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Rnssp-rmd-templates

State Emergency Department template (state_ed_report)

11/16/2021 The State Emergency Department template has been updated. This version has:

  • Modified algorithm for trajectory analysis to improve state and county-level trend classifications.

  • Improved figure sizing to accommodate the selection of many categories.

  • Improved time series visualizations, color palettes.

  • Added interactive sparklines to DT table, Improve table formatting.

6/8/2021 State Emergency Department template available.

Text Analysis Interactive Dashboard template (text_mining)

2/14/2023 The Text Mining template has been updated.

This version contains uses the 2023 updated ICD 10 codes.

8/12/2022 The Text Mining template has been updated.

This version:

  • Uses the quanteda library for pre-processing, cleansing, and tokenization of chief complaint free text and discharge diagnosis codes to optimize render time for larger data sets.
  • Includes improvements for removal of discharge diagnosis codes from the chief complaint parsed field and free text from the discharge diagnosis field.
  • Displays “ICD-9, SNOMED, or unknown DD code” for non-ICD-10 discharge diagnosis code descriptions rather than NA values.
  • Uses an updated ICD-10 discharge diagnosis code description file that includes new codes published in late 2021.
  • Uses the visNetwork package to render interactive network graphs for term correlation graphs (for chief complaint free text and discharge diagnosis codes).
  • Includes an updated description of template parameter options on the background page.
  • No longer includes the character and token length of CC and DD fields tab.
  • Includes improved Flexdashboard formatting and theme options.
  • Uses an up-to-date list of existing ESSENCE CCDD categories, subsyndromes, and syndromes for populating the syndrome definition drop-down list in the template GUI.
  • Combines permutations of 2 chief complaint terms or discharge diagnosis codes into a single bigram that is ordered alphabetically (alphanumerically for codes) so that bigram frequencies are combined. Note that this is not applied for chief complaint or discharge diagnosis trigrams.
10/19/2021 The Text Mining template has been updated.

This version contains a custom Query field that allows users to enter their own ESSENCE query.

9/29/2021 The Text Mining template has been updated. This version:

  • Prematurely exits the knit when bad User Credentials are entered.

  • Prematurely exits the knit when an empty dataset is returned by the API.

8/9/2021 The Text Mining template has been updated. This version:

  • Asks for document title in parameter GUI

  • Includes age groups 2 - 5

  • Allows user to limit to a site or group of sites

  • Allows users to subset down to particular age groups if they wish. By default, the data pull should pull CCQV data which doesn't contain age. If a user selects full details, then the age group filtering will apply. All possible age group options have been added.

  • Fixes a typo for a parameter name - replaced "ccdd_category_string" with "definition_string"

*Changes the default CCDD Category to COVID-DD

6/19/2021 The Text Mining template has been updated. This version contains the following updates:

  • Users now have a choice to select a syndrome definition from a list of all CCDD categories, subsyndromes, and syndromes that are currently in the system. Users no longer need to manually paste in the query to populate on the Background tab. The input option allows for users to type and search for a definition type and name when knitting with parameters. As done in the combined category fields in ESSENCE, CCDD categories are proceeded by CCDD Category, subsyndromes by Subsyndrome, and syndrome by Syndrome.

  • Chief complaint correlation network graph (based on Pearson correlation). Terms are filtered with a correlation greater than 0.15. Opacity of the edges/lines represents the magnitude of correlation. Note that pairs that occur next to each other in the chief complaint are removed in an attempt to avoid identifying term pairs that one would expect to see and that show up in the top 200 bigrams. Also added is a search table below the graph so that users can search for correlations for a term of interest.

  • n-gram trend analysis for chief complaint and discharge diagnosis unigrams and bigrams. The sections of code that generate these have been modified to prevent errors when there are no significant terms identified.

5/21/2021 Text Mining template available.

Essence Chief Complaint and Discharge Diagnosis Categories template (essence_ccdd)

9/13/2021 The Essence Chief Complaint and Discharge Diagnosis Categories template has been updated. This version:

  • Contains some minor update to the GUI.

  • Allows users to generate the report for a specific site.

7/6/2021 The Essence Chief Complaint and Discharge Diagnosis Categories template is available.

This template generates a trend report of CCDD Categories between the MMWR weeks containing the dates you choose. Users are able to select as many of the CCDD Categories as they would like to generate, and are able to control for data quality using the Average Weekly DDI% and CoV(HasBeenE) filters.

Emergency Department ICD-10 Category Volumes template (ed_icd10_volume)

11/10/2021 The Emergency Department ICD-10 Category Volumes template has been updated. This version:
  • Has additional patient demographic stratifications
  • Provides facility level selection variables
9/28/2021 The Emergency Department ICD-10 Category Volumes template has been updated. This version:

  • Contains an Update of the medical grouping system to be chiefcomplaintsubsyndromes when a subsyndrome is selected

  • Renders properly and properly prints DDI and CoV cutpoints in the output.

9/13/2021 The Emergency Department ICD-10 Category Volumes template is available.

This template explores the top N categories by volume for the new ICD Chapter, Section, Diagnosis, and CCSR queries. It generates heat maps of the top N ICD-10-CM codes by ICD-10-CM chapter, ICD-10-CM section, ICD-10-CM diagnosis code, and the corresponding clinical classifications software refined (CCSR) category. Users are able to select the geographic region of interest, time frame, data quality filters, and ESSENCE age group category.

Syndrome Definition Evaluation template (syndrome_eval)

8/12/2022 The Syndrome Definition Evaluation template has been updated.

This update allows the user to input Free Text Queries or CSV type NSSP-ESSENCE DataDetails API URL as a custom query.

1/14/2022 The Syndrome Definition Evaluation template has been updated.

This update allows the user to input up to three CCDD Free Text Queries.

1/6/2022 The Syndrome Definition Evaluation template has been updated.

This update adds a functionality to perform the data pull by chunks of one day.

11/3/2021 The Syndrome Definition Evaluation template has been updated.

This critical update fixes an issue related to API URLs being ill-constructed when syndromes or subsyndromes are selected.

11/1/2021 The Syndrome Definition Evaluation template has been updated for performance and efficiency. It contains:

  • An update to the detect_elements() helper function solving therefore a memory limit issue preventing a successful render of the template when large datasets are pulled.

  • Some minor improvements that remove large datasets from the memory stack when they are not used.

9/13/2021 The Syndrome Definition Evaluation template is available.

This template allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time.

Word Alerts Report template (word_alerts)

8/18/2022 The Word Alerts Report template has been updated. This version:
  • Includes a new parameter list to limit to existing ESSENCE age grouping systems.
  • Includes an option for "All" under the Limit to Site parameter drop-down list when using the Facility Location (Full Details) data source.
  • Allows users to either enter a custom CCDD query or complex query (API URL option) if they do not wish to run the template on an existing ESSENCE syndrome definition.
  • Provides more flexibility for selecting start and end dates.
  • Uses an up-to-date list of existing ESSENCE CCDD categories, subsyndromes, and syndromes for populating the syndrome definition drop-down list in the template GUI.
  • Includes enhanced summary visualizations of the number of alerts by field and n-gram
  • Includes terms with alerts over the entire date range selected in the sparkline tables rather than those with alerts for the most recent date
  • Uses daily time chunked API pulls for the Facility Location (Full Details) data source with a progress bar.
  • Includes a summary parameter table at the beginning of the report to display parameters that a user selects.
  • Includes a report appendix section at the end to summarize example stop words by class.
11/15/2021 The Word Alerts Report template has been updated. This version:

  • Updated the API for site-level full data details to use the Syndrome Subsyndrome CCDD Combined Category field to simplify the code.

  • Added a new parameter, has_been_E, so that data can be limited to ED data if specified. This only applies to ESSENCE API pulls as CCQV backup table does not have a has_been_E field.

  • Removed duplicate cat() statements when no alerts are found.

  • Default date range is now the most recent 90 days. Default start and end dates are calculated using base R.

11/9/2021 The Word Alerts Report template is available.

The Word Alerts Report template summarizes daily chief complaint and discharge diagnosis term alerts for a selected syndrome definition.

The purpose of the word alert algorithm is to seek anomalous chief complaint free text terms and discharge diagnosis codes relative to a 28-day sliding baseline.

The current implementation of word alerts in NSSP-ESSENCE is limited to data from the past 7 days. This template provides users the capability of running the word alert algorithm on any selected date range spanning up to 90 days.

Data Quality Filter Matrix template (dq_filters)

02/15/2024 The Data Quality Filter Matrix template has been updated. This version:

  • Added a parameters to allow for selection of multiple sites, facility type, and visit type.

  • Added a parameter to define earliest year data quality filters will be applied for the report output.

  • Extended the time period to 10 year back data quality filters.

  • Reduced Comparing Facility DDI and CoV section to single loop to streamline future updates.

4/5/2022 The Data Quality Filter Matrix template is available.

This template summarizes the DDI Avg Weekly Percent (DDI) and Data Quality CoV (HasBeenE) (CoV (HasBeenE)) filters individually and in conjunction with one another.

State Data Quality Report template (state_dq_report)

9/1/2023 The State Data Quality Report template has been updated. In this version:

  • Table cell conditional logic has been corrected.

  • Tables have been updated to use either the DT or reactable R packages.

  • An NSSP-themed color palette has been added.

  • The regular expression that assesses Race_Code validity has been corrected (the previous version did not throw an error when a non-code value was received after a valid code value).

  • The regular expressions that assess Ethnicity_Code and Ethnicity_Description validity have been corrected to use the correct "UNK" and "OTH" values.

1/31/2023 The State Data Quality Report template is available.

This template summarizes data quality metrics, including timeliness, completeness, and validity. It Currently includes NSSP Priority 1 & NSSP Priority 2 elements.

Lab Pathogen Surveillance Report template (lab_pathogen_trend)

8/02/2023 The Lab Pathogen Surveillance Report template is available.

This template generates a trend report of testing volume and the percent of tests that are positive for all Lab A LabCategory2 options in the ESSENCE Laboratory by Results data source.

Lab Reason for Testing Report template (lab_testing_reason)

8/02/2023 The Lab Reason for Testing Report template is available.

This template summarizes the types of tests and patient demographics of a user defined reason for testing query. Users are able to select the geographic region (national, HHS region, state, or county), time frames, and reason for testing.

Lab Year Over Year Trends Report template (lab_yoy_trend)

8/02/2023 The Lab Year Over Year Trends Report template is available.

This template generates a trend report of testing volume and the percent of tests that are positive for all Lab A LabCategory 2 options in the ESSENCE Laboratory by Results data source. Users are able to select a time period and geographic region (national, HHS Region, state, or county).

ICD-10 Discharge Diagnosis Code Usage and Feature Template (icd10_code_use)

11/21/2023 The ICD-10 Discharge Diagnosis Code Usage and Feature template is now available.

This template can be used to consider all discharge diagnosis codes occurring over a recent time window for a site and identify ICD-10 codes with statistically significant increases or decreases in trend. Basic demographic features such as mean and median age, and percentages by patient sex are reported for ICD-10 codes that are identified as having recent significant change in occurrence. Additionally, this template detects ICD-10 codes with significant change due to annual ICD-10 revisions imposed by CMS in October.