Package: pynssp
pynsspOverviewA Python package for the National Syndromic Surveillance Program (NSSP) and its Community of Practice. A collection of classes and methods to advance the practice of Syndromic Surveillance. This python package serves as a Python alternative to theRnssp R package.InstallationStable releaseTo installpynssp, run this command in your terminal:pipinstallpynsspThis is the preferred method to installpynssp, as it will always install the most recent stable release.Development versionYou can install the development version ofpynsspfrom Github:pipinstallgit+https://github.com/CDCgov/pynssp.gitUsagefrompynsspimport*fromdatetimeimportdate,timedeltaimportpandasaspd## Creating a user profile (token)myProfile=create_token_profile()## Creating a user profile (username and password)myProfile=create_profile()## JSON URL from NSSP-ESSENCE APIurl="https://essence.syndromicsurveillance.org/nssp_essence/api/alerts/regionSyndromeAlerts?end_date=31Jan2021&start_date=29Jan2021"## Update Start and End dates in NSSP-ESSENCE API URLstartDate=date.today()-timedelta(days=30)endDate=date.today()url=change_dates(url,start_date=startDate,end_date=endDate)## Pull Time Series Data from NSSP-ESSENCEapi_data=get_api_data(url,profile=myProfile)## Inspect data object structureapi_data.columns## Extract table of interestapi_data=pd.json_normalize(api_data["regionSyndromeAlerts"][0])## Get a glimpse of the pulled datasetapi_data.head()Contributing to this projectShould you want to contribute to this project, submit a push request to this Github repository and consider submitting a request to be added as a developer togazondekon@cdc.gov.Getting HelpIf you encounter a clear bug, please consider emailing the author atgazondekon@cdc.govand/orfile an issuewith a minimal reproducible example.Public Domain Standard NoticeThis 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
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the work worldwide are waived through theCC0 1.0 Universal public domain dedication.
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copyright interest.License Standard NoticeThe repository utilizes code licensed under the terms of the Apache Software
License and therefore is licensed under ASL v2 or later.This 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
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PARTICULAR PURPOSE. See the Apache Software License for more details.You should have received a copy of the Apache Software License along with this
program. If not, seehttp://www.apache.org/licenses/LICENSE-2.0.htmlThe source code forked from other open source projects will inherit its license.Privacy Standard NoticeThis repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by theDisclaimerandCode of Conduct.
For more information about CDC's privacy policy, please visithttp://www.cdc.gov/other/privacy.html.Contributing Standard NoticeAnyone is encouraged to contribute to the repository byforkingand submitting a pull request. (If you are new to GitHub, you might start with abasic tutorial.) By contributing
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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 athttp://www.cdc.gov/other/privacy.html.Records Management Standard NoticeThis 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 theCDC web site.Release Notes0.1.0 (2023-06-22)First release on PyPI.FeaturesCredentials Managementcreate_profile()initializes aCredentialsobject from a username and password.create_token_profile()initializes aTokenobject from a REST API token.REST API data pullsget_api_response()retrieves a response from an API service using a provided profile of typeCredentialsorToken. Used as a wrapper to the.get_api_response()method of a provided profile of typeCredentialsorToken.get_api_data()retrieves data (in JSON or CSV) from an API service using a provided profile of typeCredentialsorToken. Used as a wrapper to the.get_api_data()method of a provided profile of typeCredentialsorToken.get_api_graph()retrieves a graph from an API service using a provided profile of typeCredentialsorToken. Used as a wrapper to the.get_api_graph()method of a provided profile of typeCredentialsorToken.get_essence_data()retrieves data from the NSSP-ESSENCE API service using a provided profile of typeCredentialsorToken.Anomaly Detection and Trend Classificationalert_ewma()implements the EWMA time series anomaly detection algorithm.alert_regression()implements the Multiple Adaptive Regression time series anomaly detection algorithm.alert_switch()implements the Regression/EWMA Switch time series anomaly detection algorithmalert_nbinom()implements the Negative Binomial Regression time series anomaly detection algorithm.alert_serfling()implements the original and modified Serfling method for time series anomaly detection.classify_trend()fits rolling binomial models to a daily time series of percentages or proportions to classify the overall trend.Added Dataload_simulated_ts()loads a dataframe of simulated time series.load_nssp_stopwords()loads a dataframe of NSSP-curated stopwords.get_scenario1()loads a a subset of the simulated time series data ("scenario #1").get_scenario2()loads a a subset of the simulated time series data ("scenario #2").Utility Functionschange_dates()modifies the start and end dates in a given URL to new dates, if provided.webscrape_icd()scrapes ICD Codes from the Web.ClassesCredentialsis an abstract representation of a profile object given a username and password strings.Tokenis an abstract representation of a profile object given a token string.APIGraphis an abstract representation of a graph object returns from an API service.NSSPContainerencapsulates a value or an object to store.