Closed njtp111 closed 4 months ago
Hi Jiacong,
Thanks for raising this issue!
Your dataset import does not seem to work (none of the datasets are enabled for you yet, indicated by the red x
next to each dataset). Have you tried installing the demo data as a package yet? This should automatically enable the demo data for you. You can install the package via:
install.packages(
"mimic.demo",
repos = "https://eth-mds.github.io/physionet-demo"
)
I suspect that the above is the reason for your error. Could you please try the above and see if this fixes it? Once we have done that, we can then figure out why your import_src
didn't work.
Hi Jiacong,
Thanks for raising this issue!
Your dataset import does not seem to work (none of the datasets are enabled for you yet, indicated by the red
x
next to each dataset). Have you tried installing the demo data as a package yet? This should automatically enable the demo data for you. You can install the package via:install.packages( "mimic.demo", repos = "https://eth-mds.github.io/physionet-demo" )
I suspect that the above is the reason for your error. Could you please try the above and see if this fixes it? Once we have done that, we can then figure out why your
import_src
didn't work.
hi, Robin,
I'm having the same problem as him. And when installing the demo packages no dataset was added.
> install.packages(
+ "mimic.demo",
+ repos = "https://eth-mds.github.io/physionet-demo"
+ )
trying URL 'https://eth-mds.github.io/physionet-demo/src/contrib/mimic.demo_1.0.1.tar.gz'
Content type 'application/gzip' length 9987043 bytes (9.5 MB)
downloaded 9.5 MB
ββ ricu 0.5.3 ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
The following data sources are configured to be attached:
(the environment variable `RICU_SRC_LOAD` controls this)
β mimic: 0 of 26 tables available
β mimic_demo: 0 of 25 tables available
β eicu: 0 of 31 tables available
β eicu_demo: 0 of 31 tables available
β hirid: 0 of 5 tables available
β aumc: 0 of 7 tables available
β miiv: 0 of 27 tables available
ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
Error in `assert_that()` at prockenschaub-ricu-package-1942e93/R/concept-utils.R:701:2:
! x is not a list
Backtrace:
β
1. ββricu::load_dictionary(cfg_dirs = concept_path)
2. ββricu:::parse_dictionary(...) at prockenschaub-ricu-package-1942e93/R/concept-utils.R:1313:2
3. ββricu (local) do_new(concepts, dict) at prockenschaub-ricu-package-1942e93/R/concept-utils.R:1428:2
4. ββbase::lapply(lst_xtr(sub, "concepts"), do_new, ful) at prockenschaub-ricu-package-1942e93/R/concept-utils.R:1414:6
5. ββricu (local) FUN(X[[i]], ...)
6. ββbase::lapply(lst_xtr(sub, "concepts"), do_new, ful) at prockenschaub-ricu-package-1942e93/R/concept-utils.R:1414:6
7. ββricu (local) FUN(X[[i]], ...)
8. ββbase::lapply(Map(c, name = names(sub), sub), do_call, do_cncpt) at prockenschaub-ricu-package-1942e93/R/concept-utils.R:1418:4
9. ββricu (local) FUN(X[[i]], ...)
10. ββbase::do.call(fun, c(x, list(...))) at prockenschaub-ricu-package-1942e93/R/utils-misc.R:190:11
11. ββricu (local) `<fn>`(...)
12. ββricu::new_item(itms) at prockenschaub-ricu-package-1942e93/R/concept-utils.R:1381:6
13. ββricu:::assert_that(is.list(x), all_fun(x, is_itm)) at prockenschaub-ricu-package-1942e93/R/concept-utils.R:701:2
14. ββrlang::abort(msg, class = cls) at prockenschaub-ricu-package-1942e93/R/assertions.R:24:2
Execution halted
Thank you for your reaching out. I believe you are both running into an issue where the R profile will try to load the proper scripts which it can not do without the dependencies that do not get installed.
source("renv/activate.R")
(use comments (#) to prevent the rest from executing). install.packages("units")
install.packages(c("mimic.demo", "eicu.demo"), repos = "https://eth-mds.github.io/physionet-demo")
This should at least get your environment up and running. You can try out the cohort generation with: Rscript "base_cohort.R" --src mimic_demo
hi, Robin
When I run
Rscript "base_cohort.R" --src mimic_demo
, there is a error. Before that , I runricu::import_src('mimic_demo','/data/mjc/icu/mimic-iii-clinical-database-demo-1.4/')
to import data toricu
.Thanks for your help.
Best, Jiacong Mi