uncertainty: Uncertainty summary

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

Uncertainty summary

Description

Uncertainty summary

Arguments

uncertainty_summary_method	One of these options: 'original estimate - CI from bootstrap estimates'. The confidence interval is built using bootstrapped estimates and centered around the original estimates. 'bagged mean - CI from bootstrap estimates'. The confidence interval is built using bootstrapped estimates and centered around the mean of bootstrapped estimates and original estimates.
original_values	Optional. Values of reference used to construct the uncertainty interval around. Typically, these are estimates obtained on the original data. Must be a dataframe with a timestep index column named index_col and a value column named value_col. The index column must not contain any NA value.
bootstrapped_values	Bootstrap replicates of the original data. Must be a dataframe in the long format with a timestep index column named index_col, a bootstrap replicate index column named bootstrap_id_col, and a value column named value_col. The index column must not contain any NA value.
central_values	Values around which the confidence interval is going to be centered. Must be a dataframe with a timestep index column named index_col and a value column named value_col. The index column must not contain any NA value.
alpha	value between 0 and 1. Confidence level of the confidence interval.
combine_bootstrap_and_estimation_uncertainties	boolean. Combine uncertainty from Re estimation with uncertainty from observation process? If TRUE, the credible intervals for Re estimates must be passed via Re_HPDs. The output credible intervals will be the union of bootstrapping intervals and Re estimation intervals.
Re_HPDs	Optional. Credible intervals for Re estimates. Use only if combine_bootstrap_and_estimation_uncertainties is TRUE.
value_col	string. Name of the column containing values.
bootstrap_id_col	string. Name of the column containing bootstrap samples numbering. Id 0 must correspond to values associated to the original data.
index_col	string. Name of the index column. The index tracks which data point in bootstrapped values corresponds to which data point in the original values.
output_value_col	string. Name of the output column with estimated values.
prefix_up	string. prefix to add to output_value_col to name the column containing the upper limit of confidence interval
prefix_down	string. prefix to add to output_value_col to name the column containing the lower limit of confidence interval

covid-19-Re/estimateR documentation built on Sept. 14, 2024, 5:49 a.m.