syn_nssp_df

A synthetic dataset containing the number of incident cases indexed by
reference date and report date. While data of this form could be from any
source, this data is meant to represent the output of pre-processing the
syn_nssp_line_list dataset, which is a synthetic patient-level line list
data from the United State's National Syndromic Surveillance System (NSSP).

datasets

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

syn_nssp_df function

A data.frame with 3795 rows and 3 columns.<dl>
<dt>reference_date</dt>
<dd>Date the primary event occurred (e.g. date of
hospital admissions, specimen collection date, symptom onset), formatted
in ISO8601 standards as YYYY-MM-DD.</dd><dt>report_date</dt>
<dd>Date the event was reported into the surveillance
system, formatted as YYYY-MM-DD.</dd><dt>count</dt>
<dd>Number of incident events (e.g. cases) occurring on the
specified reference date and reported on the report date.</dd>
</dl>

Format

A synthetic dataset containing the number of incident cases indexed by
reference date and report date. While data of this form could be from any
source, this data is meant to represent the output of pre-processing the
syn_nssp_line_list dataset, which is a synthetic patient-level line list
data from the United State's National Syndromic Surveillance System (NSSP). — syn_nssp_df

A data.frame with 3795 rows and 3 columns.<dl>
<dt>reference_date</dt>
<dd>Date the primary event occurred (e.g. date of
hospital admissions, specimen collection date, symptom onset), formatted
in ISO8601 standards as YYYY-MM-DD.</dd>

<dt>report_date</dt>
<dd>Date the event was reported into the surveillance
system, formatted as YYYY-MM-DD.</dd>

<dt>count</dt>
<dd>Number of incident events (e.g. cases) occurring on the
specified reference date and reported on the report date.</dd>


</dl>

A synthetic dataset containing the number of incident cases indexed by
reference date and report date. While data of this form could be from any
source, this data is meant to represent the output of pre-processing the
syn_nssp_line_list dataset, which is a synthetic patient-level line list
data from the United State's National Syndromic Surveillance System (NSSP).

Description

Usage

Arguments

Format

See Also