sje-notes.md

Notes on codecheck for covid-19

Installs

A list of the key packages to install is listed in install.R and describes what extra Unix packages might be needed.

Docker

Am working on a Dockerfile to run the jobs in a container.

Single point of truth

Would suggest moving this duplicate code into a small script, e.g. setup.R or paths.R:

# Set path
# Set this path to the base directory of the repository.
covid_uk_path = "./"

# covidm options
cm_path = paste0(covid_uk_path, "/covidm/");
if(grepl(Sys.info()["user"], pattern = "^adamkuchars(ki)?$")){cm_path = "~/Documents/GitHub/covidm/"}

Suggestion: use file.path() not paste0()

file.path() is the recommended way by R to construct a portable path name, rather than paste0() (which is admittedly what I also do). So, e.g. this would make changes like:

source(paste0(cm_path, "/R/covidm.R"))

to

source(file.path(cm_path, "R", "covidm.R"))

Mapping of figures to paper

NB: Table 1 and Table 3 of the preprint from April 1 are missing (presumably deleted?).