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pynssp

A 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.

https://github.com/cdcgov/pynssp

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.2%) to scientific vocabulary

Keywords

cdc essence essence-api nssp nssp-cop

Keywords from Contributors

mesh interactive
Last synced: 6 months ago · JSON representation ·

Repository

A 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.

Basic Info
Statistics
  • Stars: 7
  • Watchers: 4
  • Forks: 7
  • Open Issues: 4
  • Releases: 1
Topics
cdc essence essence-api nssp nssp-cop
Created about 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Authors

README.md

pynssp

pynssp Pipeline pynssp documentation Project Status: Active Lifecycle: experimental PyPI - Downloads PyPI <!-- badges: end -->

Overview

A 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 the Rnssp R package.

Installation

Stable release

To install pynssp, run this command in your terminal:

sh pip install pynssp

This is the preferred method to install pynssp, as it will always install the most recent stable release.

Development version

You can install the development version of pynssp from Github:

sh pip install git+https://github.com/CDCgov/pynssp.git

Usage

```python from pynssp import * from datetime import date, timedelta import pandas as pd

Creating a user profile (token)

myProfile = createtokenprofile()

Creating a user profile (username and password)

myProfile = create_profile()

JSON URL from NSSP-ESSENCE API

url = "https://essence.syndromicsurveillance.org/nsspessence/api/alerts/regionSyndromeAlerts?enddate=31Jan2021&start_date=29Jan2021"

Update Start and End dates in NSSP-ESSENCE API URL

startDate = date.today() - timedelta(days=30) endDate = date.today()

url = changedates(url, startdate = startDate, end_date = endDate)

Pull Time Series Data from NSSP-ESSENCE

apidata = getapi_data(url, profile=myProfile)

Inspect data object structure

api_data.columns

Extract table of interest

apidata = pd.jsonnormalize(api_data["regionSyndromeAlerts"][0])

Get a glimpse of the pulled dataset

api_data.head() ```

Contributing to this project

Should 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 to gazondekon@cdc.gov.

Getting Help

If you encounter a clear bug, please consider emailing the author at gazondekon@cdc.gov and/or file an issue with a minimal reproducible example.

Public 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.

License Standard Notice

The 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 later version.

This 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.

You 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

The source code forked from other open source projects will inherit its license.

Privacy 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's privacy policy, please visit http://www.cdc.gov/other/privacy.html.

Contributing Standard Notice

Anyone 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.

All 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.

Records 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.

Owner

  • Name: Centers for Disease Control and Prevention
  • Login: CDCgov
  • Kind: organization
  • Email: data@cdc.gov
  • Location: Atlanta, GA

CDC's collaborative software projects to protect America from health, safety, and security threats, both foreign and in the U.S.

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it using these metadata."
authors:
  - family-names: Azondekon
    given-names: Gbedegnon Roseric
    orcid: "https://orcid.org/0000-0001-9155-4153"
title: "pynssp: A Python package for the National Syndromic Surveillance Program (NSSP)"
version: 0.1.0
date-released: 2023-06-22
license: "Apache License (>= 2)"
repository-code: "https://github.com/CDCgov/Rnssp"

GitHub Events

Total
  • Issues event: 7
  • Watch event: 3
  • Issue comment event: 4
  • Pull request review event: 2
  • Pull request event: 2
  • Fork event: 5
Last Year
  • Issues event: 7
  • Watch event: 3
  • Issue comment event: 4
  • Pull request review event: 2
  • Pull request event: 2
  • Fork event: 5

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 254
  • Total Committers: 2
  • Avg Commits per committer: 127.0
  • Development Distribution Score (DDS): 0.008
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Azondekon p****2@c****v 252
dependabot[bot] 4****] 2
Committer Domains (Top 20 + Academic)
cdc.gov: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 6
  • Total pull requests: 4
  • Average time to close issues: about 11 hours
  • Average time to close pull requests: about 13 hours
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.75
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 5
  • Pull requests: 1
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: about 2 hours
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.4
  • Average comments per pull request: 2.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rosericazondekon (4)
  • huyndao (1)
  • shawneeunion (1)
Pull Request Authors
  • amanigaultw (2)
  • dependabot[bot] (2)
  • huyndao (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 20 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
pypi.org: pynssp

A 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.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 20 Last month
Rankings
Dependent packages count: 7.3%
Forks count: 23.1%
Average: 25.0%
Stargazers count: 28.2%
Dependent repos count: 41.4%
Maintainers (1)
rosericazondekon
Last synced: 6 months ago

Dependencies

.github/workflows/check-standard.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/gh-pages.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • peaceiris/actions-gh-pages v3 composite
.github/workflows/pypi_publish.yaml actions
  • actions/checkout v3 composite
  • pypa/gh-action-pypi-publish release/v1 composite
requirements_dev.txt pypi
  • Sphinx * development
  • bump2version >=1.0.1 development
  • coverage >=6.2 development
  • cryptography * development
  • flake8 * development
  • m2r * development
  • matplotlib * development
  • pandas * development
  • pillow * development
  • pytest * development
  • requests * development
  • scikit-image * development
  • scipy * development
  • sphinx_rtd_theme * development
  • statsmodels * development
  • tox >=4.0.0a9 development
  • twine >=3.8.0 development
  • watchdog ==2.2.1 development
  • wheel >=0.37.1 development
setup.py pypi