README.md

In amgeronimo/chicaslab---stsmodel_africa: Do the hhh4 model and make maps and plots

stsmodel

This folder is now an R package. A rudimentary one, for sure, but it can be loaded using devtools.

Working from a folder containing this one, you can now do:

R> library(devtools)
R> load_all("./stsmodel")
R> area_gpkg ="path/to/UK2019mod_pop.gpkg"
R> linelist = "path/to/Anonymised Combined Line List 20200713.xlsx"
R> trafficdata = "path/to/200616_COVID19_road_traffic_national_table.xlsx"
R> flow = "path/to/mergedflows.rds"
R> alldata = read_all(cases=linelist, flows=flow, traffic=trafficdata, areas=area_gpkg)
[this reads in all the XLSX, CSV etc]
R> launch(outputdir, alldata)

where the parameters to launch are the folder for the output, and this alldata list with all the inputs read into it.

Docker

The image build process is

docker build -t stsmodel .

This creates an image with a version of R with all the needed packages installed. It does not include the package itself. To run the code in the package in the docker image you can mount the stsmodel folder into the container and run it from R.

System Architecture

The overall system architecture will be something like:

• stsmodel is scheduled to run regularly on fhm-chicas-gpu0 using the docker image.
• it writes outputs to a directory in another repository, stsweb, say.
• these outputs can be written to a directory according to the current date, hence keeping historical output runs.
• stsweb is committed and pushed to gitlab.com, and this triggers a CI process that builds a public Gitlab Pages site.

amgeronimo/chicaslab---stsmodel_africa documentation built on Oct. 9, 2020, 2:28 a.m.