Mathematical epidemiology in a data-rich world

This repository contains the data and sources for my paper Mathematical epidemiology in a data-rich world, published in Infectious Disease Modelling in 2020 (link). Due to editing constraints, the R code in the paper was converted to images by the publisher, meaning the code is not selectable there; the PDF file here does not have this issue (you will need to download the PDF file, though, as the github PDF vewier does not allow any selection at all).

To generate the pdf file

Here are a few remarks concerning the production of the PDF from the RMD file.

1. The version here is slightly different from the article itself: I am not using the elsarticle class, just the standard article class. Later, I might put online the code needed to create the elsarticle version.
2. The option to tidy the code in the echoed chunks does not cut lines properly. A workaround is to use a forked formatR function that can be found by issuing the following 2 R commands. See details here.

library(devtools)
install_github("pablo14/formatR")

3. The last chunk in the RMD file crops the figures before compilation. You might not need it. If you do need it and are using Windows, you will need to figure out how to install pdfcrop. (Hint: you will also have to install Perl.)
4. The file download_and_save_variables.R is an R script that .. downloads and saves variables. It puts in one single place all the downloads that are carried out in the paper and saves the result where the main RMD file gets them.
5. Beware of Wikipedia. If you run into issues when compiling the RMD file, that is most likely where your problem lies. As indicated in the text, Wikipedia editors tend to use tables for a bit everything on a page, which leads to frequent changes in the order in which tables appear in a page. If things break down because, for instance, the renaming of columns complains that the table has fewer columns than the names you are trying to assign, you might have to change the which = command to another value.

Some recent updates (February 2022)

A few things have changed since the paper was originally published.

1. The package wb has evolved and most of the functions I was using became depreciated. Also, some of the arguments changed. For instance, startdate now needs to be typeset as start_date. The code in the Rmd file and the file download_and_save_variables.R was adapted to this change.
2. Final years were also adapted to run to 2022.
3. There was a change in the way the WHO xml is formatted. The measles data query still works as before, since it grabs the csv directly. The code to parse the xml is currently broken.
4. The INVS data has changed from csv to xlsx (Excel) format, requiring to use another package.
5. Loading a data frame does not require stringsAsFactor anymore since R version 4.0, as it is now automatic.