# Per-Protocol: Censoring Analysis

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

    library(SEQTaRget)

## Per-protocol, censoring, weights in pre-expanded data and no truncation, no excused conditions (i.e. static interventions)

    options <- SEQopts(# tells SEQuential to create Kaplan-Meier curves
                       km.curves = TRUE,
                       # tells SEQuential to weight the outcome model
                       weighted = TRUE,
                       # tells SEQuential to build weights from the pre-expanded data
                       weight.preexpansion = TRUE)

    # use some example data in the package
    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 = "censoring",
                        options = options)
    #> Non-required columns provided, pruning for efficiency
    #> Pruned
    #> Expanding Data...
    #> Expansion Successful
    #> Moving forward with censoring analysis
    #> censoring model created successfully
    #> Creating Survival curves
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> Completed

    # retrieve risk plot
    km_curve(model, plot.type = "risk")
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> [[1]]

    # retrieve survival and risk data
    survival_data <- km_data(model)
    risk_data(model)
    #> [[1]]
    #>       Method      A      Risk
    #>       <char> <char>     <num>
    #> 1: censoring      0 0.6596589
    #> 2: censoring      1 0.9243520
    risk_comparison(model)
    #> [[1]]
    #>       A_x    A_y Risk Ratio Risk Difference
    #>    <fctr> <fctr>      <num>           <num>
    #> 1: risk_0 risk_1  1.4012576       0.2646931
    #> 2: risk_1 risk_0  0.7136447      -0.2646931

## Per-protocol, censoring, weights in post-expanded data and no truncation, no excused conditions (i.e. static interventions)

    options <- SEQopts(km.curves = TRUE,
                       weighted = TRUE,
                       # tells SEQuential to build weights from the post-expanded data
                       weight.preexpansion = FALSE)

    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 = "censoring",
                        options = options)
    #> Non-required columns provided, pruning for efficiency
    #> Pruned
    #> Expanding Data...
    #> Expansion Successful
    #> Moving forward with censoring analysis
    #> censoring model created successfully
    #> Creating Survival curves
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> Completed

    km_curve(model, plot.type = "risk")
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> [[1]]

    risk_data(model)
    #> [[1]]
    #>       Method      A      Risk
    #>       <char> <char>     <num>
    #> 1: censoring      0 0.6533049
    #> 2: censoring      1 0.9281893
    risk_comparison(model)
    #> [[1]]
    #>       A_x    A_y Risk Ratio Risk Difference
    #>    <fctr> <fctr>      <num>           <num>
    #> 1: risk_0 risk_1  1.4207598       0.2748844
    #> 2: risk_1 risk_0  0.7038488      -0.2748844

## Per-protocol, censoring, weights in pre-expanded data and no truncation, excused conditions for initiators and non-initiators (i.e. dynamic interventions)

    options <- SEQopts(km.curves = TRUE,
                       weighted = TRUE,
                       weight.preexpansion = TRUE,
                       # tells SEQuential to run a dynamic intervention
                       excused = TRUE,
                       # tells SEQuential to use columns excusedOne and
                       # excusedZero as excused conditions for treatment switches
                       excused.cols = c("excusedZero", "excusedOne"),
                       # tells SEQuential to expect treatment levels 0, 1
                       # (mapping to the same positions as the list in excused.cols)
                       treat.level = c(0, 1))
    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 = "censoring",
                        options = options)
    #> Expanding Data...
    #> Expansion Successful
    #> Moving forward with censoring analysis
    #> censoring model created successfully
    #> Creating Survival curves
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> Completed

    km_curve(model, plot.type = "risk")
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> [[1]]

    risk_data(model)
    #> [[1]]
    #>       Method      A      Risk
    #>       <char> <char>     <num>
    #> 1: censoring      0 0.9647942
    #> 2: censoring      1 0.9627635
    risk_comparison(model)
    #> [[1]]
    #>       A_x    A_y Risk Ratio Risk Difference
    #>    <fctr> <fctr>      <num>           <num>
    #> 1: risk_0 risk_1  0.9978953    -0.002030621
    #> 2: risk_1 risk_0  1.0021092     0.002030621

## Per-protocol, censoring, weights in post-expanded data and no truncation, excused conditions for initiators and non-initiators (i.e. dynamic interventions)

    options <- SEQopts(km.curves = TRUE,
                       weighted = TRUE,
                       weight.preexpansion = FALSE,
                       excused = TRUE,
                       excused.cols = c("excusedZero", "excusedOne"),
                       treat.level = c(0, 1),
                       weight.p99 = TRUE)
    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 = "censoring",
                        options = options)
    #> Expanding Data...
    #> Expansion Successful
    #> Moving forward with censoring analysis
    #> censoring model created successfully
    #> Creating Survival curves
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> Completed

    km_curve(model, plot.type = "risk")
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> [[1]]

    risk_data(model)
    #> [[1]]
    #>       Method      A      Risk
    #>       <char> <char>     <num>
    #> 1: censoring      0 0.6371076
    #> 2: censoring      1 0.9909442
    risk_comparison(model)
    #> [[1]]
    #>       A_x    A_y Risk Ratio Risk Difference
    #>    <fctr> <fctr>      <num>           <num>
    #> 1: risk_0 risk_1  1.5553797       0.3538366
    #> 2: risk_1 risk_0  0.6429298      -0.3538366

## Per-protocol, censoring, weights in post-expanded data and no truncation, excused conditions for initiators and non-initiators (i.e. dynamic interventions) and a competing event

    options <- SEQopts(km.curves = TRUE,
                       weighted = TRUE,
                       weight.preexpansion = FALSE,
                       excused = TRUE,
                       excused.cols = c("excusedZero", "excusedOne"),
                       treat.level = c(0, 1),
                       # add a 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 = "censoring",
                        options = options)
    #> Non-required columns provided, pruning for efficiency
    #> Pruned
    #> Expanding Data...
    #> Expansion Successful
    #> Moving forward with censoring analysis
    #> censoring model created successfully
    #> Creating Survival curves
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> Completed

    km_curve(model, plot.type = "risk")
    #> Scale for colour is already present.
    #> Adding another scale for colour, which will replace the existing scale.
    #> [[1]]

    risk_data(model)
    #> [[1]]
    #>       Method      A       Risk
    #>       <char> <char>      <num>
    #> 1: censoring      0 0.02761456
    #> 2: censoring      1 0.01770405
    risk_comparison(model)
    #> [[1]]
    #>       A_x    A_y Risk Ratio Risk Difference
    #>    <fctr> <fctr>      <num>           <num>
    #> 1: risk_0 risk_1  0.6411128    -0.009910512
    #> 2: risk_1 risk_0  1.5597880     0.009910512

## Per-protocol, censoring, weights in post-expanded data and no truncation, excused conditions for initiators and non-initiators (i.e. dynamic interventions) and hazard ratio

    options <- SEQopts(# tell SEQuential to run hazard ratios
                       hazard = TRUE,
                       weighted = TRUE,
                       weight.preexpansion = FALSE,
                       excused = TRUE,
                       excused.cols = c("excusedZero", "excusedOne"),
                       weight.p99 = TRUE)

    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 = "censoring",
                        options = options)
    #> Expanding Data...
    #> Expansion Successful
    #> Moving forward with censoring analysis
    #> Completed
    hazard_ratio(model)
    #> [[1]]
    #>  Hazard     LCI     UCI
    #> 3.02765      NA      NA