Closed hejatibor closed 2 weeks ago
it looks like you have an older version of the repo, please pull and should be fine. (use the renvlock and DUS1_point4.R code) but the rest should be from the repo
the object is in the individual_indications.R file
Thanks, with the refreshed repo I've got this error:
→ Start summary of data, at 2024-07-14 19:42:18
✔ Summary finished, at 2024-07-14 19:42:19
! names of group will be ignored
! names of strata will be ignored
ℹ The following estimates will be computed:
• number_exposures: min, q05, q25, median, q75, q95, max, mean, sd,
count_missing, percentage_missing
• duration: min, q05, q25, median, q75, q95, max, mean, sd, count_missing,
percentage_missing
• cumulative_quantity: min, q05, q25, median, q75, q95, max, mean, sd,
count_missing, percentage_missing
• number_eras: min, q05, q25, median, q75, q95, max, mean, sd, count_missing,
percentage_missing
• initial_quantity: min, q05, q25, median, q75, q95, max, mean, sd,
count_missing, percentage_missing
• impute_daily_dose_percentage: min, q05, q25, median, q75, q95, max, mean, sd,
count_missing, percentage_missing
• impute_duration_percentage: min, q05, q25, median, q75, q95, max, mean, sd,
count_missing, percentage_missing
• initial_daily_dose: min, q05, q25, median, q75, q95, max, mean, sd,
count_missing, percentage_missing
• cumulative_dose: min, q05, q25, median, q75, q95, max, mean, sd,
count_missing, percentage_missing
! Table is collected to memory as not all requested estimates are supported on
the database side
→ Start summary of data, at 2024-07-14 19:42:29
✔ Summary finished, at 2024-07-14 19:42:30
Error in if (cdm[["concept"]] %>% dplyr::filter(.data$concept_id == .env$ingredientConceptId) %>% :
argument is of length zero
Calls: .rs.sourceWithProgress ... lapply -> FUN -> eval -> eval -> checkIngredientConceptId
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
Could you help, please, what to do? Thanks Tibor
thanks which version of DrugUtilisation PatientProfiles CDMConnector and omopgenerics are you using? @hejatibor
In case you are using the correct version of DrugUtilisation (0.6.0) this check throws the error:
conceptSet <- list(
cdm[["drug_strength"]] |>
dplyr::filter(.data$ingredient_concept_id == .env$ingredientConceptId) |>
dplyr::pull("drug_concept_id")
)
**names(conceptSet) <- cdm[["concept"]] |>
dplyr::filter(.data$concept_id == .env$ingredientConceptId) |>
dplyr::pull("concept_name")**
can you double check that you have the concept_names for all the ingredients in your cdm$concept table?
ingredients <- as.integer(c(19098548, 1347450, 1594587, 912803, 40171288, 780442, 45892599, 1741122, 45892906, 1333379, 40239665, 1536743, 1742432, 1348407, 1525746, 1734104, 1750500, 1729720, 1728416, 1713332, 1759842, 1777806, 1774470, 1709170, 1778162, 1746114, 19136187, 1307515, 1186087, 42904205, 1510627, 1361580, 1151789, 937368, 912263,36857573, 19041065, 1114375, 19080982, 1397141, 718583, 40242044, 40168938, 36878937, 35200405, 37003361, 1311078,902730,36863408, 1311799, 19078097, 903643, 19012565, 19034726, 19010482, 950637, 1503983, 40174604, 42800246, 36878851 ))
plus, I would need your log.txt from the storage folder to see at which drug it fails. we have had problems with 36857573 and 36863408, so if those are the trouble makers then you can just comment them out as follows: .... 912263, #36857573, 19041065, 1114375, 19080982, 1397141, 718583, 40242044, 40168938, 36878937, 35200405, 37003361, 1311078,902730, #36863408, ......
plus in the names:
......
"certolizumab pegol", # "CERTOLIZUMAB",
"golimumab",
"anakinra",
"ranibizumab",
"bevacizumab",
"nicotine",
"icatibant",
"ecallantide",
"Conestat alfa",
"lanadelumab",
"berotralstat",
"cytarabine","Cytarabine liposomal", # "CYTARABINE 5'-PHOSPHATE",
......
these are quite a few steps, but hope it helps to figure out the problem. In any case, showing me the log would always be a good idea.
Thank you for your help, I really appreciate it. With these modifications I was able to run the DUS code succesfully.
Using DUS_14.R (from #53 ) the following error came:
The log from the storage is attached SUCD_log.txt