Intention-To-Treat Analysis

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Here, we’ll go over some examples of using ITT. First we need to load the library before getting in to some sample use cases.

library(SEQTaRget)

ITT With 5 bootstrap samples

options <- SEQopts(# tells SEQuential to create kaplan meier curves
                   km.curves = TRUE,
                   # tells SEQuential to bootstrap
                   bootstrap = TRUE,
                   # tells SEQuential to run bootstraps 5 times
                   bootstrap.nboot = 5)

# use example data
data <- SEQdata                             
model <- SEQuential(data, id.col = "ID", 
                          time.col = "time", 
                          eligible.col = "eligible", 
                          treatment.col = "tx_init", 
                          outcome.col = "outcome", 
                          time_varying.cols = c("N", "L", "P"), 
                          fixed.cols = "sex",
                          method = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")        # retrieve risk plot
survival_data <- km_data(model)            # retrieve survival and risk data

ITT with 5 bootstrap samples and losses-to-followup

options <- SEQopts(km.curves = TRUE,               
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,
                   # tells SEQuential to expect LTFU as the censoring column
                   cense = "LTFU",
                   # tells SEQuential to treat this column as the 
                   # censoring eligibility column
                   cense.eligible = "eligible_cense")

# use example data for LTFU
data <- SEQdata.LTFU
model <- SEQuential(data, id.col = "ID", 
                          time.col = "time", 
                          eligible.col = "eligible", 
                          treatment.col = "tx_init", 
                          outcome.col = "outcome", 
                          time_varying.cols = c("N", "L", "P"), 
                          fixed.cols = "sex",
                          method = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")
survival_data <- km_data(model)

ITT with 5 bootstrap samples and competing events

options <- SEQopts(km.curves = TRUE,               
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,
                   # Using LTFU as our competing event
                   compevent = "LTFU")

data <- SEQdata.LTFU
model <- SEQuential(data, id.col = "ID", 
                          time.col = "time", 
                          eligible.col = "eligible", 
                          treatment.col = "tx_init", 
                          outcome.col = "outcome", 
                          time_varying.cols = c("N", "L", "P"), 
                          fixed.cols = "sex",
                          method = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")
survival_data <- km_data(model)

ITT hazard ratio with 5 bootstrap samples and competing events

options <- SEQopts(# km.curves must be set to FALSE to turn on hazard 
                   # ratio creation
                   km.curves = FALSE,
                   # set hazard to TRUE for hazard ratio creation
                   hazard = TRUE,
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,     
                   compevent = "LTFU")

data <- SEQdata.LTFU                          
model <- SEQuential(data, id.col = "ID", 
                          time.col = "time", 
                          eligible.col = "eligible", 
                          treatment.col = "tx_init", 
                          outcome.col = "outcome", 
                          time_varying.cols = c("N", "L", "P"), 
                          fixed.cols = "sex",
                          method = "ITT", 
                          options = options)

# retrieve hazard ratios
hazard_ratio(model)

ITT with 5 bootstrap samples and competing events in subgroups defined by sex

options <- SEQopts(km.curves = TRUE,               
                   bootstrap = TRUE,                
                   bootstrap.nboot = 5,     
                   compevent = "LTFU",
                   # define the subgroup
                   subgroup = "sex")

data <- SEQdata.LTFU
model <- SEQuential(data, id.col = "ID", 
                          time.col = "time", 
                          eligible.col = "eligible", 
                          treatment.col = "tx_init", 
                          outcome.col = "outcome", 
                          time_varying.cols = c("N", "L", "P"), 
                          fixed.cols = "sex",
                          method = "ITT", 
                          options = options)

km_curve(model, plot.type = "risk")
survival_data <- km_data(model)

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