Canadian Notifiable Disease Incidence Dataset (CANDID)

This repository contains all code used to produce the CANDID manuscript and associated figures, tables, and statistics. The published version is here.

The following steps from a unix-like command line will reproduce the manuscript if all the dependencies are available.

Rscript install-iidda-r-pkgs.R
./configure
make

The first step, Rscript install-iidda-r-pkgs.R, is not necessary if you already have up-to-date installations of iidda, iidda.analysis, and iidda.api. These are packages that we developed, which are not on CRAN.

The configure command does the following.

1. Check that R is installed and has version 4.0 or greater
2. Check that required R packages are installed (see install-r-pkgs.R for some tips)
3. Warns if R package versions are different from those listed in r-package-recommendations.R
4. Check that pdflatex and bibtex are installed
5. Check that required LaTeX packages are available
6. Pull the CANDID datasets and store them as rdata files

The make command creates a PDF of the manuscript and all statistics, images, and tables that either appear in the PDF, will appear in the published article, or on this repository. The figure files, Fig1.tif to Fig8.tif, are those that appear in the main text of the manuscript. The document containing supplementary information, S1_Appendix.pdf, is also produced.

A pre-rendered version of the manuscript is output/ms.pdf, and this output directory contains pre-rendered versions of other related files.