syn_nssp_line_list

For an example of how to produce a nowcast from this data, see
<code>vignette("nssp_nowcast")</code>.

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_line_list function

A data.frame with 25 rows and 8 columns.<dl>
<dt>C_Processed_BioSenseID</dt>
<dd>Unique identifier for each patient</dd><dt>CCDDParsed</dt>
<dd>Character string indicating primary symptoms and
corresponding diagnoses codes.</dd><dt>DischargeDiagnosisMDTUpdates</dt>
<dd>Character string formatted as a
dictionary with indices and corresponding time stamps formatted as
YYYY-MM-DD HH:MM:SS.</dd><dt>DischargeDiagnosisUpdates</dt>
<dd>Character string formatted as a
dictionary with indices and corresponding diagnoses codes pertaining to
this diagnosis associated with that event.</dd><dt>HasBeenAdmitted</dt>
<dd>Numeric indicating whether the patient was
admitted (0 for no, 1 for admission).</dd><dt>C_Visit_Date_Time</dt>
<dd>Date-time indicating the time stamp of the
the patient registering in the emergency department, in
YYYY-MM-DD HH:MM:SS format.</dd><dt>c_race</dt>
<dd>Character string indicating the race/ethnicity of the
patient.</dd><dt>sex</dt>
<dd>Character string indicating the sex of the patient.</dd>
</dl>

Format

A synthetic dataset resembling line-list (each row is a patient) data from
the United States' National Syndromic Surveillance System (NSSP)
accessed via the Essence platform. All entries are synthetic, formatted to
look as close to the real raw data as possible. — syn_nssp_line_list

A data.frame with 25 rows and 8 columns.<dl>
<dt>C_Processed_BioSenseID</dt>
<dd>Unique identifier for each patient</dd>

<dt>CCDDParsed</dt>
<dd>Character string indicating primary symptoms and
corresponding diagnoses codes.</dd>

<dt>DischargeDiagnosisMDTUpdates</dt>
<dd>Character string formatted as a
dictionary with indices and corresponding time stamps formatted as
YYYY-MM-DD HH:MM:SS.</dd>

<dt>DischargeDiagnosisUpdates</dt>
<dd>Character string formatted as a
dictionary with indices and corresponding diagnoses codes pertaining to
this diagnosis associated with that event.</dd>

<dt>HasBeenAdmitted</dt>
<dd>Numeric indicating whether the patient was
admitted (0 for no, 1 for admission).</dd>

<dt>C_Visit_Date_Time</dt>
<dd>Date-time indicating the time stamp of the
the patient registering in the emergency department, in
YYYY-MM-DD HH:MM:SS format.</dd>

<dt>c_race</dt>
<dd>Character string indicating the race/ethnicity of the
patient.</dd>

<dt>sex</dt>
<dd>Character string indicating the sex of the patient.</dd>


</dl>

A synthetic dataset resembling line-list (each row is a patient) data from
the United States' National Syndromic Surveillance System (NSSP)
accessed via the Essence platform. All entries are synthetic, formatted to
look as close to the real raw data as possible.

syn_nssp_line_list: A synthetic dataset resembling line-list (each row is a patient) data from the United States' National Syndromic Surveillance System (NSSP) accessed via the Essence platform. All entries are synthetic, formatted to look as close to the real raw data as possible.

Description

Usage

Arguments

Format

See Also