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 usingshiny
.docs/
: the HTML output files which are rendered to a GitHub pages website.notebooks/
: anrmarkdown
notebook describing the model.build.R
: contains functions used to generate the notebook and dashboard (generated into thedocs/
folder).
- The R programming language (use of the RStudio IDE is recommended).
- 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:
- Clone the GitHub repository to a directory of your choice using
gh repo clone athowes/amr-poct
- 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