.validate_strata_cols

Validate each of the strata columns passed to baselinenowcast

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

.validate_strata_cols function

<dl><dt>strata_cols</dt>
<dd>Vector of character strings indicating the names of the
columns in <code>data</code> that determine how to stratify the data for nowcasting.
The unique combinations of the entries in the <code>strata_cols</code> denote the
unit of a single nowcast. Within a strata, there can be no repeated
unique combinations of reference dates and report dates. Default is <code>NULL</code>
which assumes that the data.frame being passed in represents a single
strata (only one nowcast will be produced). All columns that are not
part of the <code>strata_cols</code> will be removed.</dd>
<dt>data</dt>
<dd>Data.frame in a long tidy format with counts by reference date
and report date for one or more strata. Must contain the following
columns:
- <code>reference_date</code>: Column of type <code>Date</code> containing the dates
of the primary event occurrence.<ul>
<li><code>report_date</code>: Column of type <code>Date</code> containing the dates of
report of the primary event.</li>
<li><code>count</code>: Column of numeric or integer indicating the new confirmed
counts pertaining to that reference and report date.
Additional columns indicating the columns which set the unit of a single
can be included. The user can specify these columns with the
<code>strata_cols</code> argument, otherwise it will be assumed that the <code>data</code>
contains only data for a single strata.</li>
</ul></dd></dl>

Arguments

Validate each of the strata columns passed to baselinenowcast — .validate_strata_cols

<dl>

<dt>strata_cols</dt>
<dd>Vector of character strings indicating the names of the
columns in <code>data</code> that determine how to stratify the data for nowcasting.
The unique combinations of the entries in the <code>strata_cols</code> denote the
unit of a single nowcast. Within a strata, there can be no repeated
unique combinations of reference dates and report dates. Default is <code>NULL</code>
which assumes that the data.frame being passed in represents a single
strata (only one nowcast will be produced). All columns that are not
part of the <code>strata_cols</code> will be removed.</dd>


<dt>data</dt>
<dd>Data.frame in a long tidy format with counts by reference date
and report date for one or more strata. Must contain the following
columns:
- <code>reference_date</code>: Column of type <code>Date</code> containing the dates
of the primary event occurrence.<ul>
<li><code>report_date</code>: Column of type <code>Date</code> containing the dates of
report of the primary event.</li>
<li><code>count</code>: Column of numeric or integer indicating the new confirmed
counts pertaining to that reference and report date.
Additional columns indicating the columns which set the unit of a single
can be included. The user can specify these columns with the
<code>strata_cols</code> argument, otherwise it will be assumed that the <code>data</code>
contains only data for a single strata.</li>
</ul></dd>

</dl>

.validate_strata_cols: Validate each of the strata columns passed to baselinenowcast

Description

Usage

Arguments