Patient Event Sequencing: Multi Site, Anomaly Detection, Cross-Sectional Analysis


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2024-12-17

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Domain

Category

Parameters

Publisher

PEDSnet

Abstract

The Patient Event Sequencing module computes the days between two user-specified events and summarizes the distribution within the cohort. It assesses the plausibility of the sequence of two user-provided clinical events as they appear in a patient’s record. This allows the user to ensure that the two events, like a cancer diagnosis and chemotherapy, occur in a sensible order and within an expected length of time.

Data Requirements

cohort , n_event_a , n_event_b , pes_event_file , omop_or_pcornet , multi_or_single_site , anomaly_or_exploratory , age_groups , patient_level_tbl , p_value , time

Probe

Clinical Assessment

Access Package

# install.packages("devtools") devtools::install_github('ssdqa/patienteventsequencing')

Visualization Output

This check outputs a dot and star plot for each threshold window to identify sites with anomalous proportion of patients whose time between event falls within the window. Color of the dot represents proportion, size represents mean, and shape represents whether or not the site is anomalous.

Raw Output

This check produces a raw data output containing 21 columns of data:

Column Data Type Definition
site character the name of the site being targeted
threshold_cutoff character a string indicating the threshold for the number of days between the two events, including a label for patients who do not have one or both events
total_pts numeric the total number of patients in the cohort at the site
user_cutoff numeric the user provided threshold for days between the events
event_a_name character the name of event A
event_b_name character the name of event B
n_pts_thrs numeric the number of patients meeting the threshold_cutoff criteria
prop_pts_thrs numeric the proportion of patients meeting the threshold_cutoff criteria (n_pts_thrs / total_pts)
mean_val numeric the mean proportion of prop_pts_thrs across sites
median_val numeric the median prop_pts_thrs across sites
sd_val numeric the standard deviation of prop_pts_thrs across sites
mad_val numeric the median absolute deviation of prop_pts_thrs across sites
cov_val numeric the coefficient of variance of prop_pts_thrs across sites
max_val numeric the maximum prop_pts_thrs across sites
min_val numeric the minimum prop_pts_thrs across sites
range_val numeric the range of the prop_pts_thrs across sites
total_ct numeric the total number of group members
analysis_eligible character a string indicating whether the group is eligible for anomaly detection analysis
lower_tail numeric the lower bound used to identify low anomalies
upper_tail numeric the upper bound used to identify high anomalies
anomaly_yn character a string indicating whether the value is anomalous or not

Affiliation(s)

PEDSnet Data Coordinating Center

Funder(s)

This research was made possible through the generous support of Patient-Centered Outcomes Research Institute. The statements presented in this work are solely the responsibility of the author(s) and do not necessarily represent the views of PCORI, its Board of Governors, or its Methodology Committee.

Provenance

Description

Development Code

https://github.com/ssdqa/patienteventsequencing

Clinical Subjects Headings

Related Data Quality Result

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Patient Event Sequencing Study Results III: PRESERVE
Created:2025-04-08Affiliation:PEDSnet Data Coordinating Center
The results of a Patient Event Sequencing check using the Multi-Site, Anomaly Detection, Cross-Sectional parameters. This check evaluates anomalous lengths of time between a patient's cohort entry date and an antihypertensive prescription at each institution.

Related Person

Related Code

Thumbnail Image
Study-Specific Quality, Utility, and Breadth Assessment
Created:2025-11Affiliation:PEDSnet Data Coordinating Center
This suite of R packages allows one to investigate multiple facets of data quality and customize analyses based on your study-specific needs. Each module allows up to 8 different analyses in either the OMOP or PCORnet CDM, all aimed at taking a different view of the data while still addressing the same data quality probe.

##### [View pkgdown summary here.](https://ssdqa.github.io/squba/)

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Creative Commons license

a CC-BY Attribution 4.0 License.
Except where otherwised noted, this item's license is described as a CC-BY Attribution 4.0 License.

Cite this Data Quality Check

PEDSnet Data Coordinating Center. (2024, December). Patient Event Sequencing: Multi Site, Anomaly Detection, Cross-Sectional Analysis. [D Q Check]. PEDSpace Knowledge Bank. https://doi.org/10.24373/pdsp-411