TimeToStatus: Extract the time to an event

In ropensci/EndoMineR: Functions to mine endoscopic and associated pathology datasets

Extract the time to an event

Description

This function selects patients who have had a start event and an end event of the users choosing so you can determine things like how long it takes to get a certain outcome. For example, how long does it take to get a patient into a fully squamous oesophagus after Barrett's ablation for dysplasia?

Usage

TimeToStatus(dataframe, HospNum, EVENT, indicatorEvent, endEvent)

Arguments

dataframe	The dataframe
HospNum	The Hospital Number column
EVENT	The column that contains the outcome of choice
indicatorEvent	The name of the start event (can be a regular expression)
endEvent	The name of the endpoint (can be a regular expression)

See Also

Other Basic Analysis - Surveillance Functions: HowManyOverTime(), SurveilFirstTest(), SurveilLastTest(), SurveilTimeByRow()

Examples

# Firstly relevant columns are extrapolated from the
# Mypath demo dataset. These functions are all part of Histology data
# cleaning as part of the package.
v <- Mypath
v$NumBx <- HistolNumbOfBx(v$Macroscopicdescription, "specimen")
v$BxSize <- HistolBxSize(v$Macroscopicdescription)

# The histology is then merged with the Endoscopy dataset. The merge occurs
# according to date and Hospital number
v <- Endomerge2(
  Myendo, "Dateofprocedure", "HospitalNumber", v, "Dateofprocedure",
  "HospitalNumber"
)

# The function relies on the other Barrett's functions being run as well:
b1 <- Barretts_PragueScore(v, "Findings")
b1$IMorNoIM <- Barretts_PathStage(b1, "Histology")
colnames(b1)[colnames(b1) == "pHospitalNum"] <- "HospitalNumber"

# The function groups the procedures by patient and gives
# all the procedures between
# the indicatorEvent amd the procedure just after the endpoint.
# Eg if the start is RFA and the
# endpoint is biopsies then it will give all RFA procedures and
# the first biopsy procedure

b1$EndoscopyEvent <- EndoscopyEvent(
  b1, "Findings", "ProcedurePerformed",
  "Macroscopicdescription", "Histology"
)
nn <- TimeToStatus(b1, "eHospitalNum", "EndoscopyEvent", "rfa", "dilat")
rm(v)

ropensci/EndoMineR documentation built on Sept. 3, 2024, 7:12 a.m.