## ----include = FALSE---------------------------------------------------------- NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true") knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, message = FALSE, comment = "#>", eval = NOT_CRAN ) ## ----setup-------------------------------------------------------------------- # library(omock) # library(dplyr) # library(CodelistGenerator) # library(CohortConstructor) # library(CohortCharacteristics) # library(visOmopResults) # library(ggplot2) ## ----------------------------------------------------------------------------- # cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb") ## ----------------------------------------------------------------------------- # warfarin_codes <- getDrugIngredientCodes(cdm, "warfarin") # cdm$warfarin <- conceptCohort(cdm = cdm, # conceptSet = warfarin_codes, # name = "warfarin") # cohortCount(cdm$warfarin) ## ----------------------------------------------------------------------------- # cdm$gi_bleed <- conceptCohort(cdm = cdm, # conceptSet = list("gi_bleed" = 192671L), # name = "gi_bleed") ## ----------------------------------------------------------------------------- # cdm$warfarin_gi_bleed <- cdm$warfarin |> # requireCohortIntersect(intersections = c(1,Inf), # targetCohortTable = "gi_bleed", # targetCohortId = 1, # indexDate = "cohort_start_date", # window = c(-Inf, 0), # name = "warfarin_gi_bleed") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_gi_bleed) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$warfarin_no_gi_bleed <- cdm$warfarin |> # requireCohortIntersect(intersections = 0, # targetCohortTable = "gi_bleed", # targetCohortId = 1, # indexDate = "cohort_start_date", # window = c(-Inf, 0), # name = "warfarin_no_gi_bleed") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_no_gi_bleed) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$injuries <- conceptCohort( # cdm = cdm, # name = "injuries", # conceptSet = list( # "ankle_sprain" = 81151, # "ankle_fracture" = 4059173, # "forearm_fracture" = 4278672, # "hip_fracture" = 4230399 # ), # exit = "event_start_date" # ) # # # cdm$warfarin_any_injury <- cdm$warfarin |> # requireCohortIntersect(intersections = c(1, Inf), # cohortCombinationCriteria = "any", # targetCohortTable = "injuries", # indexDate = "cohort_start_date", # window = c(-Inf, 0), # name = "warfarin_any_injury") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_any_injury) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$warfarin_any_injury <- cdm$warfarin |> # requireCohortIntersect(intersections = c(1, Inf), # cohortCombinationCriteria = "all", # targetCohortTable = "injuries", # indexDate = "cohort_start_date", # window = c(-Inf, 0), # name = "warfarin_any_injury") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_any_injury) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$warfarin_any_injury <- cdm$warfarin |> # requireCohortIntersect(intersections = c(1, Inf), # cohortCombinationCriteria = c(2, Inf), # targetCohortTable = "injuries", # indexDate = "cohort_start_date", # window = c(-Inf, 0), # name = "warfarin_any_injury") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_any_injury) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$warfarin_gi_bleed <- cdm$warfarin |> # requireConceptIntersect(conceptSet = list("gi_bleed" = 192671), # indexDate = "cohort_start_date", # window = c(-Inf, 0), # name = "warfarin_gi_bleed") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_gi_bleed) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$warfarin_no_gi_bleed <- cdm$warfarin |> # requireConceptIntersect(intersections = 0, # conceptSet = list("gi_bleed" = 192671), # indexDate = "cohort_start_date", # window = c(-Inf, 0), # name = "warfarin_no_gi_bleed") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_no_gi_bleed) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$warfarin_visit <- cdm$warfarin |> # requireTableIntersect(tableName = "visit_occurrence", # indexDate = "cohort_start_date", # window = c(-Inf, -1), # name = "warfarin_visit") # # summary_attrition <- summariseCohortAttrition(cdm$warfarin_visit) # plotCohortAttrition(summary_attrition)