new_baselinenowcast_df

Combines data from a nowcast dataframe, a named list of the
strata associated with the nowcast dataframe, and a vector of reference
dates corresponding to the time column in the <code>baselinenowcast_df</code>

Nowcasting right-truncated epidemiological data is critical
for timely public health decision-making, as reporting delays can create
misleading impressions of declining trends in recent data. This package
provides nowcasting methods based on using empirical
delay distributions and uncertainty from past performance. It is also designed
to be used as a baseline method for developers of new nowcasting methods.
For more details on the performance of the method(s) in this package applied
to case studies of COVID-19 and norovirus, see our recent paper at
<https://wellcomeopenresearch.org/articles/10-614>. The package supports
standard data frame inputs with reference date, report date, and
count columns, as well as the direct use of reporting triangles, and is
compatible with 'epinowcast' objects. Alongside
an opinionated default workflow, it has a low-level pipe-friendly modular
interface, allowing context-specific workflows. It can accommodate a wide
spectrum of reporting schedules, including mixed patterns of reference and
reporting (daily-weekly, weekly-daily). It also supports sharing delay
distributions and uncertainty estimates between strata,
as well as custom uncertainty models and delay estimation methods.

Kaitlyn Johnson

baselinenowcast

Baseline Nowcasting for Right-Truncated Epidemiological Data

Emily Tyszka

Johannes Bracher

Sebastian Funk

Sam Abbott

Tim Taylor

new_baselinenowcast_df function

<dl><dt>baselinenowcast_df</dt>
<dd>Data.frame containing information for multiple
draws with columns for the reference time (<code>time</code>), the predicted counts
(<code>pred_count</code>), and the draw number (<code>draw</code>).</dd>
<dt>reference_dates</dt>
<dd>Vector of reference dates corresponding to the
reference times in the <code>baselinenowcast_df</code>.</dd>
<dt>output_type</dt>
<dd>Character string indicating whether the output should be
samples (<code>"samples"</code>) from the estimate with full uncertainty or whether to
return the point estimate (<code>"point"</code>). Default is <code>"samples"</code>. If
<code>"point"</code>estimates are specified, the minimum number of reference times
needed is the number needed for delay estimation, otherwise, if
<code>"samples"</code> are specified, at least 2 additional reference times are
required for uncertainty estimation.</dd></dl>

Arguments

Combine data from a nowcast dataframe, strata, and reference dates — new_baselinenowcast_df

<dl>

<dt>baselinenowcast_df</dt>
<dd>Data.frame containing information for multiple
draws with columns for the reference time (<code>time</code>), the predicted counts
(<code>pred_count</code>), and the draw number (<code>draw</code>).</dd>


<dt>reference_dates</dt>
<dd>Vector of reference dates corresponding to the
reference times in the <code>baselinenowcast_df</code>.</dd>


<dt>output_type</dt>
<dd>Character string indicating whether the output should be
samples (<code>"samples"</code>) from the estimate with full uncertainty or whether to
return the point estimate (<code>"point"</code>). Default is <code>"samples"</code>. If
<code>"point"</code>estimates are specified, the minimum number of reference times
needed is the number needed for delay estimation, otherwise, if
<code>"samples"</code> are specified, at least 2 additional reference times are
required for uncertainty estimation.</dd>

</dl>

new_baselinenowcast_df: Combine data from a nowcast dataframe, strata, and reference dates

Description

Usage

Value

Arguments

See Also