Final code for "Prospective forecasts of annual dengue hemorrhagic fever incidence in Thailand, 2010-2014"

Updated manuscript, supplement, figures, and bibliography from reviewers feedback. To run, see read me file below.

code for "Prospective forecasts of annual dengue hemorrhagic fever incidence in Thailand, 2010-2014"

Added license and an annual data set needed for compiling the manuscript (though it wasn't necessary for running the forecasts).

Please use the README to see instructions for use.

Reproducible code and data for "Prospective forecasts of annual dengue hemorrhagic fever incidence in Thailand, 2010-2014"

Instructions for use

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

1. download this repository
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 unzipped folder and save the file
4. run the shell script (on a Mac in the Terminal write: sh path/to/package/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 a 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

updated code, pre-publication manuscript draft

1.0

updated utilities to be able to conduct the analysis; added steps nee…

code and data, no manuscript

This pre-release provides both the code and the data (including R packages) required to make the forecasts that are featured in "Prospective forecasts of annual dengue hemorrhagic fever incidence in Thailand, 2010-2014" (coming soon).