reports/make_ModFit_reports.R

#......................
# get results assuming "seroinfinity"
#......................
paths <- list.files("results/Modfits_noserorev/", full.names = TRUE)

#......................
# render
#......................
renderMyDocument <- function(path) {
  countrychar <- toupper(stringr::str_split(basename(path), "_age", simplify = T))[[1]]
  rmarkdown::render("reports/Modfit_report_base.Rmd",
                    params = list( path = path ),
                    output_file = paste0(here::here(), "/reports/", countrychar, "_NoSeroRev_report.pdf"))
}

lapply(paths, renderMyDocument)



#......................
# get results assuming seroreversion
#......................
paths <- list.files("results/Modfits_serorev/", full.names = TRUE)

#......................
# render
#......................
renderMyDocument <- function(path) {
  countrychar <- toupper(stringr::str_split(basename(path), "_age", simplify = T))[[1]]
  rmarkdown::render("reports/Modfit_report_base.Rmd",
                    params = list( path = path ),
                    output_file = paste0(here::here(), "/reports/", countrychar, "_SeroRev_report.pdf"))
}

lapply(paths, renderMyDocument)


#......................
# get results for excluding care home deaths
#......................
paths <- list.files("results/Modfits_carehomes/", full.names = TRUE)

#......................
# render
#......................
renderMyDocument <- function(path) {
  countrychar <- toupper(stringr::str_split(basename(path), "_age|_carehomes", simplify = T))[[1]]
  rmarkdown::render("reports/Modfit_report_base.Rmd",
                    params = list( path = path ),
                    output_file = paste0(here::here(), "/reports/", countrychar, "_CareHomes_report.pdf"))
}

lapply(paths, renderMyDocument)
mrc-ide/reestimate_covidIFR_analysis documentation built on Nov. 19, 2021, 12:07 p.m.