createMedicationTimeBlocks: Calculates the time block data for prescriptions

In smm52/timeBlocks: Converts Serial Measurement Data into Longitudinal Trajectory of Equally-sized Time Blocks

Calculates the time block data for prescriptions

Description

Calculates the time block data for prescriptions

Usage

createMedicationTimeBlocks(
  serialDf,
  baselineInfo,
  studyStartDate,
  studyEndDate,
  atcCode = "C09",
  blockDays = 365.25,
  useDoses = FALSE,
  idColumn = "PATIENT",
  dateColumn = "VISIT",
  atcColumn = "ATC",
  dddColumn = "cDDD",
  dataName = "prescription",
  longFormat = TRUE,
  noUseAtBaseline = FALSE
)

Arguments

serialDf	the data frame with the serial data
baselineInfo	dataframe with ID and baseline date
studyStartDate	start Date of the study (has to be of class Date)
studyEndDate	end Date of the study (has to be of class Date)
atcCode	regular expression for the class of medication ATC code (default: C09 which stands for any RAAS)
blockDays	length of a time block in days (default 365.25 days)
useDoses	flag indicating whether presence of prescription events or sum of doses should be used in a block (default FALSE)
idColumn	name of ID column: default is PATIENT
dateColumn	name of date column: default is VISIT. This column has to be of class Date
atcColumn	name of the column with the ATC codes: default is ATC
dddColumn	name of the column with the dosage information: default is cDDD
dataName	set a user specified name for the data column in the output: default is prescription

Value

time block data and dates in wide format

Examples

## Not run: 
baselinePatients <- read_tsv('../data/ourBaselinePatients.txt', guess_max = 3582) %>%
    select(PATIENT, VISIT = VISIT_TL)
allFimea <- read_tsv('../data/all_fimea_kela.txt')
allFimea <- allFimea %>% mutate(VISIT = ymd(allFimea$ostopv))
allFimea <- allFimea %>% mutate(PATIENT = fd)
allFimea <- allFimea %>% filter(!is.na(all_ddd)) #check these as they should not exists
medResLong <- createMedicationTimeBlocks(allFimea, baselinePatients,
   studyStartDate = as.Date('1995-01-01', '%Y-%m-%d'),
   studyEndDate = as.Date('2015-12-31', '%Y-%m-%d'),
   atcCode = 'C09', blockDays = 365.25, useDoses = FALSE, idColumn = "PATIENT", dateColumn = "VISIT",
   atcColumn = "ATC_FIMEA", dddColumn = 'all_ddd', dataName = "anyRAAS", longFormat = TRUE,
   noUseAtBaseline = FALSE)
medResWide <- createMedicationTimeBlocks(allFimea, baselinePatients,
   studyStartDate = as.Date('1995-01-01', '%Y-%m-%d'),
   studyEndDate = as.Date('2015-12-31', '%Y-%m-%d'),
   atcCode = 'C09', blockDays = 365.25, useDoses = FALSE, idColumn = "PATIENT", dateColumn = "VISIT",
   atcColumn = "ATC_FIMEA", dddColumn = 'all_ddd', dataName = "anyRAAS", longFormat = FALSE,
   noUseAtBaseline = FALSE)

## End(Not run)

smm52/timeBlocks documentation built on Nov. 27, 2022, 3:54 a.m.