sirfunctions

Overview

The sirfunctions package contains key functions used by the Surveillance, Innovation, and Research (SIR) team within the Polio Eradication Branch (PEB) at the Centers for Disease Control and Prevention (CDC). It includes functions to download cleaned global polio data from the World Health Organization (WHO) Polio Information System (POLIS) and geographic files. In addition, the package contains functions to visualize important epidemiological trends and perform key performance indicators such as NPAFP rates, EV rates, and stool adequacy.

Installation and Updates

Ensure that devtools is installed (if not run install.packages("devtools")). Then run the following command:

devtools::install_github("nish-kishore/sirfunctions")

Remember to update sirfunctions regularly. If no update is needed, the line of code above will automatically skip.

Usage

Use any function developed in this package using: sirfunctions::{function}

For example: sirfunctions::edav_io(io = "list")

You can find the documentation for any function by running: ?sirfunctions::{function}

For example: ?sirfunctions::edav_io

Functions

Here is a current list of core functions included in sirfunctions with brief descriptions.

NOTE: Any functions getting data or those that interact with EDAV require authenticated connection to CDC EDAV resources.

Get Data

get_all_polio_data: this is the primary function which loads all recent polio data. Parameters can be used to specify date ranges, data selection and user verification.
edav_io: perform key writing/reading/editing functions for EDAV from your R system.
load_clean_{resolution}_sp: 'resolution` can be dist, prov or ctry. Parameters can be used to specify date or spatial ranges as well as the output.
init_dr: this is the primary function to initialize the desk review analytic pipeline. This function handles folder organization and download of data for a specific country. Visualization functions in the desk review will be downloaded as well.

Communications

send_teams_message: send a message to a teams channel with attachments.
upload_to_sharepoint: upload a document to a sharepoint folder.
send_outlook_email: send an email from the validated microsoft account.

Key calculations

extract_country_data: expects a 'raw.data' object that is generated by get_all_polio_data() which includes spatial data. Generates a country specific data file along with relevant spatial objects.
f.ev.rate.01: calculate the enterovirus detection rate using CDC cleaned environmental surveillance data.
f.npafp.rate.01: calculate the non-polio (NP) acute flaccid paralysis (AFP) rate accounting for person-time at risk using CDC cleaned AFP data and appropriately matched population data.
f.stool.ad.01: calculate stool adequacy using CDC cleaned acute flaccid paralysis (AFP) data.
f.timely.detection.01: calculate the timeliness of detection of cases using CDC cleaned acute flaccid paralysis (AFP) data.
f.timely.01: calculate the timeliness of stool data using only epi data.

Visualization

create_emergence_group_gif: function to visualize the spread of specific emegrence groups.
generate_adhoc_map: function to visualize outbreaks.

Helper functions

test_EDAV_connection: Evaluates the speed of connection that users have with the CDC EDAV system.
f.color.schemes: Adds Standard color schemes used in figure creation by the SIR team.
f.expand.bbox: Expands a geographic bounding box generated for maps.
f.metadata.tag: Adds a tag using information from the CDC generated 'raw.data' file to ggplot and flextable objects.
f.plot.looks: Adds standard themes used in figure creation by the SIR team.
duplicate_check: checks for duplicates in the output of get_all_polio_data().
check_afp_guid_ctry_data: checks for GUIDS present in the AFP dataset but not in the population files.
fix_ctry_data_missing_guids: fixes unknown GUIDS in the AFP linelist by obtaining GUIDs found in the pop files based on province and district names for specific years.
compress_png: compress PNG files. Note: requires installation of the pngquant software.
get_diff_cols: get the columns where records differ in a group. Useful for identifying where duplicates differ.

Release Schedule

Please see the Releases page for specifics on previous releases.

Contact

Please send a message to Nishant Kishore at ynm2@cdc.gov for any questions or queries.

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.

License

nish-kishore/sirfunctions

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