## ----include = FALSE---------------------------------------------------------- NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true") knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, message = FALSE, comment = "#>", eval = NOT_CRAN ) ## ----------------------------------------------------------------------------- # library(omock) # library(CodelistGenerator) # library(CohortConstructor) # library(CohortCharacteristics) # library(ggplot2) # library(dplyr) ## ----------------------------------------------------------------------------- # cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb") ## ----------------------------------------------------------------------------- # acetaminophen_codes <- getDrugIngredientCodes(cdm, # name = "acetaminophen", # nameStyle = "{concept_name}") # cdm$acetaminophen <- conceptCohort(cdm = cdm, # conceptSet = acetaminophen_codes, # exit = "event_end_date", # name = "acetaminophen") ## ----------------------------------------------------------------------------- # summary_attrition <- summariseCohortAttrition(cdm$acetaminophen) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$acetaminophen <- cdm$acetaminophen |> # requireIsFirstEntry() # # summary_attrition <- summariseCohortAttrition(cdm$acetaminophen) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$acetaminophen <- conceptCohort(cdm = cdm, # conceptSet = acetaminophen_codes, # exit = "event_end_date", # name = "acetaminophen") |> # requireDuration(c(30, Inf)) # # summary_attrition <- summariseCohortAttrition(cdm$acetaminophen) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$acetaminophen <- conceptCohort(cdm = cdm, # conceptSet = acetaminophen_codes, # exit = "event_end_date", # name = "acetaminophen") # cdm$acetaminophen <- cdm$acetaminophen |> # requireIsEntry(entryRange = c(1,2)) # # summary_attrition <- summariseCohortAttrition(cdm$acetaminophen) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$acetaminophen <- conceptCohort(cdm = cdm, # conceptSet = acetaminophen_codes, # name = "acetaminophen") ## ----------------------------------------------------------------------------- # cdm$acetaminophen <- cdm$acetaminophen |> # requireInDateRange(dateRange = as.Date(c("2010-01-01", "2015-01-01"))) # # summary_attrition <- summariseCohortAttrition(cdm$acetaminophen) # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # cdm$acetaminophen <- conceptCohort(cdm = cdm, # conceptSet = acetaminophen_codes, # name = "acetaminophen") ## ----------------------------------------------------------------------------- # cdm$acetaminophen_one_night <- cdm$acetaminophen |> # requireDuration(c(2, Inf), # name = "acetaminophen_one_night") |> # renameCohort("acetaminophen_one_night") # # cdm <- bind(cdm$acetaminophen, # cdm$acetaminophen_one_night, # name = "both_cohorts") ## ----------------------------------------------------------------------------- # summary_attrition <- summariseCohortAttrition(cdm$both_cohorts) # plotCohortAttrition(summary_attrition) ## ----warning=FALSE------------------------------------------------------------ # summary_characteristics <- summariseCharacteristics(cdm$both_cohorts) # tableCharacteristics(summary_characteristics |> # filter(variable_name %in% c("Number subjects", "Days in cohort"))) ## ----------------------------------------------------------------------------- # cdm$acetaminophen_1 <- conceptCohort(cdm = cdm, # conceptSet = acetaminophen_codes, # name = "acetaminophen_1") |> # requireIsFirstEntry() |> # requireInDateRange(dateRange = as.Date(c("2010-01-01", "2016-01-01"))) |> # renameCohort("entry_before_date") # # cdm$acetaminophen_2 <- conceptCohort(cdm = cdm, # conceptSet = acetaminophen_codes, # name = "acetaminophen_2") |> # requireInDateRange(dateRange = as.Date(c("2010-01-01", "2016-01-01"))) |> # requireIsFirstEntry("date_before_entry") ## ----------------------------------------------------------------------------- # cdm <- bind(cdm$acetaminophen_1, # cdm$acetaminophen_2, # name = "both_cohorts") # summary_attrition <- summariseCohortAttrition(cdm$both_cohorts) ## ----------------------------------------------------------------------------- # plotCohortAttrition(summary_attrition) ## ----------------------------------------------------------------------------- # medication_codes <- getDrugIngredientCodes(cdm = cdm, nameStyle = "{concept_name}") # medication_codes ## ----------------------------------------------------------------------------- # cdm$medications <- conceptCohort(cdm = cdm, # conceptSet = medication_codes, # name = "medications") # # # cohortCount(cdm$medications) |> # filter(number_subjects > 0) |> # ggplot() + # geom_histogram(aes(number_subjects), # colour = "black", # binwidth = 25) + # xlab("Number of subjects") + # theme_bw() ## ----------------------------------------------------------------------------- # cdm$medications <- cdm$medications |> # requireMinCohortCount(minCohortCount = 500) # # cohortCount(cdm$medications) |> # filter(number_subjects > 0) |> # ggplot() + # geom_histogram(aes(number_subjects), # colour = "black", # binwidth = 25) + # xlim(0, NA) + # xlab("Number of subjects") + # theme_bw()