demo_analysis/3_concomitant.R

In thehyve/ohdsi-DeriveVariables: Derive Variables From the OMOP CDM

# Load package
library(OHDSIDeriveVariables)

####### Setup environment ###########
cdmDatabaseSchema <- 'cdm5'
cohortDatabaseSchema <- 'study'
cohortTableName <- 'masterfile'

connectionDetails <- createConnectionDetails(dbms="postgresql",
                                             server="localhost/ohdsi",
                                             user="postgres", password="",
                                             port=5433,
                                             schema=cdmDatabaseSchema)

# Get the study cohort as a dataframe (studyPop)
cohort <- getCohort(connectionDetails, cdmDatabaseSchema, cohortDatabaseSchema, cohortTableName)
attach(cohort)

################ Analysis ##############
## Diabetes Concomitant Morbidity ##
diabetes_ids <- c(195771,201254,201820,201826,4058243,44793114,4193704)
diabetesAtIndex <- getConditionConcomitant( diabetes_ids,
                                            connectionDetails,
                                            cohortDatabaseSchema,
                                            cohortTableName)

cont_table <- table(diabetesAtIndex, INDEX_DRUG_STRING)
print("Diabetes at index")
prop.table(cont_table, margin=2)
chisq.test(cont_table, correct = FALSE)

## Pacemaker Concomitant Morbidity ##
pacemaker_ids <- c(4018842,4035447,4048988,4049399,4050574,4051939,4085558,4099402,4125933,4140992,4142917,4144921,4179363,4183537,4199841,4203562,4204395,4216345,4242529,4243335,4244395,4246210,4281670,4286047,4296792,4331222,4332099,40481942,40487117,42709991,44782661,44783080,44783089,44790298,44790432,44790501,44811732)
pacemakerImplanted <- getProcedureHistory( pacemaker_ids,
                                           connectionDetails,
                                           cohortDatabaseSchema,
                                           cohortTableName)

cont_table_pm <-  table(pacemakerImplanted, INDEX_DRUG_STRING)
print("Pacemaker Implanted before index")
prop.table(cont_table_pm, margin=2)
chisq.test(cont_table_pm, correct = FALSE)