annual-predictions-paper

Code and data behind "Prospective forecasts of annual dengue hemorrhagic fever incidence in Thailand, 2010–2014" by Lauer et al, published in PNAS in 2018.

In order to re-run this experiment, please follow these steps:

1. download this repository by pressing the green button in the upper right-hand corner
2. unzip the downloaded folder
3. replace path/to/package in line 9 of the shell script inst/annual-forecasts-workflow.sh with the absolute path to the home directory of the unzipped folder and save the file
4. run the shell script (on a Mac in the Terminal write: sh path/to/package/annual-predictions-paper-master/inst/annual-forecasts-workflow.sh; the author does not know the PC equivalent of this command)

This shell script:

1. creates an R packrat project, which installs all of the packages used to originally run the analysis (note: this step may take 10 minutes or longer, sometimes due to the long installation of the stringi package)
2. runs make-forecasting-data.R, which puts together the forecasting data from the raw data
3. runs make-forecasts.R which conducts cross validation, model selection, and makes out-of-sample forecasts
4. runs Lauer-annual-DHF-figures.Rnw which makes the figures for the manuscript
5. runs Lauer-annual-DHF-supplement.Rnw which makes the supplement
6. runs Lauer-annual-DHF-manuscript.Rnw which makes the manuscript

If any of this process fails to work, please make an issue and I will try to help!