incidence_to_df: Export incidence model to data frame

In incidental: Implements Empirical Bayes Incidence Curves

Description

Export the output of fit_incidence to a data frame with an optional addition of a time index.

Usage

incidence_to_df(x, times = NULL, low_quantile = 0.05, high_quantile = 0.95)

Arguments

x	An "incidence_spline_model" output from fit_incidence.
times	An optional vector of time indices.
low_quantile	A scalar that specifies the low quantile value for the output CI.
high_quantile	A scalar that specifies the high quantile value for the output CI.

Value

A data frame with the following entries:

• Time – a time index; if 'ts' is 'NULL' it is the observation number;

• Reported – the value of 'reported';

• Ihat – MAP incidence curve estimate;

• Chat – expected cases given MAP incidence curve estimate;

• LowCI – lower pointwise credible interval bands around the incidence curve; and

• HighCI – higher pointwise credible interval bands around the incidence curve.

Examples

indiana_model <- fit_incidence(
                  reported = spanish_flu$Indiana, 
                  delay_dist = spanish_flu_delay_dist$proportion)
 indiana_df <- incidence_to_df(indiana_model, times = spanish_flu$Date)

incidental documentation built on Sept. 16, 2020, 5:07 p.m.