The aim of this analysis is to determine which factors are associated with (or optimistically caused) the decline of malaria in the United States. Example covariates include urbanisation, drainage and socio-economic factors.
The directories of this repository are:
| Directory | Contains |
|---|---|
make |
Scripts used to run the reports. _make.R runs everything in order. |
src |
All orderly reports. |
utils |
Helper scripts for common development tasks. |
orderlyWe use the orderly package (RESIDE, 2020) to simplify the process of doing reproducible research.
After installing orderly (from either CRAN or Github) a report, let's say called example, may be run by:
orderly::orderly_run(name = "src/example")The results of this run will appear in the draft/ folder (ignored on Github).
To commit the draft (with associated id) to the archive/ folder (also ignored on Github, and which should be treated as "read only") use:
orderly::orderly_commit(id)Any outputs of this report will then be available to use as dependencies within other reports.
The R-INLA package is not currently available on CRAN, and instead may be installed by following instructions from the project website.