Clinical Events and Specialty Agreement: Single Site, Anomaly Detection, Cross-Sectional Analysis
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This check computes types of clinical events that occur across clinician or facility specialties at a moment in time. It provides a high level summary of the quality of clinical specialty data in a study sample for a given site. The intention of the check is to evaluate the concordance of specific events (e.g., diagnosis of type I diabetes) and specialist providers or care sites (e.g., endocrinologist or endocrinology clinic) at the visit level.
Data Requirements
Probe
Clinical Assessment
Access Package
# install.packages("devtools")
devtools::install_github('ssdqa/https://github.com/ssdqa/clinicalevents.specialties')Visualization Output
This check outputs a line plot which displays the proportion of visits with each specialty over a user-selected time period. Each of the color coded lines corresponds to a specialty. Specialties can be isolated by clicking on the legend. The time variable is represented on the x-axis and the proportion of visits is captured on the y-axis. A tooltip displays each data point’s specialty name, proportion of visits value, and start time upon hover.
Raw Output
The raw data output requires the user to annotate the specialty name output before running the output function.
| Column | Data Type | Definition |
|---|---|---|
specialty_name |
character | user provided annotation |
specialty_concept_id` |
numeric / character | the concept indicating the specialty of the provider and/or care site |
specialty_concept_name |
character | if a vocabulary table is provided, the name of the specialty associated with the specialty_concept_id |
The resulting raw data output of this check produces eight columns of data:
| Column | Data Type | Definition |
|---|---|---|
specialty_concept_id` |
numeric / character | the concept indicating the specialty of the provider and/or care site |
cluster |
character | the cluster assigned in the user provided codeset; if no cluster is indicated, the name of the concept is used |
num_visits |
numeric | the number of visits associated with the specialty_concept_id & cluster |
codeset_name |
character | the name of the codeset provided for the analysis |
site |
character | the name of the site being targeted OR “combined” if multiple sites were provided for a single site analysis |
age_grp |
character | if an age group dataframe is provided, a string indicating the age grouping at the time of the specialty visit |
visit_type |
character | if a visit type dataframe is provided, the visit type of the specialty visit |
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