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).
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ICD-10 Discharge Diagnosis Code Usage and Features (icd10_code_use)
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ICD-10 Discharge Diagnosis Code Usage and Features template (icd10_code_use)
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-[{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/post/2021-11-06-knitting-with-parameters-using-the-knit-button-within-rstudio/","title":"Knitting With Parameters","tags":[],"description":"","content":"\r\rFirst, start a new R Markdown file From Template as demonstrated below:\r\rNext, Knit the template With Parameters using the Knit button in your Rstudio IDE:\r\rReferences:\rKnitting with parameters\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/stateedreport/","title":"State Emergency Department","tags":["state","county","emergency","department","glm","lm","nssp","essence","template"],"description":"","content":"name: state_ed_report fullname: Text Analysis Interactive Dashboard description: \u0026gt;An automated Text Analysis Interactive Dashboard template. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The state emergency department report template (state_ed_report) summarizes trend classification and ESSENCE alerting for the CCDD categories at the state and county level. Users can select percentages, counts, or percentages and counts for state and county-level time series. By default, trends are reported as a percent of daily emergency department visits.\nTo classify trends over time, this template applies penalized least squares smoothing splines to time series of percentages and Poisson generalized additive models to time series of counts. The slopes of the smoothed data are used to classify daily trajectory statuses into categories of increase, stable, or decrease. Slopes greater than a pre-defined slope cut point of 0.01 are classified as increasing, while slopes less than -0.01 are classified as decreasing. Slopes with an absolute value less than or equal to 0.01 are classified as stable. This method is best suited for classification of county-level time series with higher variability in day-to-day trends.\nIf you\u0026rsquo;re pulling current data, use a 3-day lag. This best practice prevents lower counts associated with lags in receiving data from biasing the most recent classification.\nTo identify stratifications with recent and anomalous increases in syndromic activity, ESSENCE alerting is overlaid on the time series for each county and CCDD category. These alerts correspond to ESSENCE's default alerting algorithm, Poisson/EWMA/Regression Switch, with alerting thresholds 0.05 (yellow) and 0.01 (red).\nDaily stratified alerting indicators and statistics are pulled along with the percentages, numerators, and denominators from the time series data table application programming interface (API).\n User Inputs Access and Magagement Center (AMC) username and password (securely encrypted) State (data are pulled by hospital state from the Facility Location [Full Details] data source CCDD Categories — currently includes all CCDD categories available in ESSENCE. Users may select as many categories as they want. The default categories are CLI CC with CLI DD and Coronavirus DD v1, CDC Pneumonia CCDD v1, and CDC COVID-Specific DD v1. Query start and end dates Time series type — percentages (default), counts, or percentages and counts Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `state_ed_report` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;state_ed_report\u0026#34;) Remove this template # Remove `state_ed_report` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;state_ed_report\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/","title":"Usage","tags":[],"description":"","content":"Usage Learn how to dynamically extend your existing Rnssp installation with Rnssp R Markdown templates.\n Requirements List available templates Add a template Manually add a template Remove a template Manage templates with Rnssp addins "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/post/2022-08-17-pull-existing-ccdd-cateogires-and-queries-with-essence-api/","title":"How to Pull CCDD Category List from NSSP-ESSENCE","tags":[],"description":"","content":" This post demonstrates how users with access to NSSP-ESSENCE can pull an up-to-date list of existing ESSENCE CCDD categories and their underlying queries using an ESSENCE API URL. These data can be pulled into RStudio in JSON format and will match the CC and DD Categories table found under the “More” tab in NSSP-ESSENCE. This example can be run either in the BioSense Platform instance of RStudio Workbench or in a local desktop instance of RStudio. Users must have the Rnssp package installed and will need to save their Access and Management Center (AMC) credentials to a myProfile object to proceed.\nThe following packages are needed to run this example:\nlibrary(tidyverse) library(Rnssp) If you haven’t already saved your AMC credentials to a myProfile object, then run the following code chunk to supply your username and password:\n myProfile \u0026lt;- create_profile() Out of convenience, you can save your myProfile object to either an .rda or .rds file in your home directory as follows:\n # .rda option save(myProfile, file = \u0026quot;~/myProfile.rda\u0026quot;) # .rds option saveRDS(myProfile, \u0026quot;~/myProfile.rds\u0026quot;) By saving your myProfile object to your home directory, only you will be able to access and load this file into your global environment. You should only need to update your credentials every 90 days after your AMC password expires. To load your credentials into your environment, you can either use the load() function for an rda file or the readRDS() function for an rds file.\n # .rda option load(\u0026quot;~/myProfile.rda\u0026quot;) # .rds option myProfile \u0026lt;- readRDS(\u0026quot;~/myProfile.rds\u0026quot;) The API URL to pull the existing list of CCDD categories and their underlying queries will pull from SyndromeDefinitionsServlet_CCDD using the action getCCDDTerms. This will import JSON-formatted data as a list of length 1 with element “categories”. This element is a standard data frame and can be extracted from this list using the pluck() function from the purrr package, which is included in tidyverse.\n url \u0026lt;- \u0026quot;https://essence.syndromicsurveillance.org/nssp_essence/servlet/SyndromeDefinitionsServlet_CCDD?action=getCCDDTerms\u0026quot; ccdd_queries \u0026lt;- get_api_data(url) %\u0026gt;% pluck(\u0026quot;categories\u0026quot;) glimpse(ccdd_queries) The ccdd_queries data frame will contain the following elements:\n updateInfo: Information on recent updates. All categories currently have a value of “No Updates”. termId: CCDD category ID (row number) groupName: Name of the group to which the CCDD category belongs. All categories currently have a value of “Uncategorized” dateCreated Date the CCDD category was added to the system. notes: Supplemental notes or details accompanying the CCDD category. All categories currently have a value of “No Notes” lastUpdate: Date the CCDD category or accompanying metadata was last updated. description: Summary text describing the purpose of the CCDD category and how the query was developed. definition: The underlying query of the CCDD category and fields that are searched. isAdmin: Boolean indicator that is TRUE for all CCDD categories category: Name of the CCDD category fieldsSearched: List of query fields that are searched. All categories currently have a value of “Undefined”. This information can be found in the defintion field described above. Typically, only the category and definition fields will be of interest. The extraneous fields can be removed by using the select() function:\n ccdd_queries \u0026lt;- get_api_data(url) %\u0026gt;% pluck(\u0026quot;categories\u0026quot;) %\u0026gt;% select(category, definition) head(ccdd_queries) "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/","title":"Available Templates","tags":[],"description":"","content":"Available Templates Explore and learn how to use the Rnssp R Markdown templates.\n State Emergency Department Text Analysis Dashboard ESSENCE CCDD Categories ED ICD-10 Category Volumes Syndrome Definition Evaluation Word Alerts Report Data Quality Filter Matrix State Data Quality Report Lab Pathogen Surveillance Lab Reason for Testing Lab Year Over Year Trends ICD-10 Discharge Diagnosis Code Usage and Features "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/requirements/","title":"Requirements","tags":["requirements","R","Rstudio","demo","IDE"],"description":"","content":"For a pleasant experience with the Rnssp R Markdown templates, users' system requirements must satisfy the following requirements:\n Proper installation and configuration of R (\u0026gt;= 3.6.0) Proper installation and configuration of an RStudio Integrated Development Environment Installation of the Rnssp R package The development version of the Rnssp R package can be installed from Github using the devtools or the remotes R package:\n# install the Rnssp package using devtools devtools::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;) # devtools::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;, force = TRUE) or\n# install the Rnssp package using remotes remotes::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;) # remotes::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;, force = TRUE) Shown below is a demo of the installation of the Rnssp R package using the devtools R package.\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/textmining/","title":"Text Analysis Dashboard","tags":["text","analysis","dashboard","mining","nssp","essence","template"],"description":"","content":"name: text_mining fullname: State Emergency Department Report description: \u0026gt;An automated state emergency department report template summarizing CCDD categories. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program. Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The Interactive Text Analysis Dashboard template (text_mining) summarizes the chief complaint text and discharge diagnosis codes as part of an initial description of the content of these fields. Drop-down menus allow users to select from existing ESSENCE syndrome definitions, including CCDD categories, syndromes, and subsyndromes. Users can also input a custom query of the CCDD field or the API URL for complex queries that search multiple fields.\nThis template can access two different data sources, including the Chief Complaint Query Validation (CCQV) data source in NSSP ESSENCE and Facility Location Full Details. Please be aware that when using the CCQV data source some sites have opted out of contributing their data, including Arizona, Idaho, Illinois, Marion County, Indiana, Massachusetts, North Dakota, and Ohio. To accomodate site-level users, the Facility Location Full Details data source can be selected so that data are pulled at the individual state-level. Note: The API URL for the full details data source limits to CCQV fields only.\nThe visualizations in this template include total weekly volume of encounters, the 200 most frequent n-gram frequencies of chief complaint terms and discharge diagnosis codes, term co-occurrence network graphs for the ChiefComplaintParsed and CCDD fields, a chief complaint and discharge diagnosis term correlation network graph, and n-grams with significant increases or decreases in occurrence over time. Potential clusters or groupings of terms are visualized by node color in term co-occurrence and correlation network graphs and can be selected from the \u0026ldquo;Select by group\u0026rdquo; drop-down menu. Clusters are determined by the Louvain algorithm, an unsupervised method to detect communities in networks by maximizing modularity.\nInteractive widgets were produced with the plotly and visNetwork packages. These packages provide hovering functionality to display data point values and ICD-10 code descriptions.\n User Inputs Access and Management Center (AMC) username and password (securely encrypted) Query start and end dates Has been Emergency: TRUE/FALSE option for limiting to emergency department visits Data source: options include the Chief Complaint Query Validation (CCQV) data source or Facility Location [Full Details] Site: dropdown list of all sites reporting to the NSSP (applies only when using Facility Location [Full Details] Age Groups: options include all existing ESSENCE age grouping systems Syndrome definition: CCDD category, subsyndrome, or syndrome. CCDD Query: option for custom chief complaint and discharge diagnosis free-text queries Complex Query: option to paste in API URL for complex queries searching multiple fields Title: custom title of Flexdashboard HTML output Output When knit with parameters, this template generates a Flexible Dashboard report in HTML format.\n Add this template # Add `text_mining` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;text_mining\u0026#34;) Remove this template # Remove `text_mining` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;text_mining\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/essenceccdd/","title":"ESSENCE CCDD Categories","tags":["chief complaint","discharge diagnosis","essence","nssp","template"],"description":"","content":"name: essence_ccdd fullname: Essence CCDD Categories Trends description: \u0026gt;This template generates a trend report of Chief Complaint and Discharge Diagnosis (CCDD) Categories between the MMWR weeks containing the dates you choose. You are able to select as many of the CCDD Categories as you would like to generate this report and are able to control for data quality using the Average Weekly DDI% and CoV(HasBeenE) filters. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: false Detailed Description This template (essence_ccdd) generates a trend report of Chief Complaint and Discharge Diagnosis (CCDD) Categories between the MMWR weeks containing the dates you choose. Users able to select as many of the CCDD Categories as they would like to knit this template and are able to control for data quality using the Average Weekly DDI% and CoV(HasBeenE) filters.\nThis template depicts Essence CCDD categories by count of visits and percentage of visits, stratified by year.\nEmergency department visits are categorized via free-text queries of the chief complaint and discharge diagnosis fields. The availability and informativeness of these fields varies at a facility level. To ensure enough information is consistently provided to NSSP-ESSENCE for categorization, facilities are included if they met the following standards:\n Average Weekly Discharge Diagnosis Informative Percent (DDI%) - A measure of how informative the information in the discharge diagnosis fields are over time. The DDI% is used to control for the quality of the discharge diagnosis field. Facilities were included in the report if they had a DDI greater than or equal to 75% over the past two years. Data Quality Coefficient of Variation (CoV) - A measure of total volume volatility over time. The CoV is used to control for onboarding of new facilities over the time period of interest. Facilities are included if they had a COV less than or equal to 40 over the past two years. User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP ESSENCE account password Start Date: Automatically modified to the start date to be the first day of the MMWR week of the selected start date. End Date: recommended to be at least 2 weeks prior to date of running the report to account for a lag in discharge diagnosis data. Automatically modified to be the last day of the MMWR week of the selected end date. CCDD Categories: can be any categories of interest. If no categories are selected the report will default to include all available categories. Avg Weekly Discharge Diagnosis Informative (DDI) Greater than or equal to: Threshold for facility level average weekly discharge diagnosis informative. Helps control for informativeness of the discharge diagnosis field. It is recommended to select an average weekly DDI of 75 or greater. If no value is entered the report will default to not filter facilities by this data quality metric. Coefficient of Variance (CoV HasBeenE) Less than or equal to: Threshold for the coefficient of variance (CoV) for ED visits. Helps control for total volume volatility for the selected time period. It is recommended to select a CoV of 40 or less. If no value is entered the report will default to not filter facilities by this data quality metric. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `essence_ccdd` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;essence_ccdd\u0026#34;) Remove this template # Remove `essence_ccdd` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;essence_ccdd\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/listtemplates/","title":"List available templates","tags":["load","library","list","template","demo"],"description":"","content":"Rnssp R Markdown templates are being designed and released regularly. All available templates can be explored on the publicly accessible Rnssp RMD templates Github repository.\nThe Rnssp R package provides various utility functions to easily manage templates. One of those utility functions is the Rnssp::list_templates() function.\nFirst, load the Rnssp R package:\n# Load the Rnssp package library(Rnssp) Next, get the current list of available packages:\n# List all available templates list_templates() To get a tabular and more detailed view of the available templates, run:\n# Detailed table view of the available templates list_templates(as.table = TRUE) %\u0026gt;% View() Here\u0026rsquo;s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/post/","title":"Posts","tags":[],"description":"","content":"Posts Knitting With Parameters How to Pull CCDD Category List from NSSP-ESSENCE "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/utilityaddtemplate/","title":"Add a template","tags":["add","template","demo"],"description":"","content":"After loading the Rnssp R package (library(Rnssp)), use the add_rmd_template() utility function to add/update a template.\nThis example uses the essence_ccdd template:\n# Add the `essence_ccdd` template add_rmd_template(\u0026#34;essence_ccdd\u0026#34;) ALWAYS RESTART YOUR R SESSION after adding or updating a template to your Rnssp R package installation.\n Here’s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/edicd10volume/","title":"ED ICD-10 Category Volumes","tags":["emergency","department","icd10","volumes","heatmap","nssp","essence","template"],"description":"","content":"name: ed_icd10_volume fullname: Emergency Department ICD-10 Category Volumes description: \u0026gt;This template generates heatmaps 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. The user is able to select the geographic region of interest, time frame, data quality filters, and ESSENCE age group category. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description This template (ed_icd10_volume) generates heatmaps 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. The user is able to select the geographic region of interest, time frame, data quality filters, and ESSENCE age group category.\nICD-10-CM Chapters, Sections, and Codes: The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) classifies over 70,000 diagnosis codes into chapters and sections. ESSENCE uses the first three characters (e.g., A00 or J21) into 1 of 22 chapters, 284 sections, and 1,911 diagnosis code categories. More information on ICD-10-CM can be found here.\nCCSR Diagnostic Categories: The Healthcare Cost and Utilization Project (HCUP) Clinical Classifications Software Refined (CCSR) aggregates over 70,000 ICD-10-CM diagnosis codes into 530 meaningful diagnostic categories. More information on the CCSR and mapping schema can be found here.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP ESSENCE account password Start Date: Start date End Date: Recommended to be at least 2 weeks prior to date of running the report to account for a lag in discharge diagnosis data. Site: Geographic region, can be national, a Department of Health and Human Services (DHHS) region, or participating site. Automatically defaults to national data. Site Facility: A Facility Level ESSENCE API with the facility or facilities of interest selected. Overwrites site parameter to run the report for a specific facility. Facility Name: Label the report with the facility name(s). Stratification Variable: Can be one of the age, sex, race, or ethnicity classifications in ESSENCE. Add Unknown: TRUE/FALSE option as to whether Unknown or Not Reported categories should be considered. Default is FALSE. Top N conditions to rank: Default is 10. Avg Weekly Discharge Diagnosis Informative (DDI) Greater than or equal to: Threshold for facility level average weekly discharge diagnosis informative. Helps control for informativeness of the discharge diagnosis field. It is recommended to select an average weekly DDI of 75 or greater. If no value is entered, the report will default to not filter facilities by this data quality metric. To remove the average weekly DDI filter, enter 0. Coefficient of Variance (CoV HasBeenE) Less than or equal to: Threshold for the coefficient of variance (CoV) for ED visits. Helps control for total volume volatility for the selected time period. It is recommended to select a CoV of 40 or less. If no value is entered the report will default to not filter facilities by this data quality metric. To remove the CoV HasBeenE filter, enter 1000000. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `ed_icd10_volume` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;ed_icd10_volume\u0026#34;) Remove this template # Remove `ed_icd10_volume` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;ed_icd10_volume\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/manualaddtemplate/","title":"Manually add a template","tags":["manually","add","template","demo"],"description":"","content":"A template may manually be added to the existing Rnssp installation by using the add_rmd_template() utility function.\nUsers may download a template zip archive from the Rnssp RMD templates Github repository and manually add it to the existing Rnssp installation.\nIn fact, when executed without any parameter, the add_rmd_template() utility function opens a file explorer dialog box that allows users to load a template zip file.\nMake sure that the Rnssp package is loaded (library(Rnssp)), as shown below:\n# Manually add a template add_rmd_template() # with no argument ALWAYS RESTART YOUR R SESSION after adding or updating a template to your Rnssp R package installation.\n Here\u0026rsquo;s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/syndromeeval/","title":"Syndrome Definition Evaluation","tags":["syndrome","definition","evaluation","nssp","essence","template","demo"],"description":"","content":"name: syndrome_eval fullname: Syndrome Definition Evaluation description: \u0026gt;An automated report template that allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time. Original Script By: Sara Chronister (Maricopa County, AZ). Revamped and Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The Syndrome Definition Evaluation template (syndrome_eval) allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time.\nThis template parses syndrome terms, identifies their type and count their CCDD matches.\nThe syndrome definition evaluation template generates:\n A table summarizing individual definition information by syndrome definition An interactive visualization comparing visits by syndrome definition over time A comparative bar chart of total visits identified by all syndrome definitions combined A summary table of the number and percent of identified visits captured by each observed combination of definitions A Venn diagram, an Euler diagram, and an upset plot as visual representations of the number of identified visits captured by each observed combination of definitions Summary plots of the top five occurring terms for each definition and each field of interest User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP ESSENCE account password Site: A participating site Start Date: Automatically modified to be the first day of the MMWR week of the selected start date End Date: Recommended to be at least 2 weeks prior to date of running the report to account for a lag in discharge diagnosis data. Automatically modified to be the last day of the MMWR week of the selected end date. Has been Emergency: TRUE/FALSE option for limiting to emergency department visits Chunk data pull (per day)?: TRUE/FALSE option for pull the data by chunks (time resolution: one day) Grouping systems (Up to 3): When more than 3 are supplied, only the first 3 are considered by the template Custom Query 1: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API Custom Query Label 1: A string labeling Custom Query 1 Custom Query 2: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API Custom Query Label 1: A string labeling Custom Query 2 Custom Query 3: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API Custom Query Label 3: A string labeling Custom Query 3 A title for the report Export Data: TRUE/FALSE option as to whether to save export and save datasets on the disk. When TRUE, a folder named Output is automatically created in the working directory and receives exported data in .csv format. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `syndrome_eval` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;syndrome_eval\u0026#34;) Remove this template # Remove `syndrome_eval` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;syndrome_eval\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/removetemplate/","title":"Remove a template","tags":["remove","template","demo"],"description":"","content":"When an Rnssp R Markdown template is no longer needed, you can dispose of it by using the remove_rmd_template() utility function.\nHere\u0026rsquo;s how to delete the essence_ccdd template:\n# Remove the `essence_ccdd` template remove_rmd_template(\u0026#34;essence_ccdd\u0026#34;) # or remove_rmd_template(template = \u0026#34;essence_ccdd\u0026#34;) ALWAYS RESTART YOUR R SESSION after removing a template from your Rnssp R package installation.\n Here\u0026rsquo;s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/wordalerts/","title":"Word Alerts Report","tags":["word","alerts","chief complaint","discharge diagnosis","algorithm","CCQV","datamart","nssp","essence","template"],"description":"","content":"name: word_alerts fullname: Word Alerts Report description: \u0026gt;The word alerts template summarizes daily chief complaints and discharge diagnosis term alerts for a selected syndrome definition. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The Word Alerts Report template (word_alerts) summarizes daily chief complaints and discharge diagnosis term alerts for a selected syndrome definition.\nThe 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.\nThe current implementation of word alerts in NSSP-ESSENCE is limited to data from the past 7 days. This template lets users run the word alert algorithm on any selected date range spanning up to 90 days.\n Description of Word Alert Algorithm The ESSENCE word alert algorithm uses 28-day baselines over which unigram and bigram frequencies are computed. As with the univariate temporal anomaly detection algorithms, a 2-day guardband is used to separate the baseline and test date. For each term that occurred in the testing block (test date), contingency tables are formed to count the number of emergency department encounters with the term/code occurring in the chief complaint/discharge diagnosis and the number of emergency department encounters without the term/code in the chief complaint/discharge diagnosis for both the testing and baseline blocks.\nTwo-by-two contingency table for RASH SKIN Block Visits with Term Visits without Term Test Date (Last 24 Hours) A: 136 B: 5,111 Baseline (28 Days) C: 2,851 D: 149,477 To test for anomalous increases in term occurrence on the test date relative to the baseline, either Fisher’s Exact Test or a Chi-squared Test is applied. Fisher’s Exact Test is applied for moderate counts, whereas a Chi-squared Test is applied for large counts. Terms are determined to have moderate counts if the number of visits in the baseline with the term is less than 1,000 or if the number of visits on the test date without the term is less than 1,000, i.e., min(B,C) \u0026lt; 1,000. Unigrams and bigrams are considered anomalous if the resulting p-value is less than 0.001.\n Pre-processing of Chief Complaints and Discharge Diagnoses Pre-processing of chief complaint free text includes removal of punctuation, discharge diagnosis codes, uninformative patterns, medical processing terms, and common first names. Duplicate terms in the same chief complaint and discharge diagnosis are also removed. For discharge diagnosis bigrams, pairings of codes are arranged in alphanumeric order so that permutations of the same codes are not counted separately.\n Report Interactivity This HTML report includes interactive visualizations and tables that accommodate hovering to display additional information. ICD-9 and ICD-10 code descriptions can be displayed by hovering over discharge diagnosis codes. Note that descriptions for SNOMED codes are not available.\n User Inputs Access and Management Center (AMC) username and password (securely encrypted) Query start and end dates Has Been Emergency (Full Details only): Option to limit data where HasBeenE = Yes Data source: CCQV Datamart Backup (NSSP User Only!) or Facility Location (Full Details) Limit to Site (Full Details only): Limit to Site or All Sites Age Groups: Options include all existing ESSENCE age grouping systems. Syndrome Definition: CCDD Category, subsyndrome, or syndrome. CCDD Query (Full Details only): Option for custom chief complaint and discharge diagnosis free-text queries. Complex Query (Full Details only): Option to paste in API URL for complex queries searching multiple fields. Title: Custom title for HTML output. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `word_alerts` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;word_alerts\u0026#34;) Remove this template # Remove `word_alerts` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;word_alerts\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/dqfilters/","title":"Data Quality Filter Matrix","tags":["data quality","discharge diagnosis informative","coefficient of variation","filters","DDI","CoV"],"description":"","content":"name: dq_filters fullname: Data Quality Filter Matrix description: \u0026gt;This template summarizes the DDI Avg Weekly Percent (DDI) and Data Quality CoV (HasBeenE) (CoV (HasBeenE)) filters individually and in conjuction with one another. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description This template summarizes the DDI Avg Weekly Percent (DDI) and Data Quality CoV (HasBeenE) (CoV (HasBeenE)) filters individually and in conjuction with one another.\nMatrices summarize the weekly number of facilities reporting data and the overall visit volume for each data quality filter duration (current year, one year back, two years back, three years back, and four years back) for DDI cutpoints of 70%, 75%, and 80%, and CoV (HasBeenE) cut points of 30, 35, 40, and 45.\nA table is included that lists the DDI and CoV (HasBeenE) values for each data quality filter year for all facilities included in the report.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Site ID: Geographic region. Can be national or a participating site. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `dq_filters` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;dq_filters\u0026#34;) Remove this template # Remove `dq_filters` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;dq_filters\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/templatemanager/","title":"Manage templates with Rnssp addins","tags":["template","rnssp","addins","list","add","update","remove"],"description":"","content":"Starting from Rnssp v. 0.1.0, RStudio users may manage Rnssp R Markdown template with Rnssp Addins.\nLaunch the addin In RStudio, you can use the Addins menu:\nList Available Rnssp templates Users may check the list of all the currently available Rnssp R Markdown templates with the List Rnssp Templates addin:\nOr in the R console :\nRnssp:::list_templates() Add/Update Rnssp Templates A unique feature of the Rnssp package is the ability to add R Markdown templates dynamically to an existing installation of the package. Rnssp R Markdown templates can be dynamically added or updated via the Add/Update Rnssp Templates addin:\nOr in the R console :\nRnssp:::add_rmd_template_gui() Remove Rnssp Templates When one or more Rnssp templates are no longer needed, they can be removed via the Remove Rnssp Templates addin:\nOr in the R console :\nRnssp:::remove_rmd_template_gui() "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/statedqreport/","title":"State Data Quality Report","tags":["data quality","data quality metrics","timeliness","completeness","validity","NSSP priority elements"],"description":"","content":"name: state_dq_report fullname: State Data Quality Report description: \u0026gt;This template summarizes data quality metrics, including timeliness, completeness, and validity. It currently includes NSSP Priority 1 \u0026amp; NSSP Priority 2 elements. Original Code By: Andrew Farrey (Kentucky Injury Prevention and Research Center). Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The state data quality template calculates and summarizes syndromic surveillance data quality metrics pulled from the BioSense platform and the ESSENCE application programming interface (API) similar to the NSSP Data Quality Dashboards. The template assesses coverage, timeliness, completeness, and validity of patient encounters limited to the selected calculated patient class (C_Patient_Class) that occurred during the chosen date range. The default start and end dates include the previous two weeks of data, with the recommended two day lag time reflected. Note that selecting a date range longer than 90 days will result in extensive rendering time.\nCoverage visualizations include interactive plots of the total active facility count, total patient encounters limited to the selected C_Patient_Class, total HL7 messages received by BioSense for patient encounters limited to the selected C_Patient_Class, and a table of currently onboarding facilities.\nTimeliness visualizations include an overall timeliness plot (depicting first message timeliness), an interactive plot of message counts by NSSP Timeliness Category by facility, an interactive plot of message percentages by NSSP timeliness count by facility, a table containing mean and median first message timeliness by facility, a table containing mean and median chief complaint timeliness by facility (chief complaint lag/delay), and a table containing mean and median diagnosis code timeliness by facility (diagnosis code lag/delay). BioSense platform arrival date time stamps have been adjusted to reflect the user’s selected time zone to avoid adversely affecting timeliness calculations.\nThe template assesses all NSSP Priority 1 and NSSP Priority 2 data elements for completeness and validity. Completeness is assessed by data element across the entire patient encounter (required data fields must be present at least once per C_Biosense_ID), while validity is assessed by data element on a per message or per patient encounter basis, depending on each data field’s requirement level (see the validity definition table in the template for more information).\nCompleteness visualizations include overall completeness plots for each NSSP priority level broken down by data element, time series plots of CCAvailable and DDAvailable pulled using the ESSENCE API, and a table containing chief complaint and diagnosis code completeness by facility. Validity visualizations include overall validity plots for both NSSP priority levels broken down by data element, validity tables for both NSSP priority level data elements by facility, time series plots of CCInformative and DDInformative pulled using the ESSENCE API, an interactive plot containing messages sent to the user\u0026rsquo;s site exceptions table, and a table containing error message counts by facility received during the selected date range.\nInteractive plots were created using the plotly package. Interactive tables were created using the DT package and the kableExtra package.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Site ID: Geographic region. Must select one participating site. Start Date: Start date End Date: End date Patient Class: Can be either \u0026ldquo;E (Emergency Department)\u0026rdquo;, \u0026ldquo;I (Inpatient)\u0026rdquo;, or \u0026ldquo;O (Outpatient)\u0026rdquo; Time Zone: User\u0026rsquo;s time zone. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `state_dq_report` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;state_dq_report\u0026#34;) Remove this template # Remove `state_dq_report` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;state_dq_report\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/labpathogentrend/","title":"Lab Pathogen Surveillance","tags":["lab","laboratory","pathogen","surveillance","trend","volume","demographics","response"],"description":"","content":"name: lab_pathogen_trend fullname: Lab Pathogen Surveillance description: \u0026gt;Generates a report of all tests for a selected laboratory A laboratory category 2 pathogen by user selected time period and demographic stratification. Users can select to return the percent of tests with negative results or positive results. Original Code By: Jourdan Devies \u0026amp; Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description 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. Users are able to select a time period and geographic region (national, HHS Region, state, or county). Time periods less than or equal to 60 days will return daily timeseries, greater than 60 days and less than 1 year will return MMWR week timeseries, and greater than 1 year will return monthly timeseries.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Start Date: Start date (February 1, 2019 or later) End Date: End date Lab Category 2 Selection: User selected Lab Result Category 2 option from the list to run the report. Test Type(s): Select the laboratory test type to be included in the output (e.g. All, Antibody, Antigen, etc) Percent Calculation: Choose between graphing the percent of tests with a positive result or percent of tests with a negative result. Geographic Region: Geographic region. Can be national, HHS Region, or state. User Selected County: A Laboratory by Results (Full Details) ESSENCE API with the county or counties of interest selected. Overwrites site parameter to run the report for a specific facility. User Selected County Label: Label the report with the county name(s). Age Group: Can be one of the age, sex, race, or ethnicity classifications in ESSENCE laboratory data. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `lab_pathogen_trend` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;lab_pathogen_trend\u0026#34;) Remove this template # Remove `lab_pathogen_trend` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;lab_pathogen_trend\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/labtestingreason/","title":"Lab Reason for Testing","tags":["lab","laboratory","pathogen","surveillance","trend","volume","demographics","testing","reason"],"description":"","content":"name: lab_testing_reason fullname: Lab Reason for Testing description: \u0026gt;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. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description 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.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Start Date: Start date (February 1, 2019 or later) End Date: End date Geographic Region: Geographic region. Can be national, HHS Region, or state. User Selected County: A Laboratory by Results (Full Details) ESSENCE API with the county or counties of interest selected. Overwrites site parameter to run the report for a specific facility. Free Text Query: ESSENCE syntax for free-text search of codes in the reason for testing field (e.g. ^[;/ ]J02^) Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `lab_testing_reason` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;lab_testing_reason\u0026#34;) Remove this template # Remove `lab_testing_reason` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;lab_testing_reason\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/labyoytrend/","title":"Lab Year Over Year Trends","tags":["lab","laboratory","pathogen","surveillance","trend","volume","routine"],"description":"","content":"name: lab_yoy_trend fullname: Lab Year Over Year Trends description: \u0026gt;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. Original Code By: Dylan Johns \u0026amp; Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description 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).\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Start Date: Start date (February 1, 2019 or later) End Date: End date Lab Category 1 Selections: Laboratory category 1 options to be included in the report. Geographic Region: Geographic region. Can be national, HHS Region, or state. User Selected County: A Laboratory by Results (Full Details) ESSENCE API with the county or counties of interest selected. Overwrites site parameter to run the report for a specific facility. User Selected County Label: Label the report with the county name(s). Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `lab_yoy_trend` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;lab_yoy_trend\u0026#34;) Remove this template # Remove `lab_yoy_trend` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;lab_yoy_trend\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/icd10codeuse/","title":"ICD-10 Discharge Diagnosis Code Usage and Features","tags":["icd10","discharge diagnosis","trend analysis","glm","asyndromic","nssp","essence","emergency","department"],"description":"","content":"name: icd10_code_use fullname: ICD-10 Discharge Diagnosis Code Usage and Features description: \u0026gt;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. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Michael Sheppard. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description This template supports asyndromic surveillance by considering all ICD-10 discharge diagnosis codes occurring in a site\u0026rsquo;s emergency department records over a recent time window and identifying codes with statistically significant increases or decreases in trend over an 11-week period. The data pulled does not limit to a specific CCDD Category, syndrome, or query and includes all records occurring in the date range specified by the user. The report includes a summary of discharge diagnosis code types received (i.e., ICD-10, ICD-9, or SNOMED), summary statistics reporting on total unique codes, mean and median character length, and weekly trends of unique code types. The main section of this report includes HTML sparkline tables displaying weekly trends for codes identified as having significant increases/decreases, ESSENCE time series URL links, and associated demographic features. Features include overall code frequencies, mean and median age, and patient sex breakdowns. Please note that the sparklines represent discharge diagnosis unigram trends that are calculated by dividing the weekly number of occurrences of a code by the total summed frequency of all codes occurring in that week. The trends will therefore mirror trends in the ESSENCE time series figure (after clicking on the URL), however the numeric values will not match as the ESSENCE time series displays the percentage of ED visits in which the code occurred. Lastly, this template includes a summary of ICD-10 discharge diagnosis codes that were identified as having significant increases or decreases due to ICD-10 code revisions imposed by CMS in October of each year. Users can define an end date that is constrained to occur on a Saturday (end of an MMWR week) to include a full week\u0026rsquo;s worth of data for the ending week. The start date will automatically be populated as 17 weeks earlier than the end week to include 18 total weeks of data. Keep in mind that trend significance is only assessed for the last 11 weeks of this 18-week period. Lastly, users will choose their site and indicate whether or not they want to limit to records where Has Been E is Yes.\n User Inputs NSSP Username: AMC and ESSENCE account username NSSP Password: AMC and ESSENCE account password End Date: Saturday end date of the last week to include Has been Emergency: Checked by default to limit to ED encounters. If unchecked, records from other facility types (i.e., urgent care visits) will be included. Site: Site name Title: Customized title, otherwise set to ICD-10 Discharge Diagnosis Code Usage and Feature Template by default Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `icd10_code_use` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;icd10_code_use\u0026#34;) Remove this template # Remove `icd10_code_use` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;icd10_code_use\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/","title":"Rnssp RMD Templates","tags":["intro","help","home","Rnssp"],"description":"","content":"Rnssp R Markdown Templates This catalog of Rnssp R Markdown Templates has been created by the developers of the Rnssp R package in collaboration with the members of the Community of Practice (CoP) and the National Syndromic Surveillance Program (NSSP).\nOur goal is to make a wide collection of report templates accessible and easily distributable via the Rnssp R package.\nThis online documentation serves as a repository of support material for NSSP members. This documentation provides:\n instructions on how to add, use, and remove a template from an existing Rnssp R package installation; detailed description of each template; and blog posts on various topics related to R Markdown templates. Importantly, the documentation promotes collaboration and encourages outreach.\nTo use the Rnssp R Markdown Templates, please install the Rnssp R package first.\n Contributing to this Documentation To contribute to this project, please submit a request to gazondekon@cdc.gov.\nGetting Help If you encounter a bug using the templates, we encourage you to email the author at gazondekon@cdc.gov or file an issue. Include a reproducible example.\nPublic Domain Standard Notice This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC ? 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.\nLicense Standard Notice The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.\nThis source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.\nThis source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY, without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.\nYou should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html\nThe source code forked from other open-source projects will inherit its license.\nPrivacy Standard Notice This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC\u0026rsquo;s privacy policy, please visit http://www.cdc.gov/other/privacy.html.\nContributing Standard Notice Everyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.\nAll comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.\nRecords Management Standard Notice This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/add/","title":"add","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/addins/","title":"addins","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/alerts/","title":"alerts","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/algorithm/","title":"algorithm","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/analysis/","title":"analysis","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/asyndromic/","title":"asyndromic","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/categories/","title":"Categories","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/ccqv/","title":"CCQV","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/change/","title":"change","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/changelogs/","title":"Change Logs","tags":["news","update","logs","change"],"description":"","content":"State Emergency Department template (state_ed_report) 11/16/2021 The State Emergency Department template has been updated. This version has:\n Modified algorithm for trajectory analysis to improve state and county-level trend classifications.\n Improved figure sizing to accommodate the selection of many categories.\n Improved time series visualizations, color palettes.\n Added interactive sparklines to DT table, Improve table formatting.\n 6/8/2021 State Emergency Department template available.\n Text Analysis Interactive Dashboard template (text_mining) 2/14/2023 The Text Mining template has been updated.\nThis version contains uses the 2023 updated ICD 10 codes.\n 8/12/2022 The Text Mining template has been updated. This version:\n 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.\n Includes improvements for removal of discharge diagnosis codes from the chief complaint parsed field and free text from the discharge diagnosis field.\n Displays “ICD-9, SNOMED, or unknown DD code” for non-ICD-10 discharge diagnosis code descriptions rather than NA values.\n Uses an updated ICD-10 discharge diagnosis code description file that includes new codes published in late 2021.\n Uses the visNetwork package to render interactive network graphs for term correlation graphs (for chief complaint free text and discharge diagnosis codes).\n Includes an updated description of template parameter options on the background page.\n No longer includes the character and token length of CC and DD fields tab.\n Includes improved Flexdashboard formatting and theme options.\n 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.\n 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.\n 10/19/2021 The Text Mining template has been updated.\nThis version contains a custom Query field that allows users to enter their own ESSENCE query.\n 9/29/2021 The Text Mining template has been updated. This version:\n Prematurely exits the knit when bad User Credentials are entered.\n Prematurely exits the knit when an empty dataset is returned by the API.\n 8/9/2021 The Text Mining template has been updated. This version:\n Asks for document title in parameter GUI\n Includes age groups 2 - 5\n Allows user to limit to a site or group of sites\n Allows users to subset down to particular age groups if they wish. By default, the data pull should pull CCQV data which doesn\u0026rsquo;t contain age. If a user selects full details, then the age group filtering will apply. All possible age group options have been added.\n Fixes a typo for a parameter name - replaced \u0026ldquo;ccdd_category_string\u0026rdquo; with \u0026ldquo;definition_string\u0026rdquo;\n Changes the default CCDD Category to COVID-DD\n 6/19/2021 The Text Mining template has been updated. This version contains the following updates:\n 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.\n 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 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.\n 5/21/2021 Text Mining template available.\n 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:\n Contains some minor update to the GUI.\n Allows users to generate the report for a specific site.\n 7/6/2021 The Essence Chief Complaint and Discharge Diagnosis Categories template is available.\nThis 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.\n 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:\n Has additional patient demographic stratifications\n Provides facility level selection variables\n 9/28/2021 The Emergency Department ICD-10 Category Volumes template has been updated. This version:\n Contains an Update of the medical grouping system to be chiefcomplaintsubsyndromes when a subsyndrome is selected\n Renders properly and properly prints DDI and CoV cutpoints in the output.\n 9/13/2021 The Emergency Department ICD-10 Category Volumes template is available.\nThis 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.\n Syndrome Definition Evaluation template (syndrome_eval) 8/12/2022 The Syndrome Definition Evaluation template has been updated.\nThis update allows the user to input Free Text Queries or a CSV type URL from NSSP-ESSENCE DataDetails API as a custom query.\n 1/14/2022 The Syndrome Definition Evaluation template has been updated.\nThis update allows the user to input up to three CCDD Free Text Queries.\n 1/6/2022 The Syndrome Definition Evaluation template has been updated.\nThis update adds a functionality to perform the data pulls by chunks of one day.\n 11/3/2021 The Syndrome Definition Evaluation template has been updated.\nThis critical update fixes an issue related to API URLs being ill-constructed when syndromes or subsyndromes are selected.\n 11/1/2021 The Syndrome Definition Evaluation template has been updated for performance and efficiency. It contains:\n 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.\n Some minor improvements that remove large datasets from the memory stack when they are not used.\n 9/13/2021 The Syndrome Definition Evaluation template is available.\nThis template allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time.\n Word Alerts Report template (word_alerts) 8/18/2022 The Word Alerts Report template has been updated. This version:\n Includes a new parameter list to limit to existing ESSENCE age grouping systems.\n Includes an option for \u0026ldquo;All\u0026rdquo; under the Limit to Site parameter drop-down list when using the Facility Location (Full Details) data source.\n 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.\n Provides more flexibility for selecting start and end dates.\n 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.\n Includes enhanced summary visualizations of the number of alerts by field and n-gram.\n Includes terms with alerts over the entire date range selected in the sparkline tables rather than those with alerts for the most recent date.\n Uses daily time chunked API pulls for the Facility Location (Full Details) data source with a progress bar.\n Includes a summary parameter table at the beginning of the report to display parameters that a user selects.\n Includes a report appendix section at the end to summarize example stop words by class.\n 11/15/2021 The Word Alerts Report template has been updated. This version:\n Updated the API for site-level full data details to use the Syndrome Subsyndrome CCDD Combined Category field to simplify the code.\n 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.\n Removed duplicate cat() statements when no alerts are found.\n Default date range is now the most recent 90 days. Default start and end dates are calculated using base R.\n 11/9/2021 The Word Alerts Report template is available.\nThe Word Alerts Report template summarizes daily chief complaints and discharge diagnosis term alerts for a selected syndrome definition.\nThe purpose of the word alert algorithm is to seek anomalous chief complaints free text terms and discharge diagnosis codes relative to a 28-day sliding baseline.\nThe 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.\n Data Quality Filter Matrix template (dq_filters) 4/5/2022 The Data Quality Filter Matrix template is available.\nThis template summarizes the DDI Avg Weekly Percent (DDI) and Data Quality CoV (HasBeenE) (CoV (HasBeenE)) filters individually and in conjunction with one another.\n State Data Quality Report template (state_dq_report) 1/31/2023 The State Data Quality Report template is available.\nThis template summarizes data quality metrics, including timeliness, completeness, and validity. It Currently includes NSSP Priority 1 \u0026amp; NSSP Priority 2 elements.\n Lab Pathogen Surveillance template (lab_pathogen_trend) 8/02/2023 The Lab Pathogen Surveillance template is available.\nThis 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.\n Lab Reason for Testing template (lab_testing_reason) 8/02/2023 The Lab Reason for Testing template is available.\nThis 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.\n Lab Year Over Year Trends template (lab_yoy_trend) 8/02/2023 The Lab Year Over Year Trends template is available.\nThis 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).\n ICD-10 Discharge Diagnosis Code Usage and Features (icd10_code_use) 11/21/2023 The ICD-10 Discharge Diagnosis Code Usage and Features template is available.\nThis template generates an HTML file with sparkline tables displaying ICD-10 discharge diagnosis codes identified as having recent statistically significant increases or decreases in trend. Data pulled are all encounters for a site and are not limited to a specific CCDD Category, syndrome, or query. Users are able to select an end date, their site, and specify whether or not they want to limit to visits where Has Been Emergency is Yes.\n "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/chief-complaint/","title":"chief complaint","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/coefficient-of-variation/","title":"coefficient of variation","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/completeness/","title":"completeness","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/contribute/","title":"contribute","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/contributor/","title":"contributor","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/county/","title":"county","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/cov/","title":"CoV","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/credits/","title":"Credits","tags":["credits","contribute","contributor","developers","ideas"],"description":"","content":"We would like to acknowledge the following persons for their support and contribution:\nOriginal Idea and Concept Roseric Azondekon Documentation Development Roseric Azondekon Template Ideas and Development Aaron Kite-Powell Michael Sheppard Kelly Carey Andrew Farrey Sara Chronister Roseric Azondekon The National Syndromic Surveillance Program (NSSP) and the NSSP Community of Practice Tooling Netlify - Continuous deployment and hosting of this documentation Hugo - The world’s fastest framework for building websites Grav - A Modern Flat-File Content Management System R - An Environment for Statistical Computing RStudio - An Integrated Development Environment for R "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/credits/","title":"credits","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/dashboard/","title":"dashboard","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/data-quality/","title":"data quality","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/data-quality-metrics/","title":"data quality metrics","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/datamart/","title":"datamart","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/ddi/","title":"DDI","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/definition/","title":"definition","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/demo/","title":"demo","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/demographics/","title":"demographics","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/department/","title":"department","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/developers/","title":"developers","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/discharge-diagnosis/","title":"discharge diagnosis","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/discharge-diagnosis-informative/","title":"discharge diagnosis informative","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/emergency/","title":"emergency","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/essence/","title":"essence","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/evaluation/","title":"evaluation","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/filters/","title":"filters","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/glm/","title":"glm","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/heatmap/","title":"heatmap","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/help/","title":"help","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/home/","title":"home","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/icd10/","title":"icd10","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/ide/","title":"IDE","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/ideas/","title":"ideas","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/intro/","title":"intro","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/lab/","title":"lab","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/laboratory/","title":"laboratory","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/library/","title":"library","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/list/","title":"list","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/lm/","title":"lm","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/load/","title":"load","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/logs/","title":"logs","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/manually/","title":"manually","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/mining/","title":"mining","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/news/","title":"news","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/nssp/","title":"nssp","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/nssp-priority-elements/","title":"NSSP priority elements","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/pathogen/","title":"pathogen","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/r/","title":"R","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/reason/","title":"reason","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/remove/","title":"remove","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/requirements/","title":"requirements","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/response/","title":"response","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/rnssp/","title":"Rnssp","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/routine/","title":"routine","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/rstudio/","title":"Rstudio","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/state/","title":"state","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/surveillance/","title":"surveillance","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/syndrome/","title":"syndrome","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/","title":"Tags","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/template/","title":"template","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/testing/","title":"testing","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/text/","title":"text","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/timeliness/","title":"timeliness","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/trend/","title":"trend","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/trend-analysis/","title":"trend analysis","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/update/","title":"update","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/validity/","title":"validity","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/volume/","title":"volume","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/volumes/","title":"volumes","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/word/","title":"word","tags":[],"description":"","content":""}]
\ No newline at end of file
+[{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/post/2021-11-06-knitting-with-parameters-using-the-knit-button-within-rstudio/","title":"Knitting With Parameters","tags":[],"description":"","content":"\r\rFirst, start a new R Markdown file From Template as demonstrated below:\r\rNext, Knit the template With Parameters using the Knit button in your Rstudio IDE:\r\rReferences:\rKnitting with parameters\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/stateedreport/","title":"State Emergency Department","tags":["state","county","emergency","department","glm","lm","nssp","essence","template"],"description":"","content":"name: state_ed_report fullname: Text Analysis Interactive Dashboard description: \u0026gt;An automated Text Analysis Interactive Dashboard template. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The state emergency department report template (state_ed_report) summarizes trend classification and ESSENCE alerting for the CCDD categories at the state and county level. Users can select percentages, counts, or percentages and counts for state and county-level time series. By default, trends are reported as a percent of daily emergency department visits.\nTo classify trends over time, this template applies penalized least squares smoothing splines to time series of percentages and Poisson generalized additive models to time series of counts. The slopes of the smoothed data are used to classify daily trajectory statuses into categories of increase, stable, or decrease. Slopes greater than a pre-defined slope cut point of 0.01 are classified as increasing, while slopes less than -0.01 are classified as decreasing. Slopes with an absolute value less than or equal to 0.01 are classified as stable. This method is best suited for classification of county-level time series with higher variability in day-to-day trends.\nIf you\u0026rsquo;re pulling current data, use a 3-day lag. This best practice prevents lower counts associated with lags in receiving data from biasing the most recent classification.\nTo identify stratifications with recent and anomalous increases in syndromic activity, ESSENCE alerting is overlaid on the time series for each county and CCDD category. These alerts correspond to ESSENCE's default alerting algorithm, Poisson/EWMA/Regression Switch, with alerting thresholds 0.05 (yellow) and 0.01 (red).\nDaily stratified alerting indicators and statistics are pulled along with the percentages, numerators, and denominators from the time series data table application programming interface (API).\n User Inputs Access and Magagement Center (AMC) username and password (securely encrypted) State (data are pulled by hospital state from the Facility Location [Full Details] data source CCDD Categories — currently includes all CCDD categories available in ESSENCE. Users may select as many categories as they want. The default categories are CLI CC with CLI DD and Coronavirus DD v1, CDC Pneumonia CCDD v1, and CDC COVID-Specific DD v1. Query start and end dates Time series type — percentages (default), counts, or percentages and counts Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `state_ed_report` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;state_ed_report\u0026#34;) Remove this template # Remove `state_ed_report` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;state_ed_report\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/","title":"Usage","tags":[],"description":"","content":"Usage Learn how to dynamically extend your existing Rnssp installation with Rnssp R Markdown templates.\n Requirements List available templates Add a template Manually add a template Remove a template Manage templates with Rnssp addins "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/post/2022-08-17-pull-existing-ccdd-cateogires-and-queries-with-essence-api/","title":"How to Pull CCDD Category List from NSSP-ESSENCE","tags":[],"description":"","content":" This post demonstrates how users with access to NSSP-ESSENCE can pull an up-to-date list of existing ESSENCE CCDD categories and their underlying queries using an ESSENCE API URL. These data can be pulled into RStudio in JSON format and will match the CC and DD Categories table found under the “More” tab in NSSP-ESSENCE. This example can be run either in the BioSense Platform instance of RStudio Workbench or in a local desktop instance of RStudio. Users must have the Rnssp package installed and will need to save their Access and Management Center (AMC) credentials to a myProfile object to proceed.\nThe following packages are needed to run this example:\nlibrary(tidyverse) library(Rnssp) If you haven’t already saved your AMC credentials to a myProfile object, then run the following code chunk to supply your username and password:\n myProfile \u0026lt;- create_profile() Out of convenience, you can save your myProfile object to either an .rda or .rds file in your home directory as follows:\n # .rda option save(myProfile, file = \u0026quot;~/myProfile.rda\u0026quot;) # .rds option saveRDS(myProfile, \u0026quot;~/myProfile.rds\u0026quot;) By saving your myProfile object to your home directory, only you will be able to access and load this file into your global environment. You should only need to update your credentials every 90 days after your AMC password expires. To load your credentials into your environment, you can either use the load() function for an rda file or the readRDS() function for an rds file.\n # .rda option load(\u0026quot;~/myProfile.rda\u0026quot;) # .rds option myProfile \u0026lt;- readRDS(\u0026quot;~/myProfile.rds\u0026quot;) The API URL to pull the existing list of CCDD categories and their underlying queries will pull from SyndromeDefinitionsServlet_CCDD using the action getCCDDTerms. This will import JSON-formatted data as a list of length 1 with element “categories”. This element is a standard data frame and can be extracted from this list using the pluck() function from the purrr package, which is included in tidyverse.\n url \u0026lt;- \u0026quot;https://essence.syndromicsurveillance.org/nssp_essence/servlet/SyndromeDefinitionsServlet_CCDD?action=getCCDDTerms\u0026quot; ccdd_queries \u0026lt;- get_api_data(url) %\u0026gt;% pluck(\u0026quot;categories\u0026quot;) glimpse(ccdd_queries) The ccdd_queries data frame will contain the following elements:\n updateInfo: Information on recent updates. All categories currently have a value of “No Updates”. termId: CCDD category ID (row number) groupName: Name of the group to which the CCDD category belongs. All categories currently have a value of “Uncategorized” dateCreated Date the CCDD category was added to the system. notes: Supplemental notes or details accompanying the CCDD category. All categories currently have a value of “No Notes” lastUpdate: Date the CCDD category or accompanying metadata was last updated. description: Summary text describing the purpose of the CCDD category and how the query was developed. definition: The underlying query of the CCDD category and fields that are searched. isAdmin: Boolean indicator that is TRUE for all CCDD categories category: Name of the CCDD category fieldsSearched: List of query fields that are searched. All categories currently have a value of “Undefined”. This information can be found in the defintion field described above. Typically, only the category and definition fields will be of interest. The extraneous fields can be removed by using the select() function:\n ccdd_queries \u0026lt;- get_api_data(url) %\u0026gt;% pluck(\u0026quot;categories\u0026quot;) %\u0026gt;% select(category, definition) head(ccdd_queries) "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/","title":"Available Templates","tags":[],"description":"","content":"Available Templates Explore and learn how to use the Rnssp R Markdown templates.\n State Emergency Department Text Analysis Dashboard ESSENCE CCDD Categories ED ICD-10 Category Volumes Syndrome Definition Evaluation Word Alerts Report Data Quality Filter Matrix State Data Quality Report Lab Pathogen Surveillance Lab Reason for Testing Lab Year Over Year Trends ICD-10 Discharge Diagnosis Code Usage and Features "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/requirements/","title":"Requirements","tags":["requirements","R","Rstudio","demo","IDE"],"description":"","content":"For a pleasant experience with the Rnssp R Markdown templates, users' system requirements must satisfy the following requirements:\n Proper installation and configuration of R (\u0026gt;= 3.6.0) Proper installation and configuration of an RStudio Integrated Development Environment Installation of the Rnssp R package The development version of the Rnssp R package can be installed from Github using the devtools or the remotes R package:\n# install the Rnssp package using devtools devtools::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;) # devtools::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;, force = TRUE) or\n# install the Rnssp package using remotes remotes::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;) # remotes::install_github(\u0026#34;cdcgov/Rnssp\u0026#34;, force = TRUE) Shown below is a demo of the installation of the Rnssp R package using the devtools R package.\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/textmining/","title":"Text Analysis Dashboard","tags":["text","analysis","dashboard","mining","nssp","essence","template"],"description":"","content":"name: text_mining fullname: State Emergency Department Report description: \u0026gt;An automated state emergency department report template summarizing CCDD categories. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program. Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The Interactive Text Analysis Dashboard template (text_mining) summarizes the chief complaint text and discharge diagnosis codes as part of an initial description of the content of these fields. Drop-down menus allow users to select from existing ESSENCE syndrome definitions, including CCDD categories, syndromes, and subsyndromes. Users can also input a custom query of the CCDD field or the API URL for complex queries that search multiple fields.\nThis template can access two different data sources, including the Chief Complaint Query Validation (CCQV) data source in NSSP ESSENCE and Facility Location Full Details. Please be aware that when using the CCQV data source some sites have opted out of contributing their data, including Arizona, Idaho, Illinois, Marion County, Indiana, Massachusetts, North Dakota, and Ohio. To accomodate site-level users, the Facility Location Full Details data source can be selected so that data are pulled at the individual state-level. Note: The API URL for the full details data source limits to CCQV fields only.\nThe visualizations in this template include total weekly volume of encounters, the 200 most frequent n-gram frequencies of chief complaint terms and discharge diagnosis codes, term co-occurrence network graphs for the ChiefComplaintParsed and CCDD fields, a chief complaint and discharge diagnosis term correlation network graph, and n-grams with significant increases or decreases in occurrence over time. Potential clusters or groupings of terms are visualized by node color in term co-occurrence and correlation network graphs and can be selected from the \u0026ldquo;Select by group\u0026rdquo; drop-down menu. Clusters are determined by the Louvain algorithm, an unsupervised method to detect communities in networks by maximizing modularity.\nInteractive widgets were produced with the plotly and visNetwork packages. These packages provide hovering functionality to display data point values and ICD-10 code descriptions.\n User Inputs Access and Management Center (AMC) username and password (securely encrypted) Query start and end dates Has been Emergency: TRUE/FALSE option for limiting to emergency department visits Data source: options include the Chief Complaint Query Validation (CCQV) data source or Facility Location [Full Details] Site: dropdown list of all sites reporting to the NSSP (applies only when using Facility Location [Full Details] Age Groups: options include all existing ESSENCE age grouping systems Syndrome definition: CCDD category, subsyndrome, or syndrome. CCDD Query: option for custom chief complaint and discharge diagnosis free-text queries Complex Query: option to paste in API URL for complex queries searching multiple fields Title: custom title of Flexdashboard HTML output Output When knit with parameters, this template generates a Flexible Dashboard report in HTML format.\n Add this template # Add `text_mining` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;text_mining\u0026#34;) Remove this template # Remove `text_mining` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;text_mining\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/essenceccdd/","title":"ESSENCE CCDD Categories","tags":["chief complaint","discharge diagnosis","essence","nssp","template"],"description":"","content":"name: essence_ccdd fullname: Essence CCDD Categories Trends description: \u0026gt;This template generates a trend report of Chief Complaint and Discharge Diagnosis (CCDD) Categories between the MMWR weeks containing the dates you choose. You are able to select as many of the CCDD Categories as you would like to generate this report and are able to control for data quality using the Average Weekly DDI% and CoV(HasBeenE) filters. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: false Detailed Description This template (essence_ccdd) generates a trend report of Chief Complaint and Discharge Diagnosis (CCDD) Categories between the MMWR weeks containing the dates you choose. Users able to select as many of the CCDD Categories as they would like to knit this template and are able to control for data quality using the Average Weekly DDI% and CoV(HasBeenE) filters.\nThis template depicts Essence CCDD categories by count of visits and percentage of visits, stratified by year.\nEmergency department visits are categorized via free-text queries of the chief complaint and discharge diagnosis fields. The availability and informativeness of these fields varies at a facility level. To ensure enough information is consistently provided to NSSP-ESSENCE for categorization, facilities are included if they met the following standards:\n Average Weekly Discharge Diagnosis Informative Percent (DDI%) - A measure of how informative the information in the discharge diagnosis fields are over time. The DDI% is used to control for the quality of the discharge diagnosis field. Facilities were included in the report if they had a DDI greater than or equal to 75% over the past two years. Data Quality Coefficient of Variation (CoV) - A measure of total volume volatility over time. The CoV is used to control for onboarding of new facilities over the time period of interest. Facilities are included if they had a COV less than or equal to 40 over the past two years. User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP ESSENCE account password Start Date: Automatically modified to the start date to be the first day of the MMWR week of the selected start date. End Date: recommended to be at least 2 weeks prior to date of running the report to account for a lag in discharge diagnosis data. Automatically modified to be the last day of the MMWR week of the selected end date. CCDD Categories: can be any categories of interest. If no categories are selected the report will default to include all available categories. Avg Weekly Discharge Diagnosis Informative (DDI) Greater than or equal to: Threshold for facility level average weekly discharge diagnosis informative. Helps control for informativeness of the discharge diagnosis field. It is recommended to select an average weekly DDI of 75 or greater. If no value is entered the report will default to not filter facilities by this data quality metric. Coefficient of Variance (CoV HasBeenE) Less than or equal to: Threshold for the coefficient of variance (CoV) for ED visits. Helps control for total volume volatility for the selected time period. It is recommended to select a CoV of 40 or less. If no value is entered the report will default to not filter facilities by this data quality metric. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `essence_ccdd` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;essence_ccdd\u0026#34;) Remove this template # Remove `essence_ccdd` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;essence_ccdd\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/listtemplates/","title":"List available templates","tags":["load","library","list","template","demo"],"description":"","content":"Rnssp R Markdown templates are being designed and released regularly. All available templates can be explored on the publicly accessible Rnssp RMD templates Github repository.\nThe Rnssp R package provides various utility functions to easily manage templates. One of those utility functions is the Rnssp::list_templates() function.\nFirst, load the Rnssp R package:\n# Load the Rnssp package library(Rnssp) Next, get the current list of available packages:\n# List all available templates list_templates() To get a tabular and more detailed view of the available templates, run:\n# Detailed table view of the available templates list_templates(as.table = TRUE) %\u0026gt;% View() Here\u0026rsquo;s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/post/","title":"Posts","tags":[],"description":"","content":"Posts Knitting With Parameters How to Pull CCDD Category List from NSSP-ESSENCE "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/utilityaddtemplate/","title":"Add a template","tags":["add","template","demo"],"description":"","content":"After loading the Rnssp R package (library(Rnssp)), use the add_rmd_template() utility function to add/update a template.\nThis example uses the essence_ccdd template:\n# Add the `essence_ccdd` template add_rmd_template(\u0026#34;essence_ccdd\u0026#34;) ALWAYS RESTART YOUR R SESSION after adding or updating a template to your Rnssp R package installation.\n Here’s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/edicd10volume/","title":"ED ICD-10 Category Volumes","tags":["emergency","department","icd10","volumes","heatmap","nssp","essence","template"],"description":"","content":"name: ed_icd10_volume fullname: Emergency Department ICD-10 Category Volumes description: \u0026gt;This template generates heatmaps 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. The user is able to select the geographic region of interest, time frame, data quality filters, and ESSENCE age group category. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description This template (ed_icd10_volume) generates heatmaps 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. The user is able to select the geographic region of interest, time frame, data quality filters, and ESSENCE age group category.\nICD-10-CM Chapters, Sections, and Codes: The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) classifies over 70,000 diagnosis codes into chapters and sections. ESSENCE uses the first three characters (e.g., A00 or J21) into 1 of 22 chapters, 284 sections, and 1,911 diagnosis code categories. More information on ICD-10-CM can be found here.\nCCSR Diagnostic Categories: The Healthcare Cost and Utilization Project (HCUP) Clinical Classifications Software Refined (CCSR) aggregates over 70,000 ICD-10-CM diagnosis codes into 530 meaningful diagnostic categories. More information on the CCSR and mapping schema can be found here.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP ESSENCE account password Start Date: Start date End Date: Recommended to be at least 2 weeks prior to date of running the report to account for a lag in discharge diagnosis data. Site: Geographic region, can be national, a Department of Health and Human Services (DHHS) region, or participating site. Automatically defaults to national data. Site Facility: A Facility Level ESSENCE API with the facility or facilities of interest selected. Overwrites site parameter to run the report for a specific facility. Facility Name: Label the report with the facility name(s). Stratification Variable: Can be one of the age, sex, race, or ethnicity classifications in ESSENCE. Add Unknown: TRUE/FALSE option as to whether Unknown or Not Reported categories should be considered. Default is FALSE. Top N conditions to rank: Default is 10. Avg Weekly Discharge Diagnosis Informative (DDI) Greater than or equal to: Threshold for facility level average weekly discharge diagnosis informative. Helps control for informativeness of the discharge diagnosis field. It is recommended to select an average weekly DDI of 75 or greater. If no value is entered, the report will default to not filter facilities by this data quality metric. To remove the average weekly DDI filter, enter 0. Coefficient of Variance (CoV HasBeenE) Less than or equal to: Threshold for the coefficient of variance (CoV) for ED visits. Helps control for total volume volatility for the selected time period. It is recommended to select a CoV of 40 or less. If no value is entered the report will default to not filter facilities by this data quality metric. To remove the CoV HasBeenE filter, enter 1000000. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `ed_icd10_volume` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;ed_icd10_volume\u0026#34;) Remove this template # Remove `ed_icd10_volume` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;ed_icd10_volume\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/manualaddtemplate/","title":"Manually add a template","tags":["manually","add","template","demo"],"description":"","content":"A template may manually be added to the existing Rnssp installation by using the add_rmd_template() utility function.\nUsers may download a template zip archive from the Rnssp RMD templates Github repository and manually add it to the existing Rnssp installation.\nIn fact, when executed without any parameter, the add_rmd_template() utility function opens a file explorer dialog box that allows users to load a template zip file.\nMake sure that the Rnssp package is loaded (library(Rnssp)), as shown below:\n# Manually add a template add_rmd_template() # with no argument ALWAYS RESTART YOUR R SESSION after adding or updating a template to your Rnssp R package installation.\n Here\u0026rsquo;s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/syndromeeval/","title":"Syndrome Definition Evaluation","tags":["syndrome","definition","evaluation","nssp","essence","template","demo"],"description":"","content":"name: syndrome_eval fullname: Syndrome Definition Evaluation description: \u0026gt;An automated report template that allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time. Original Script By: Sara Chronister (Maricopa County, AZ). Revamped and Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The Syndrome Definition Evaluation template (syndrome_eval) allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time.\nThis template parses syndrome terms, identifies their type and count their CCDD matches.\nThe syndrome definition evaluation template generates:\n A table summarizing individual definition information by syndrome definition An interactive visualization comparing visits by syndrome definition over time A comparative bar chart of total visits identified by all syndrome definitions combined A summary table of the number and percent of identified visits captured by each observed combination of definitions A Venn diagram, an Euler diagram, and an upset plot as visual representations of the number of identified visits captured by each observed combination of definitions Summary plots of the top five occurring terms for each definition and each field of interest User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP ESSENCE account password Site: A participating site Start Date: Automatically modified to be the first day of the MMWR week of the selected start date End Date: Recommended to be at least 2 weeks prior to date of running the report to account for a lag in discharge diagnosis data. Automatically modified to be the last day of the MMWR week of the selected end date. Has been Emergency: TRUE/FALSE option for limiting to emergency department visits Chunk data pull (per day)?: TRUE/FALSE option for pull the data by chunks (time resolution: one day) Grouping systems (Up to 3): When more than 3 are supplied, only the first 3 are considered by the template Custom Query 1: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API Custom Query Label 1: A string labeling Custom Query 1 Custom Query 2: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API Custom Query Label 1: A string labeling Custom Query 2 Custom Query 3: Free Text Query or a CSV type URL from NSSP-ESSENCE DataDetails API Custom Query Label 3: A string labeling Custom Query 3 A title for the report Export Data: TRUE/FALSE option as to whether to save export and save datasets on the disk. When TRUE, a folder named Output is automatically created in the working directory and receives exported data in .csv format. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `syndrome_eval` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;syndrome_eval\u0026#34;) Remove this template # Remove `syndrome_eval` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;syndrome_eval\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/removetemplate/","title":"Remove a template","tags":["remove","template","demo"],"description":"","content":"When an Rnssp R Markdown template is no longer needed, you can dispose of it by using the remove_rmd_template() utility function.\nHere\u0026rsquo;s how to delete the essence_ccdd template:\n# Remove the `essence_ccdd` template remove_rmd_template(\u0026#34;essence_ccdd\u0026#34;) # or remove_rmd_template(template = \u0026#34;essence_ccdd\u0026#34;) ALWAYS RESTART YOUR R SESSION after removing a template from your Rnssp R package installation.\n Here\u0026rsquo;s a demo:\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/wordalerts/","title":"Word Alerts Report","tags":["word","alerts","chief complaint","discharge diagnosis","algorithm","CCQV","datamart","nssp","essence","template"],"description":"","content":"name: word_alerts fullname: Word Alerts Report description: \u0026gt;The word alerts template summarizes daily chief complaints and discharge diagnosis term alerts for a selected syndrome definition. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The Word Alerts Report template (word_alerts) summarizes daily chief complaints and discharge diagnosis term alerts for a selected syndrome definition.\nThe 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.\nThe current implementation of word alerts in NSSP-ESSENCE is limited to data from the past 7 days. This template lets users run the word alert algorithm on any selected date range spanning up to 90 days.\n Description of Word Alert Algorithm The ESSENCE word alert algorithm uses 28-day baselines over which unigram and bigram frequencies are computed. As with the univariate temporal anomaly detection algorithms, a 2-day guardband is used to separate the baseline and test date. For each term that occurred in the testing block (test date), contingency tables are formed to count the number of emergency department encounters with the term/code occurring in the chief complaint/discharge diagnosis and the number of emergency department encounters without the term/code in the chief complaint/discharge diagnosis for both the testing and baseline blocks.\nTwo-by-two contingency table for RASH SKIN Block Visits with Term Visits without Term Test Date (Last 24 Hours) A: 136 B: 5,111 Baseline (28 Days) C: 2,851 D: 149,477 To test for anomalous increases in term occurrence on the test date relative to the baseline, either Fisher’s Exact Test or a Chi-squared Test is applied. Fisher’s Exact Test is applied for moderate counts, whereas a Chi-squared Test is applied for large counts. Terms are determined to have moderate counts if the number of visits in the baseline with the term is less than 1,000 or if the number of visits on the test date without the term is less than 1,000, i.e., min(B,C) \u0026lt; 1,000. Unigrams and bigrams are considered anomalous if the resulting p-value is less than 0.001.\n Pre-processing of Chief Complaints and Discharge Diagnoses Pre-processing of chief complaint free text includes removal of punctuation, discharge diagnosis codes, uninformative patterns, medical processing terms, and common first names. Duplicate terms in the same chief complaint and discharge diagnosis are also removed. For discharge diagnosis bigrams, pairings of codes are arranged in alphanumeric order so that permutations of the same codes are not counted separately.\n Report Interactivity This HTML report includes interactive visualizations and tables that accommodate hovering to display additional information. ICD-9 and ICD-10 code descriptions can be displayed by hovering over discharge diagnosis codes. Note that descriptions for SNOMED codes are not available.\n User Inputs Access and Management Center (AMC) username and password (securely encrypted) Query start and end dates Has Been Emergency (Full Details only): Option to limit data where HasBeenE = Yes Data source: CCQV Datamart Backup (NSSP User Only!) or Facility Location (Full Details) Limit to Site (Full Details only): Limit to Site or All Sites Age Groups: Options include all existing ESSENCE age grouping systems. Syndrome Definition: CCDD Category, subsyndrome, or syndrome. CCDD Query (Full Details only): Option for custom chief complaint and discharge diagnosis free-text queries. Complex Query (Full Details only): Option to paste in API URL for complex queries searching multiple fields. Title: Custom title for HTML output. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `word_alerts` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;word_alerts\u0026#34;) Remove this template # Remove `word_alerts` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;word_alerts\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/dqfilters/","title":"Data Quality Filter Matrix","tags":["data quality","discharge diagnosis informative","coefficient of variation","filters","DDI","CoV"],"description":"","content":"name: dq_filters fullname: Data Quality Filter Matrix description: \u0026gt;This template summarizes the DDI Avg Weekly Percent (DDI) and Data Quality CoV (HasBeenE) (CoV (HasBeenE)) filters individually and in conjuction with one another. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description This template summarizes the DDI Avg Weekly Percent (DDI) and Data Quality CoV (HasBeenE) (CoV (HasBeenE)) filters individually and in conjuction with one another.\nMatrices summarize the weekly number of facilities reporting data and the overall visit volume for each data quality filter duration (current year, one year back, two years back, three years back, and four years back) for DDI cutpoints of 70%, 75%, and 80%, and CoV (HasBeenE) cut points of 30, 35, 40, and 45.\nA table is included that lists the DDI and CoV (HasBeenE) values for each data quality filter year for all facilities included in the report.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Site ID: Geographic region. Can be national or a participating site. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `dq_filters` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;dq_filters\u0026#34;) Remove this template # Remove `dq_filters` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;dq_filters\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/usage/templatemanager/","title":"Manage templates with Rnssp addins","tags":["template","rnssp","addins","list","add","update","remove"],"description":"","content":"Starting from Rnssp v. 0.1.0, RStudio users may manage Rnssp R Markdown template with Rnssp Addins.\nLaunch the addin In RStudio, you can use the Addins menu:\nList Available Rnssp templates Users may check the list of all the currently available Rnssp R Markdown templates with the List Rnssp Templates addin:\nOr in the R console :\nRnssp:::list_templates() Add/Update Rnssp Templates A unique feature of the Rnssp package is the ability to add R Markdown templates dynamically to an existing installation of the package. Rnssp R Markdown templates can be dynamically added or updated via the Add/Update Rnssp Templates addin:\nOr in the R console :\nRnssp:::add_rmd_template_gui() Remove Rnssp Templates When one or more Rnssp templates are no longer needed, they can be removed via the Remove Rnssp Templates addin:\nOr in the R console :\nRnssp:::remove_rmd_template_gui() "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/statedqreport/","title":"State Data Quality Report","tags":["data quality","data quality metrics","timeliness","completeness","validity","NSSP priority elements"],"description":"","content":"name: state_dq_report fullname: State Data Quality Report description: \u0026gt;This template summarizes data quality metrics, including timeliness, completeness, and validity. It currently includes NSSP Priority 1 \u0026amp; NSSP Priority 2 elements. Original Code By: Andrew Farrey (Kentucky Injury Prevention and Research Center). Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description The state data quality template calculates and summarizes syndromic surveillance data quality metrics pulled from the BioSense platform and the ESSENCE application programming interface (API) similar to the NSSP Data Quality Dashboards. The template assesses coverage, timeliness, completeness, and validity of patient encounters limited to the selected calculated patient class (C_Patient_Class) that occurred during the chosen date range. The default start and end dates include the previous two weeks of data, with the recommended two day lag time reflected. Note that selecting a date range longer than 90 days will result in extensive rendering time.\nCoverage visualizations include interactive plots of the total active facility count, total patient encounters limited to the selected C_Patient_Class, total HL7 messages received by BioSense for patient encounters limited to the selected C_Patient_Class, and a table of currently onboarding facilities.\nTimeliness visualizations include an overall timeliness plot (depicting first message timeliness), an interactive plot of message counts by NSSP Timeliness Category by facility, an interactive plot of message percentages by NSSP timeliness count by facility, a table containing mean and median first message timeliness by facility, a table containing mean and median chief complaint timeliness by facility (chief complaint lag/delay), and a table containing mean and median diagnosis code timeliness by facility (diagnosis code lag/delay). BioSense platform arrival date time stamps have been adjusted to reflect the user’s selected time zone to avoid adversely affecting timeliness calculations.\nThe template assesses all NSSP Priority 1 and NSSP Priority 2 data elements for completeness and validity. Completeness is assessed by data element across the entire patient encounter (required data fields must be present at least once per C_Biosense_ID), while validity is assessed by data element on a per message or per patient encounter basis, depending on each data field’s requirement level (see the validity definition table in the template for more information).\nCompleteness visualizations include overall completeness plots for each NSSP priority level broken down by data element, time series plots of CCAvailable and DDAvailable pulled using the ESSENCE API, and a table containing chief complaint and diagnosis code completeness by facility. Validity visualizations include overall validity plots for both NSSP priority levels broken down by data element, validity tables for both NSSP priority level data elements by facility, time series plots of CCInformative and DDInformative pulled using the ESSENCE API, an interactive plot containing messages sent to the user\u0026rsquo;s site exceptions table, and a table containing error message counts by facility received during the selected date range.\nInteractive plots were created using the plotly package. Interactive tables were created using the DT package and the kableExtra package.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Site ID: Geographic region. Must select one participating site. Start Date: Start date End Date: End date Patient Class: Can be either \u0026ldquo;E (Emergency Department)\u0026rdquo;, \u0026ldquo;I (Inpatient)\u0026rdquo;, or \u0026ldquo;O (Outpatient)\u0026rdquo; Time Zone: User\u0026rsquo;s time zone. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `state_dq_report` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;state_dq_report\u0026#34;) Remove this template # Remove `state_dq_report` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;state_dq_report\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/labpathogentrend/","title":"Lab Pathogen Surveillance","tags":["lab","laboratory","pathogen","surveillance","trend","volume","demographics","response"],"description":"","content":"name: lab_pathogen_trend fullname: Lab Pathogen Surveillance description: \u0026gt;Generates a report of all tests for a selected laboratory A laboratory category 2 pathogen by user selected time period and demographic stratification. Users can select to return the percent of tests with negative results or positive results. Original Code By: Jourdan Devies \u0026amp; Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description 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. Users are able to select a time period and geographic region (national, HHS Region, state, or county). Time periods less than or equal to 60 days will return daily timeseries, greater than 60 days and less than 1 year will return MMWR week timeseries, and greater than 1 year will return monthly timeseries.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Start Date: Start date (February 1, 2019 or later) End Date: End date Lab Category 2 Selection: User selected Lab Result Category 2 option from the list to run the report. Test Type(s): Select the laboratory test type to be included in the output (e.g. All, Antibody, Antigen, etc) Percent Calculation: Choose between graphing the percent of tests with a positive result or percent of tests with a negative result. Geographic Region: Geographic region. Can be national, HHS Region, or state. User Selected County: A Laboratory by Results (Full Details) ESSENCE API with the county or counties of interest selected. Overwrites site parameter to run the report for a specific facility. User Selected County Label: Label the report with the county name(s). Age Group: Can be one of the age, sex, race, or ethnicity classifications in ESSENCE laboratory data. Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `lab_pathogen_trend` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;lab_pathogen_trend\u0026#34;) Remove this template # Remove `lab_pathogen_trend` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;lab_pathogen_trend\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/labtestingreason/","title":"Lab Reason for Testing","tags":["lab","laboratory","pathogen","surveillance","trend","volume","demographics","testing","reason"],"description":"","content":"name: lab_testing_reason fullname: Lab Reason for Testing description: \u0026gt;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. Original Code By: Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description 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.\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Start Date: Start date (February 1, 2019 or later) End Date: End date Geographic Region: Geographic region. Can be national, HHS Region, or state. User Selected County: A Laboratory by Results (Full Details) ESSENCE API with the county or counties of interest selected. Overwrites site parameter to run the report for a specific facility. Free Text Query: ESSENCE syntax for free-text search of codes in the reason for testing field (e.g. ^[;/ ]J02^) Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `lab_testing_reason` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;lab_testing_reason\u0026#34;) Remove this template # Remove `lab_testing_reason` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;lab_testing_reason\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/labyoytrend/","title":"Lab Year Over Year Trends","tags":["lab","laboratory","pathogen","surveillance","trend","volume","routine"],"description":"","content":"name: lab_yoy_trend fullname: Lab Year Over Year Trends description: \u0026gt;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. Original Code By: Dylan Johns \u0026amp; Kelly Carey. Adapted to the Rnssp Package by: Gbedegnon Roseric Azondekon. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description 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).\n User Inputs NSSP Username: NSSP ESSENCE account username NSSP Password: NSSP account password Start Date: Start date (February 1, 2019 or later) End Date: End date Lab Category 1 Selections: Laboratory category 1 options to be included in the report. Geographic Region: Geographic region. Can be national, HHS Region, or state. User Selected County: A Laboratory by Results (Full Details) ESSENCE API with the county or counties of interest selected. Overwrites site parameter to run the report for a specific facility. User Selected County Label: Label the report with the county name(s). Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `lab_yoy_trend` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;lab_yoy_trend\u0026#34;) Remove this template # Remove `lab_yoy_trend` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;lab_yoy_trend\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/templates/icd10codeuse/","title":"ICD-10 Discharge Diagnosis Code Usage and Features","tags":["icd10","discharge diagnosis","trend analysis","glm","asyndromic","nssp","essence","emergency","department"],"description":"","content":"name: icd10_code_use fullname: ICD-10 Discharge Diagnosis Code Usage and Features description: \u0026gt;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. Original Code By: Michael Sheppard. Adapted to the Rnssp Package by: Michael Sheppard. National Syndromic Surveillance Program (NSSP). Centers for Disease Control and Prevention (CDC). create_dir: true Detailed Description This template supports asyndromic surveillance by considering all ICD-10 discharge diagnosis codes occurring in a site\u0026rsquo;s emergency department records over a recent time window and identifying codes with statistically significant increases or decreases in trend over an 11-week period. The data pulled does not limit to a specific CCDD Category, syndrome, or query and includes all records occurring in the date range specified by the user. The report includes a summary of discharge diagnosis code types received (i.e., ICD-10, ICD-9, or SNOMED), summary statistics reporting on total unique codes, mean and median character length, and weekly trends of unique code types. The main section of this report includes HTML sparkline tables displaying weekly trends for codes identified as having significant increases/decreases, ESSENCE time series URL links, and associated demographic features. Features include overall code frequencies, mean and median age, and patient sex breakdowns. Please note that the sparklines represent discharge diagnosis unigram trends that are calculated by dividing the weekly number of occurrences of a code by the total summed frequency of all codes occurring in that week. The trends will therefore mirror trends in the ESSENCE time series figure (after clicking on the URL), however the numeric values will not match as the ESSENCE time series displays the percentage of ED visits in which the code occurred. Lastly, this template includes a summary of ICD-10 discharge diagnosis codes that were identified as having significant increases or decreases due to ICD-10 code revisions imposed by CMS in October of each year. Users can define an end date that is constrained to occur on a Saturday (end of an MMWR week) to include a full week\u0026rsquo;s worth of data for the ending week. The start date will automatically be populated as 17 weeks earlier than the end week to include 18 total weeks of data. Keep in mind that trend significance is only assessed for the last 11 weeks of this 18-week period. Lastly, users will choose their site and indicate whether or not they want to limit to records where Has Been E is Yes.\n User Inputs NSSP Username: AMC and ESSENCE account username NSSP Password: AMC and ESSENCE account password End Date: Saturday end date of the last week to include Has been Emergency: Checked by default to limit to ED encounters. If unchecked, records from other facility types (i.e., urgent care visits) will be included. Site: Site name Title: Customized title, otherwise set to ICD-10 Discharge Diagnosis Code Usage and Feature Template by default Output When knit with parameters, this template generates a report in HTML format.\n Add this template # Add `icd10_code_use` to my existing Rnssp installation Rnssp::add_rmd_template(\u0026#34;icd10_code_use\u0026#34;) Remove this template # Remove `icd10_code_use` from my existing Rnssp installation Rnssp::remove_rmd_template(\u0026#34;icd10_code_use\u0026#34;) Latest Update!\nFor questions, ideas for improvement/collaboration, or attribution, please submit an issue here.\n Download this template "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/","title":"Rnssp RMD Templates","tags":["intro","help","home","Rnssp"],"description":"","content":"Rnssp R Markdown Templates This catalog of Rnssp R Markdown Templates has been created by the developers of the Rnssp R package in collaboration with the members of the Community of Practice (CoP) and the National Syndromic Surveillance Program (NSSP).\nOur goal is to make a wide collection of report templates accessible and easily distributable via the Rnssp R package.\nThis online documentation serves as a repository of support material for NSSP members. This documentation provides:\n instructions on how to add, use, and remove a template from an existing Rnssp R package installation; detailed description of each template; and blog posts on various topics related to R Markdown templates. Importantly, the documentation promotes collaboration and encourages outreach.\nTo use the Rnssp R Markdown Templates, please install the Rnssp R package first.\n Contributing to this Documentation To contribute to this project, please submit a request to gazondekon@cdc.gov.\nGetting Help If you encounter a bug using the templates, we encourage you to email the author at gazondekon@cdc.gov or file an issue. Include a reproducible example.\nPublic Domain Standard Notice This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC ? 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.\nLicense Standard Notice The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.\nThis source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.\nThis source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY, without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.\nYou should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html\nThe source code forked from other open-source projects will inherit its license.\nPrivacy Standard Notice This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC\u0026rsquo;s privacy policy, please visit http://www.cdc.gov/other/privacy.html.\nContributing Standard Notice Everyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.\nAll comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.\nRecords Management Standard Notice This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.\n"},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/add/","title":"add","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/addins/","title":"addins","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/alerts/","title":"alerts","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/algorithm/","title":"algorithm","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/analysis/","title":"analysis","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/asyndromic/","title":"asyndromic","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/categories/","title":"Categories","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/ccqv/","title":"CCQV","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/change/","title":"change","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/changelogs/","title":"Change Logs","tags":["news","update","logs","change"],"description":"","content":"State Emergency Department template (state_ed_report) 11/16/2021 The State Emergency Department template has been updated. This version has:\n Modified algorithm for trajectory analysis to improve state and county-level trend classifications.\n Improved figure sizing to accommodate the selection of many categories.\n Improved time series visualizations, color palettes.\n Added interactive sparklines to DT table, Improve table formatting.\n 6/8/2021 State Emergency Department template available.\n Text Analysis Interactive Dashboard template (text_mining) 2/14/2023 The Text Mining template has been updated.\nThis version contains uses the 2023 updated ICD 10 codes.\n 8/12/2022 The Text Mining template has been updated. This version:\n 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.\n Includes improvements for removal of discharge diagnosis codes from the chief complaint parsed field and free text from the discharge diagnosis field.\n Displays “ICD-9, SNOMED, or unknown DD code” for non-ICD-10 discharge diagnosis code descriptions rather than NA values.\n Uses an updated ICD-10 discharge diagnosis code description file that includes new codes published in late 2021.\n Uses the visNetwork package to render interactive network graphs for term correlation graphs (for chief complaint free text and discharge diagnosis codes).\n Includes an updated description of template parameter options on the background page.\n No longer includes the character and token length of CC and DD fields tab.\n Includes improved Flexdashboard formatting and theme options.\n 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.\n 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.\n 10/19/2021 The Text Mining template has been updated.\nThis version contains a custom Query field that allows users to enter their own ESSENCE query.\n 9/29/2021 The Text Mining template has been updated. This version:\n Prematurely exits the knit when bad User Credentials are entered.\n Prematurely exits the knit when an empty dataset is returned by the API.\n 8/9/2021 The Text Mining template has been updated. This version:\n Asks for document title in parameter GUI\n Includes age groups 2 - 5\n Allows user to limit to a site or group of sites\n Allows users to subset down to particular age groups if they wish. By default, the data pull should pull CCQV data which doesn\u0026rsquo;t contain age. If a user selects full details, then the age group filtering will apply. All possible age group options have been added.\n Fixes a typo for a parameter name - replaced \u0026ldquo;ccdd_category_string\u0026rdquo; with \u0026ldquo;definition_string\u0026rdquo;\n Changes the default CCDD Category to COVID-DD\n 6/19/2021 The Text Mining template has been updated. This version contains the following updates:\n 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.\n 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 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.\n 5/21/2021 Text Mining template available.\n 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:\n Contains some minor update to the GUI.\n Allows users to generate the report for a specific site.\n 7/6/2021 The Essence Chief Complaint and Discharge Diagnosis Categories template is available.\nThis 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.\n 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:\n Has additional patient demographic stratifications\n Provides facility level selection variables\n 9/28/2021 The Emergency Department ICD-10 Category Volumes template has been updated. This version:\n Contains an Update of the medical grouping system to be chiefcomplaintsubsyndromes when a subsyndrome is selected\n Renders properly and properly prints DDI and CoV cutpoints in the output.\n 9/13/2021 The Emergency Department ICD-10 Category Volumes template is available.\nThis 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.\n Syndrome Definition Evaluation template (syndrome_eval) 8/12/2022 The Syndrome Definition Evaluation template has been updated.\nThis update allows the user to input Free Text Queries or a CSV type URL from NSSP-ESSENCE DataDetails API as a custom query.\n 1/14/2022 The Syndrome Definition Evaluation template has been updated.\nThis update allows the user to input up to three CCDD Free Text Queries.\n 1/6/2022 The Syndrome Definition Evaluation template has been updated.\nThis update adds a functionality to perform the data pulls by chunks of one day.\n 11/3/2021 The Syndrome Definition Evaluation template has been updated.\nThis critical update fixes an issue related to API URLs being ill-constructed when syndromes or subsyndromes are selected.\n 11/1/2021 The Syndrome Definition Evaluation template has been updated for performance and efficiency. It contains:\n 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.\n Some minor improvements that remove large datasets from the memory stack when they are not used.\n 9/13/2021 The Syndrome Definition Evaluation template is available.\nThis template allows ESSENCE users to evaluate the data details (line level) results of one, two, or three syndrome definitions at a time.\n Word Alerts Report template (word_alerts) 8/18/2022 The Word Alerts Report template has been updated. This version:\n Includes a new parameter list to limit to existing ESSENCE age grouping systems.\n Includes an option for \u0026ldquo;All\u0026rdquo; under the Limit to Site parameter drop-down list when using the Facility Location (Full Details) data source.\n 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.\n Provides more flexibility for selecting start and end dates.\n 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.\n Includes enhanced summary visualizations of the number of alerts by field and n-gram.\n Includes terms with alerts over the entire date range selected in the sparkline tables rather than those with alerts for the most recent date.\n Uses daily time chunked API pulls for the Facility Location (Full Details) data source with a progress bar.\n Includes a summary parameter table at the beginning of the report to display parameters that a user selects.\n Includes a report appendix section at the end to summarize example stop words by class.\n 11/15/2021 The Word Alerts Report template has been updated. This version:\n Updated the API for site-level full data details to use the Syndrome Subsyndrome CCDD Combined Category field to simplify the code.\n 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.\n Removed duplicate cat() statements when no alerts are found.\n Default date range is now the most recent 90 days. Default start and end dates are calculated using base R.\n 11/9/2021 The Word Alerts Report template is available.\nThe Word Alerts Report template summarizes daily chief complaints and discharge diagnosis term alerts for a selected syndrome definition.\nThe purpose of the word alert algorithm is to seek anomalous chief complaints free text terms and discharge diagnosis codes relative to a 28-day sliding baseline.\nThe 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.\n Data Quality Filter Matrix template (dq_filters) 4/5/2022 The Data Quality Filter Matrix template is available.\nThis template summarizes the DDI Avg Weekly Percent (DDI) and Data Quality CoV (HasBeenE) (CoV (HasBeenE)) filters individually and in conjunction with one another.\n State Data Quality Report template (state_dq_report) 1/31/2023 The State Data Quality Report template is available.\nThis template summarizes data quality metrics, including timeliness, completeness, and validity. It Currently includes NSSP Priority 1 \u0026amp; NSSP Priority 2 elements.\n Lab Pathogen Surveillance template (lab_pathogen_trend) 8/02/2023 The Lab Pathogen Surveillance template is available.\nThis 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.\n Lab Reason for Testing template (lab_testing_reason) 8/02/2023 The Lab Reason for Testing template is available.\nThis 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.\n Lab Year Over Year Trends template (lab_yoy_trend) 8/02/2023 The Lab Year Over Year Trends template is available.\nThis 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).\n ICD-10 Discharge Diagnosis Code Usage and Features template (icd10_code_use) 11/21/2023 The ICD-10 Discharge Diagnosis Code Usage and Features template is available.\nThis template generates an HTML file with sparkline tables displaying ICD-10 discharge diagnosis codes identified as having recent statistically significant increases or decreases in trend. Data pulled are all encounters for a site and are not limited to a specific CCDD Category, syndrome, or query. Users are able to select an end date, their site, and specify whether or not they want to limit to visits where Has Been Emergency is Yes.\n "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/chief-complaint/","title":"chief complaint","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/coefficient-of-variation/","title":"coefficient of variation","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/completeness/","title":"completeness","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/contribute/","title":"contribute","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/contributor/","title":"contributor","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/county/","title":"county","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/cov/","title":"CoV","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/credits/","title":"Credits","tags":["credits","contribute","contributor","developers","ideas"],"description":"","content":"We would like to acknowledge the following persons for their support and contribution:\nOriginal Idea and Concept Roseric Azondekon Documentation Development Roseric Azondekon Template Ideas and Development Aaron Kite-Powell Michael Sheppard Kelly Carey Andrew Farrey Sara Chronister Roseric Azondekon The National Syndromic Surveillance Program (NSSP) and the NSSP Community of Practice Tooling Netlify - Continuous deployment and hosting of this documentation Hugo - The world’s fastest framework for building websites Grav - A Modern Flat-File Content Management System R - An Environment for Statistical Computing RStudio - An Integrated Development Environment for R "},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/credits/","title":"credits","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/dashboard/","title":"dashboard","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/data-quality/","title":"data quality","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/data-quality-metrics/","title":"data quality metrics","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/datamart/","title":"datamart","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/ddi/","title":"DDI","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/definition/","title":"definition","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/demo/","title":"demo","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/demographics/","title":"demographics","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/department/","title":"department","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/developers/","title":"developers","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/discharge-diagnosis/","title":"discharge diagnosis","tags":[],"description":"","content":""},{"uri":"https://cdcgov.github.io/Rnssp-rmd-templates/tags/discharge-diagnosis-informative/","title":"discharge diagnosis 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priority 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