web_update.md

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

Make a new folder

mkdir sts
cd sts

Checkout stsmap and stsmodel

git checkout [e-mail]:chicas-covid19/stsmap.git
git checkout [e-mail]:covid-19/stsmodel.git

Update or create new daily results in stsmap

Every time you want to update or create the output from new daily data, you run the model in a docker container that creates a new output folder. This output folder is in the stsmap folder and gets pushed to gitlab to create new updated gitlab pages.

Run the model in a docker container

On gpu0 there is a docker image that has R with all the required packages. Run it with the new folder mounted and /data:

docker run -v $PWD/:/app/ -v /data:/data -i -t stsmodel

Run R:

library(devtools)
load_all("./stsmodel")

Now read the data in - use the latest line listing data that has been mounted under /data:

alldata = read_all(cases="/data/covid19/PHE/PHE_2020-07-24/Anonymised Combined Line List 20200724.xlsx", 
 flows="/app/Data/Unrestricted/processed/mergedflows.rds",
 traffic="/data/covid19/DfT/2020-06-16/200616_COVID19_road_traffic_national_table.xlsx",
 areas="/app/Data/Unrestricted/original/geodata/UK2019mod_pop.gpkg")

Now run the model and map, putting the output in the stsmap repo with a date corresponding to the latest date in the data. Note this is not the date of the output file.

model_and_map(alldata,outputdir="./stsmap/days/", useDate=TRUE)
### output dir is /app/stsmap/days/2020-07-23

Quit R.

Set owner

Docker creates everything as root. This gets the UID and GID of the stsmap folder and sets the new day to that:

chown -R `stat -c %u stsmap`:`stat -c %g stsmap` stsmap/days/2020-07-23/

Now exit docker

Push new stsmap

Add the new output day to the stsmap git repo and push to gitlab:

cd stsmap
git add days/
git commit -a -m "new data `date`"
git push

When you want to run with new data, repeat the above, although you don't need to clone stsmap and stsmodel from scratch, you can just pull them for updates from the sts folder.

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