## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----------------------------------------------------------------------------- library(PatientProfiles) library(CodelistGenerator) library(CohortConstructor) library(dplyr) library(ggplot2) library(omock) cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb") cdm$ankle_sprain <- conceptCohort( cdm = cdm, conceptSet = list("ankle_sprain" = 81151), name = "ankle_sprain" ) cdm$ankle_sprain ## ----------------------------------------------------------------------------- acetaminophen_cs <- getDrugIngredientCodes( cdm = cdm, name = c("acetaminophen") ) acetaminophen_cs ## ----------------------------------------------------------------------------- cdm$ankle_sprain |> addConceptIntersectFlag( conceptSet = acetaminophen_cs, indexDate = "cohort_start_date", window = c(0, 30) ) |> glimpse() ## ----------------------------------------------------------------------------- cdm$ankle_sprain |> addConceptIntersectCount( conceptSet = acetaminophen_cs, indexDate = "cohort_start_date", window = c(0, 30) ) |> glimpse() ## ----------------------------------------------------------------------------- cdm$ankle_sprain |> addConceptIntersectDate( conceptSet = acetaminophen_cs, indexDate = "cohort_start_date", window = c(0, 30), order = "first" ) |> glimpse() ## ----------------------------------------------------------------------------- cdm$ankle_sprain |> addConceptIntersectDays( conceptSet = acetaminophen_cs, indexDate = "cohort_start_date", window = c(0, 30), order = "first" ) |> glimpse() ## ----------------------------------------------------------------------------- cdm$ankle_sprain |> addConceptIntersectFlag( conceptSet = acetaminophen_cs, indexDate = "cohort_start_date", window = list( c(-Inf, -1), c(0, 0), c(1, Inf) ) ) |> glimpse() ## ----------------------------------------------------------------------------- meds_cs <- getDrugIngredientCodes( cdm = cdm, name = c( "acetaminophen", "amoxicillin", "aspirin", "heparin", "morphine", "oxycodone", "warfarin" ) ) cdm$ankle_sprain |> addConceptIntersectFlag( conceptSet = meds_cs, indexDate = "cohort_start_date", window = list( c(-Inf, -1), c(0, 0) ) ) |> glimpse() ## ----fig.width=7-------------------------------------------------------------- acetaminophen_cs <- getDrugIngredientCodes( cdm = cdm, name = c("acetaminophen") ) cdm$acetaminophen <- conceptCohort( cdm = cdm, name = "acetaminophen", conceptSet = acetaminophen_cs ) bind_rows( cdm$ankle_sprain |> addCohortIntersectCount( targetCohortTable = "acetaminophen", window = c(-Inf, Inf) ) |> group_by(`161_acetaminophen_minf_to_inf`) |> tally() |> collect() |> arrange(desc(`161_acetaminophen_minf_to_inf`)) |> mutate(type = "cohort"), cdm$ankle_sprain |> addConceptIntersectCount( conceptSet = acetaminophen_cs, window = c(-Inf, Inf) ) |> group_by(`161_acetaminophen_minf_to_inf`) |> tally() |> collect() |> arrange(desc(`161_acetaminophen_minf_to_inf`)) |> mutate(type = "concept_set") ) |> ggplot() + geom_col(aes(`161_acetaminophen_minf_to_inf`, n, fill = type), position = "dodge" ) + theme_bw() + theme( legend.title = element_blank(), legend.position = "top" )