launch <- function(output, alldata){
write_metadata(alldata, file.path(output,"input_metadata.csv"))
last_day = max(as.Date(colnames(alldata$cases)[-1],format="%m/%d/%y"))
run_meta = list(last_day=last_day,
start=Sys.time(),
end=NA,
info = Sys.info()
)
saveRDS(run_meta, file.path(output,"run_meta.rds"))
pdf(file.path(output, "Rplots.pdf"))
# close PDF device on exit from function
on.exit(dev.off())
#THese are done in the other model
#message("Part 01")
#analysis01(output, alldata)
#message("Part 02")
#analysis02(output, alldata)
#message("There is no Part 03")
#message("Part 04")
analysis04(output)
run_meta$end = Sys.time()
run_meta$duration = run_meta$end - run_meta$start
saveRDS(run_meta, file.path(output,"run_meta.rds")) ## update when finished
}
read_all_files <- function(
area_gpkg ="./Data/Unrestricted/original/geodata/UK2019mod_pop.gpkg",
linelist = "./Data/Restricted/PHE/PHE_2020-07-13/Anonymised Combined Line List 20200713.xlsx",
trafficdata = "./Data/Restricted/Traffic/200616_COVID19_road_traffic_national_table.xlsx",
flow = "./Data/Unrestricted/processed/mergedflows.rds"
){
alldata = read_all(cases=linelist, flows=flow, traffic=trafficdata, areas=area_gpkg)
}
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