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issue with intersectCohort() #242

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patripedregal opened this issue Jul 7, 2024 · 1 comment
Open

issue with intersectCohort() #242

patripedregal opened this issue Jul 7, 2024 · 1 comment
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@patripedregal
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patripedregal commented Jul 7, 2024

When using intersectCohorts with a cohort table generated with conceptCohorts I get the following error:
image
image

@nmercadeb nmercadeb self-assigned this Jul 29, 2024
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Code to reproduce error (in intersectCohorts 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

@edward-burn edward-burn added this to the cran v0.3 milestone Sep 2, 2024
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