reconstructKM (version 0.4.0)

CIC_reconstruct: Reconstruct cumulative incidence curves

Description

In competing risks situations, papers may provide one overall KM plot for the composite outcome of event 1 or event 2 as well as cumulative incidence plots for the each event separately. We can use these three plots to reconstruct individual level data with event-specific labels (censored, event 1, or event 2). Can also handle the case when the CIC for event 2 is not given. Run this separately for each arm.

Usage

CIC_reconstruct(overallIPD, clicks1, arm, clicks2 = NULL)

Value

An augmented version of overallIPD that additionally gives the cause of the event (cause 1 or cause 2) as a fourth "event" column.

Arguments

overallIPD

The individual patient data from the overall (composite outcome) plot that has already been processed through reconstructKM. Should have three columns: time, status, and arm.

clicks1

A data.frame with "time" and "cuminc" columns that are output from the digitizing software, similar to what you would input for reconstructKM except it's a cumulative incidence function for a specific event, not a survival function (make sure first click is (0,0)).

arm

The arm corresponding to clicks1 and possibly clicks2.

clicks2

Same as clicks1 but for the second event if it's provided. Default is null.

Examples

data(pembro_clicks)
data(pembro_NAR)
augTabs <- format_raw_tabs(raw_NAR=pembro_NAR, raw_surv=pembro_clicks)
reconstruct <- KM_reconstruct(aug_NAR=augTabs$aug_NAR, aug_surv=augTabs$aug_surv)
IPD <- data.frame(arm=1, time=reconstruct$IPD_time, status=reconstruct$IPD_event)
clicks1 <- dplyr::mutate(pembro_clicks, cuminc=1-survival)
CIC_reconstruct(overallIPD = IPD, clicks1 = clicks1, arm=1, clicks2=NULL)