| analyse_sim {gestate} | R Documentation |
Analyse simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.
Description
Function for analysing simulated time-to-event trial data produced by simulate_trials() or simulate_trials_strata().
This function automatically reads in either list or matrix simulate_trials() data formats.
It performs log rank test and Cox regression analysis by default, but can also/instead perform RMST and/or landmark analyses.
Covariate adjusted (/ stratified) analysis may be selected by using the "stratum" argument.
If a stratum is specified, it will be included as a covariate in Cox and RMST analysis, and as a stratum in a stratified log-rank test and an inverse-precision-weighted landmark test.
Strata values are handled as factors, so continuous covariates are not supported.
Analysis is typically the slowest part of simulation studies, so parallel processing using the doParallel package is built in.
Parallel processing is enabled by setting the number of cores in the "parallel_cores" argument.
Use of parallel processing is recommended for largescale (e.g. 100,000 iteration) simulations.
To avoid unnecessary issues, ensure that the number of cores specified does not exceed number of threads provided by hardware.
Usage
analyse_sim(
data,
LR = TRUE,
RMST = NA,
landmark = NA,
stratum = "",
parallel_cores = 1,
Time = "Time",
Event = "Censored",
censoringOne = TRUE,
Trt = "Trt",
Iter = "Iter"
)
Arguments
data |
Output file from simulate_trials(). Only simulate_trials() or simulate_trials_strata() output is supported, in either "list" or "matrix" format. |
LR |
Requests log-rank test and Cox regression. Default=TRUE |
RMST |
Requests Restricted Mean Survival Time analysis with specified (positive integer) restriction time, leave NULL for no analysis. Default=NULL (no RMST analysis). |
landmark |
Requests Landmark analysis at specified (positive integer) time, leave NULL for no analysis. Default=NULL (no landmark analysis). |
stratum |
Specify name of column of a stratification factor and turn on stratified (LR/LM) and covariate-adjusted (Cox/RMST) analysis. By default, "", and no stratification. |
parallel_cores |
Positive integer specifying number of cores to use. If 1 specified then no parallel processing. Default=1 (no parallel processing). |
Time |
String specifying the name of the time column. Default="Time" |
Event |
String specifying the name of the censoring/event column. Default="Censored" (and by default it is a censoring column unless censoringOne=FALSE) |
censoringOne |
Boolean specifying whether censoring is denoted in the censoring/event column by a one (TRUE) or zero (FALSE). Default=TRUE (censorings denoted by 1, events by 0) |
Trt |
String specifying the name of the treatment column. Default="Trt" |
Iter |
String specifying the name of the iterations column. Default="Iter" |
Value
Returns a table with one row per simulation. Table contains the following columns:
"HR" Cox Hazard Ratio (LR/Cox analysis only)
"LogHR" Cox Log Hazard Ratio (LR/Cox analysis only)
"LogHR_SE" Cox Standard Error of log Hazard Ratio (LR/Cox analysis only)
"HR_Z" Cox Z-Score (LR/Cox analysis only)
"HR_P" 1-sided Cox p-value (LR/Cox analysis only)
"LR_Z" Log-Rank Test Z-Score (LR/Cox analysis only)
"LR_P" 1-sided Log-Rank Test p-value (LR/Cox analysis only)
"Events_Active" Events in Active arm (LR/Cox analysis only)
"Events_Control" Events in Control arm (LR/Cox analysis only)
"RMST_Time" RMST restriction time (RMST analysis only)
"RMST_Active" RMST for Active arm (RMST analysis only)
"RMST_Active_SE" RMST Standard Error for Active arm (RMST analysis only)
"RMST_Control" RMST for Control arm (RMST analysis only)
"RMST_Control_SE" RMST Standard Error for Control arm (RMST analysis only)
"RMST_Delta" RMST difference between arms active-control (RMST analysis only)
"RMST_Delta_SE" RMST difference between arms Standard Error (RMST analysis only)
"RMST_Z" Z-score for RMST (RMST analysis only)
"RMST_P" 1-sided RMST p-value (RMST analysis only)
"LM_Time" Landmark time, i.e. time of survival function comparison (Landmark analysis only)
"LM_Active" Survival function for active arm at landmark time (Landmark analysis only)
"LM_Active_SE" Greenwood standard error for active arm at landmark time (Landmark analysis only)
"LM_Control" Survival function for control arm at landmark time (Landmark analysis only)
"LM_Control_SE" Greenwood standard error for control arm at landmark time (Landmark analysis only)
"LM_Delta" Survival function difference between arms active-control at landmark time (Landmark analysis only)
"LM_Delta_SE" Greenwood standard error for difference between arms at landmark time (Landmark analysis only)
"LM_Z" Z-score for landmark analysis (Landmark analysis only)
"LM_P" 1-sided landmark analysis p-value (Landmark analysis only)
Author(s)
James Bell
References
Uno H, Claggett B, Tian L, Inoue E, Gallo P, Miyata T, Schrag D, Takeuchi M, Uyama Y, Zhao L, Skali H, Solomon S, Jacobus S, Hughes M, Packer M, Wei LJ. Moving beyond the hazard ratio in quantifying the between-group difference in survival analysis. Journal of clinical Oncology 2014,32, 2380-2385. Tian L, Zhao L, Wei LJ. Predicting the restricted mean event time with the subjects baseline covariates in survival analysis. Biostatistics 2014, 15, 222-233.
Examples
example_sim <- simulate_trials(active_ecurve=Weibull(250,0.8),control_ecurve=Weibull(100,1),
rcurve=LinearR(12,100,100), assess=20,iterations=100,seed=12345,detailed_output=TRUE)
example_analysis1 <- analyse_sim(example_sim)
example_analysis2 <- analyse_sim(data=example_sim,RMST=15,landmark=15)
example_strat_sim <- simulate_trials_strata(stratum_probs=c(0.5,0.5),
active_ecurve=c(Weibull(250,0.8),Weibull(100,1)), control_ecurve=Weibull(100,1),
rcurve=LinearR(12,100,100),assess=20,iterations=100,seed=12345)
example_strat_analysis <- analyse_sim(data=example_strat_sim,RMST=15,landmark=15,stratum="Stratum")