mkdir sts
cd sts
stsmap
and stsmodel
git checkout git@gitlab.com:chicas-covid19/stsmap.git
git checkout git@fhm-chicas-code.lancs.ac.uk:covid-19/stsmodel.git
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.
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
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.
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
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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.