We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
When using intersectCohorts with a cohort table generated with conceptCohorts I get the following error:
The text was updated successfully, but these errors were encountered:
Code to reproduce error (in intersectCohorts returnOnlyComb = FALSE --> keepOriginalCohorts = TRUE):
returnOnlyComb = FALSE
keepOriginalCohorts = TRUE
# packages --- library(Capr) library(here) library(DBI) library(CDMConnector) library(dplyr) library(tidyr) library(CodelistGenerator) library(CohortConstructor) # db with vocab ---- server_dbi <- Sys.getenv("DB_SERVER_cdm_thin_fr_202308_dbi") user <- Sys.getenv("DB_USER") password <- Sys.getenv("DB_PASSWORD") port <- Sys.getenv("DB_PORT") host <- Sys.getenv("DB_HOST") # connect db <- DBI::dbConnect(RPostgres::Postgres(), dbname = server_dbi, port = port, host = host, user = user, password = password) cdm_database_schema <- "public" vocabulary_database_schema <- cdm_database_schema results_database_schema <- "results" db_name<-"THIN_fr" table_stem <- "issue_cc" # create cdm reference ---- cdm <- cdmFromCon( con = db, cdm_schema = cdm_database_schema, write_schema = c("schema" = results_database_schema, "prefix" = table_stem), cdm_name = db_name, achilles_schema = results_database_schema ) ## OCAM + OCA drug_codes <- getDrugIngredientCodes(cdm, name = c("amoxicillin", "clarithromycin", "metronidazole")) cdm$ocam <- conceptCohort(cdm = cdm, conceptSet = drug_codes, name = "ocam") cdm$intersection_ocam <- cdm$ocam %>% CohortConstructor::intersectCohorts( gap = 0, # returnOnlyComb = FALSE, keepOriginalCohorts = TRUE, name = "intersection_ocam" )
! It needs access to THIN france
Sorry, something went wrong.
nmercadeb
No branches or pull requests
When using intersectCohorts with a cohort table generated with conceptCohorts I get the following error:
The text was updated successfully, but these errors were encountered: