reporting_triangle object
[.reporting_triangle	Subset reporting_triangle objects
[<-.reporting_triangle	Subset assignment for reporting_triangle objects