This repository contains a model developed by AMR Funding Circle to assess the possible value of developing a point of care test for antimicrobial resistance (AMR). The focus of this analysis is on neonatal sepsis in India.

• dashboard/: a simple dashboard built using shiny.
• docs/: the HTML output files which are rendered to a GitHub pages website.
• notebooks/: an rmarkdown notebook describing the model.
• build.R: contains functions used to generate the notebook and dashboard (generated into the docs/ folder).

1. The R programming language (use of the RStudio IDE is recommended).
2. The following R packages, which may be installed via:

package_names <- c("shiny", "shinylive", "rmarkdown", "purrr", "dplyr", "tidyr", "ggplot2", "colorspace")
install.packages(package_names)

To reproduce the analysis, take the following steps:

1. Clone the GitHub repository to a directory of your choice using

gh repo clone athowes/amr-poct

2. Run build.R to generate the notebook and dashboard.

The RMarkdown file for the notebook notebooks/model.Rmd can be edited as desired. The dashboard can be edited by altering the files dashboard/app.R and dashboard/functions.R.

The session information used to develop this code is as follows:

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] colorspace_2.1-0 ggplot2_3.4.4    tidyr_1.3.0      dplyr_1.1.4      purrr_1.0.2      rmarkdown_2.25   shinylive_0.1.1  shiny_1.8.0