Trocaire Somalia Community-based Management of Acute Malnutrition (CMAM) Analytics

This repository is a template for a docker-containerised, {targets}-based, {renv}-enabled R workflow for analytics of Trócaire’s Community-based Management of Acute Malnutrition (CMAM) programme in Somalia.

About the Project

Malnutrition in Somalia is among the highest globally, with around 903,000 children affected, including 150,000 who are severely malnourished. Trócaire addresses this by screening and treating children under five, providing nutrition supplements, and promoting better feeding and hygiene practices among pregnant and nursing mothers. They also train caregivers to identify and refer malnourished children for timely treatment.

This repository contains workflows that process and analyse Trócaire’s community-based management of acute malnutrition (CMAM) routine programme data.

Repository Structure

The project repository is structured as follows:

trocaire-cmam-analytics
    |-- .git-crypt/
    |-- .github/
    |-- auth/
    |-- data/
    |-- data-raw/
    |-- outputs/
    |-- R/
    |-- renv
    |-- reports
    |-- _targets.R
    |-- .env
    |-- .gitattributes
    |-- .Rprofile
    |-- packages.R
    |-- renv.lock

• .git-crypt/ contains git-crypt software specific files to manage encryption of specific files and folders in the repository.

• .github contains project testing and automated deployment of outputs workflows via continuous integration and continuous deployment (CI/CD) using Github Actions.

• auth contains encrypted authentication keys used in this project.

• data/ contains intermediate and final data outputs produced by the workflow.

• data-raw/ contains raw datasets, usually either downloaded from source or added manually, that are used in the project.

• outputs/ contains compiled reports and figures produced by the workflow.

• R/ contains functions developed/created specifically for use in this workflow.

• renv/ contains renv package specific files and directories used by the package for maintaining R package dependencies within the project. The directory renv/library, is a library that contains all packages currently used by the project. This directory, and all files and sub-directories within it, are all generated and managed by the renv package. Users should not change/edit these manually.

• reports/ contains literate code for R Markdown and/or Quarto reports rendered in the workflow.

• _targets.R file defines the steps in the workflow’s data ingest, data processing, data analysis, and reporting pipeline.

• .env is an encrypted file that contains environment variables used in this project.

• .gitattributes file contains information used by git-crypt to determine which files and/or folders in the repository to encrypt.

• .Rprofile file is a project R profile generated when initiating renv for the first time. This file is run automatically every time R is run within this project, and renv uses it to configure the R session to use the renv project library.

• packages.R file lists out all R package dependencies required by the workflow.

• renv.lock file is the renv lockfile which records enough metadata about every package used in this project that it can be re-installed on a new machine. This file is generated by the renv package and should not be changed/edited manually.

Reproducibility

R version

This project was built using R 4.5.1. To manage R versions, it is recommended to use rig - an R installation manager - to be able to install multiple versions of R and switch between them as needed.

R package dependencies

This project uses the {renv} framework to record R package dependencies and versions. Packages and versions used are recorded in renv.lock and code used to manage dependencies is in the renv directory and other files in the root project directory.

On starting an R session in the working directory of this repository, first run

renv::restore()

to install R package dependencies.

Encryption

This project uses encrypted environment variables and authentication keys for data retrieval managed using git-crypt. Collaborators will need to install git-crypt and then provide their GPG key to the authors to be added as an authorised user within the repository. To get a GPG key, download and install GPG and then generate your GPG key pair. Then provide your GPG key id to the authors.

Once given permission into the project and GPG key id added to the repository, update your local version of the repository by doing a git pull and then unlock the encrypted files/folders of the repository by running the following command in Terminal from within the project directory:

git-crypt unlock

The encrypted components of the repository will now be decrypted and accessible for running the workflow (described below).

The workflow

The current workflow has the following steps:

graph LR
  style Graph fill:#FFFFFF00,stroke:#000000;
  subgraph Graph
    direction LR
    xe1cb52acd9cb733d(["otp_admissions_by_sex_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    xc5234a98b2b6e9c0(["otp_admissions_by_sex_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x211a3b39dfafa3b3(["otp_admissions_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x7278532b2bc29c60(["otp_admissions_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x11cedfe9795e0456(["sc_admissions_by_sex_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    xe8b2466bc3ec193d(["sc_admissions_by_sex_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x51516c5a51bc6f72(["sc_admissions_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    xd02d1bbb0c19e187(["sc_admissions_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x15baf61e9ffb2262(["tsfp_u5_admissions_by_sex_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x7b12cae56451f5ec(["tsfp_u5_admissions_by_sex_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x7b6f17b702e81898(["tsfp_u5_admissions_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x6bc4301a20d74330(["tsfp_u5_admissions_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    xefcb70fd373e934d["trocaire_cmam_data_raw"]:::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    xbd3f23f4f80bc001(["tsfp_plw_admissions_by_sex_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    xa4028d0478a08c4a(["tsfp_plw_admissions_by_sex_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x77f2fe6f084dca2c(["tsfp_plw_admissions_yearly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    xc8e187d255805f46(["tsfp_plw_admissions_monthly"]):::completed --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xe1cb52acd9cb733d(["otp_admissions_by_sex_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xc5234a98b2b6e9c0(["otp_admissions_by_sex_yearly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x211a3b39dfafa3b3(["otp_admissions_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x7278532b2bc29c60(["otp_admissions_yearly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x11cedfe9795e0456(["sc_admissions_by_sex_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xe8b2466bc3ec193d(["sc_admissions_by_sex_yearly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x51516c5a51bc6f72(["sc_admissions_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xd02d1bbb0c19e187(["sc_admissions_yearly"]):::completed
    xefcb70fd373e934d["trocaire_cmam_data_raw"]:::completed --> x49ad837c8662aacd(["trocaire_cmam_data"]):::completed
    xab2ef7d5cf8c2a5a["trocaire_data_files"]:::completed --> xefcb70fd373e934d["trocaire_cmam_data_raw"]:::completed
    x768c673cc9e63582(["trocaire_data_files_list"]):::completed --> x2de3516cf4485518(["trocaire_data_file_names"]):::completed
    x2de3516cf4485518(["trocaire_data_file_names"]):::completed --> xab2ef7d5cf8c2a5a["trocaire_data_files"]:::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xbd3f23f4f80bc001(["tsfp_plw_admissions_by_sex_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xa4028d0478a08c4a(["tsfp_plw_admissions_by_sex_yearly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> xc8e187d255805f46(["tsfp_plw_admissions_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x77f2fe6f084dca2c(["tsfp_plw_admissions_yearly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x15baf61e9ffb2262(["tsfp_u5_admissions_by_sex_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x7b12cae56451f5ec(["tsfp_u5_admissions_by_sex_yearly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x7b6f17b702e81898(["tsfp_u5_admissions_monthly"]):::completed
    x49ad837c8662aacd(["trocaire_cmam_data"]):::completed --> x6bc4301a20d74330(["tsfp_u5_admissions_yearly"]):::completed
    
  end

Loading

To run the workflow, issue the following command in R from within the project directory

targets::tar_make()

or issue the following command in Terminal from within the project directory

Rscript -e  "targets::tar_make()"

Authors

• Bisharo Europe Maalim
• Proochista Ariana
• Ernest Guevarra

License

All code in this workflow is released under a GPL-3.0 license. All text and reports in this workflow is released under a CC-BY-4.0 license. Data from Trócaire’s CMAM programme is owned by Trócaire and is restricted to those who have been given permission. All other data is released under a CC0 license.