SABRENet

NOTE: This repository contains functions for SABRENet involving Airtable. However, data was removed from Airtable on May 3, 2024. Thus, while some of these functions could be useful as templates for other work, a decent portion of this code is defunct for SABRENet

This respoitory contains code associated with the SABRENet project in collaboration with the University of Pretoria, South Africa. This repository is an offshoot of code originally found in sabrenet-reports that has now become a package for use in other sabrenet-XXXX repositories. This package/repository contains useful code for functions that are used across sabrenet-XXXX repositories

These functions are used in other sabrenet repositories as a downloaded package

devtools::install_github("ecohealthalliance/sabrenetfunctions")

The base is currently maintained by Morgan Kain and Collin Schwantes

Production Base

Repository Structure and Reproducibility (across all sabrenet-XXXX repositories, some may not show up in -this- repo)

• data/ contains data from the study and a data dictionary describing all variables.
• auth/ contains creds for google service account. Click here for more info
• R/ contains functions used in this analysis.
• reports/ contains literate code for R Markdown reports generated in the analysis
• outputs/ contains compiled reports and figures.

Function and R/ naming conventions (across all sabrenet-XXXX repositories, some may not show up in -this- repo)

• First level function prefixes:
  • get_ –> retrieving data from Airtable base
    • mostly associated with data_input_targets
  • insert_ –> Adding new rows to airtable tables with local data
    • mostly associated with data_insert_targets
  • modify_ –> modifying entries in existing rows in airtable tables with local data
    • mostly associated with data_insert_targets
  • process_ , establish_ , clean_ , summarize_ –> all data manipulation/cleaning for insert_ , plot_ , or generate_
    • mostly part of data_organization_targets
  • calculate_ , estimate_ –> Analyses
    • analysis_targets
  • generate_ , plot_ , render_ –> creation of any saved output
    • table_targets , plot_targets
• Second stage prefixes (analysis classes)
  • PCR – pipeline associated with molecular analysis of samples
  • sero – pipeline associated with serology
  • GPS – any spatial stuff
  • diversity – estiamtes of viral diversity

Targets Framework

• Unlike other sabrenet-XXXX repositories this repository does not use the targets package because it just houses some functions that are meant to be sourced from within the other repositories

Versioning

• This project requires R version 4.3.2 (2023-10-31). 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 renv/ and other files in the root project directory. On starting an R session in the working directory, run renv::restore() to install R package dependencies.