Summarise the uncertainty obtained from bootstrapping — summarise

This function takes as input bootstrapped values: Re estimates or others and builds uncertainty intervals from these bootstrapped values.

summarise_uncertainty(
  bootstrapped_values,
  original_values = NULL,
  uncertainty_summary_method = "original estimate - CI from bootstrap estimates",
  value_col = "Re_estimate",
  output_value_col = "Re_estimate",
  bootstrap_id_col = "bootstrap_id",
  index_col = "idx",
  ...
)

Arguments

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.
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.
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.
value_col	string. Name of the column containing values.
output_value_col	string. Name of the output column with estimated 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.
...	Arguments passed on to `.summarise_CI_bootstrap` `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. `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

Value

A dataframe containing Re estimates (column 'Re_estimate') and confidence interval boundaries, with 4 columns like so:

index_col, the timestep index column
A column named output_value_col, containing the central values (typically these are Re estimates)
CI_up, upper limit of the confidence interval
CI_down, the lower limit of the confidence interval

Details

This function is not meant to be needed by regular users. It is exported as it can be useful when building 'pipes': sequences of computations that weave together the different modules provided by estimateR.