.perform_allocation_process

internal

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

.perform_allocation_process function

<dl><dt>reporting_triangle</dt>
<dd>A reporting_triangle object with rows
representing reference times and columns representing delays.
Can be a reporting matrix or incomplete reporting matrix.
Can also be a ragged reporting triangle, where multiple columns are
reported for the same row (e.g., weekly reporting of daily data).</dd>
<dt>scale_factor</dt>
<dd>Numeric value indicating the multiplicative factor on
the maximum delay to be used for estimation of delay and uncertainty.
Default is <code>3</code>.</dd>
<dt>prop_delay</dt>
<dd>Numeric value &lt;1 indicating what proportion of all
reference times in the reporting triangle to be used for delay
estimation. Default is <code>0.5</code>.</dd>
<dt>n_min_retro_nowcasts</dt>
<dd>Integer indicating the minimum number of
reference times needed for uncertainty estimation. Default is <code>2</code>.</dd></dl>

Arguments

Perform the allocation process — .perform_allocation_process

<dl>

<dt>reporting_triangle</dt>
<dd>A reporting_triangle object with rows
representing reference times and columns representing delays.
Can be a reporting matrix or incomplete reporting matrix.
Can also be a ragged reporting triangle, where multiple columns are
reported for the same row (e.g., weekly reporting of daily data).</dd>


<dt>scale_factor</dt>
<dd>Numeric value indicating the multiplicative factor on
the maximum delay to be used for estimation of delay and uncertainty.
Default is <code>3</code>.</dd>


<dt>prop_delay</dt>
<dd>Numeric value &lt;1 indicating what proportion of all
reference times in the reporting triangle to be used for delay
estimation. Default is <code>0.5</code>.</dd>


<dt>n_min_retro_nowcasts</dt>
<dd>Integer indicating the minimum number of
reference times needed for uncertainty estimation. Default is <code>2</code>.</dd>

</dl>

Perform the allocation process

.perform_allocation_process: Perform the allocation process

Description

Usage

Value

Arguments