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| Name | Website | Docs | Other |
|---|---|---|---|
| MIMIC | Physionet | -- | Article (description) |
| eICU | Physionet | Link | Article (description) |
| HiRID | Physionet | Link | ICU Benchmark |
| AUMCdb | Website | -- | Link |
Excellent study on 'Predicting sepsis using deep learning across international sites: a retrospective development and validation study' from Michael Moor et al, published in eClinicalMedicine, 2023 (Article, Supplementary Material, Repository)
- Calculating the sepsis3 criteria in AUMCdb (Article, Repository)
The code as it is in the repository does not work. This are just some dingings.
for (x in c("mimic")) {
if (!is_data_avail(x)) {
msg("setting up {x}\n")
setup_src_data(x)
}
dir <- file.path("./")
msg("exporting data for {x}\n")
export_data(x, dest_dir = dir)
}
for (x in c("miiv")) {
if (!is_data_avail(x)) {
msg("setting up {x}\n")
setup_src_data(x)
}
}
for (x in c("miiv")) {
msg("setting up {x}\n")
setup_src_data(x)
}
for (x in c("miiv")) {
if (!is_data_avail(x)) {
msg("setting up {x}\n")
import_src(x)
}
}
for (x in c("aumc")) {
msg("exporting data for {x}\n")
export_data(x)
}
dir <- file.path("data-export", paste0("eicu_bernard")) export_data("eicu", dest_dir = dir)
install.packages( c("mimic.demo", "eicu.demo"), repos = "https://eth-mds.github.io/physionet-demo" ) load_concepts("hr", demo, verbose = FALSE) df <- load_concepts("hr", "eicu_demo", verbose = FALSE) write_psv(df, './')
src='eicu' dest_dir <- './' atr <- list( ricu = list( id_vars = id_vars(dat$dat), index_var = index_var(dat$dat), time_unit = units(interval(dat$dat)), time_step = time_step(dat$dat) ), mcsep = list(cohorts = dat$coh) )
dat <- as.data.frame(dat) fil <- file.path(dest_dir, paste(src, packageVersion("ricu"), sep = "_"))
jsonlite::write_json(atr$mcsep$splits, file.path(cfg_path("splits"), paste0(basename(fil), ".json")), pretty = TRUE )
create_parquet(dat, fil, atr, chunk_size = 1e3)
Sys.setenv( RICU_PHYSIONET_USER = "bahp", RICU_PHYSIONET_PASS = "Imperial-5..", RICU_AUMC_TOKEN = "74ca2023-9aab-4f32-a3e6-ebec156b82ab" )
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