getpower.method2 {SimHaz} | R Documentation |
Calculate power for the Cox proportional hazard model with time-dependent exposure using method 2
Description
This functions runs nSim (Number of simulations, specified by the user) Monte Carlo simulations, each time calling tdSim.method2 internally. The function returns a data frame of scenario-specific input parameters- and also output statistical power. The user has the option to append the output to a file with file name specified in the input parameters list.
Usage
getpower.method2(nSim = 500, N, duration = 24, scenario, lambda12,
lambda23 = NULL, lambda13, HR = NULL, exp.prop, rateC, min.futime,
min.postexp.futime, output.fn, simu.plot = FALSE)
Arguments
nSim |
Number of simulations. |
N |
Number of subjects to be screened. |
duration |
Length of the study in months; the default value is 24 (months). |
scenario |
Any text string inputted by the user as an option to name a scenario that is being simulated. The use can simply put " " if he/she decides to not name the scenario. |
lambda12 |
Lambda12 parameter to control time to exposure. |
lambda23 |
Lambda23 parameter to control time to event after exposure. |
lambda13 |
Lambda13 parameter to control time to event in the control group. |
HR |
Hazard Ratio. This input is optional. If HR is set and lambda23 is not set, lambda23 = lambda13*HR. |
exp.prop |
A numeric value between 0 and 1 (not include 0 and 1) that represents the proportion of subjects that are assigned with an exposure. |
rateC |
Rate of the exponential distribution to generate censoring times. |
min.futime |
A numeric value that represents minimum follow-up time (in months). The default value is 0, which means no minimum follow-up time is considered. If it has a positive value, this argument will help exclude subjects that only spend a short amount of time in the study. |
min.postexp.futime |
A numeric value that represents minimum post-exposure follow-up time (in months). The default value is 0, which means no minimum post-exposure follow-up time is considered. If it has a positive value, this argument will help exclude subjects that only spend a short amount of time in the study after their exposure. |
output.fn |
A .csv filename to write in the output. If the filename does not exist, the function will create a new .csv file for the output. |
simu.plot |
A logical value indicating whether or not to output an incidence plot.The default value is FALSE. |
Details
The function calculates power based on the Cox regression model, which calls the coxph function from the survival library using the the simulated data from tdSim.method2.
Value
A data.frame object with columns corresponding to
i_scenario |
Scenario name specified by the user |
i_N |
Number of subjects needs to be screened, specified by the user |
i_min.futime |
Minimum follow-up time to be considered, specified by the user |
i_min.postexp.futime |
Minimum post-exposure follow-up time to be considered, specified by the user |
i_exp.prop |
Exposure rate specified by the user |
i_lambda12 |
Lambda12 parameter to control time to exposure |
i_lambda23 |
Lambda23 parameter to control time to event after exposure |
i_lambda13 |
Lambda13 parameter to control time to event in the control group |
i_rateC |
Rate of the exponential distribution to generate censoring times. Calculated from median time to censoring, which is specified by the user. i_beta Input value of regression coefficient (log hazard ratio) |
N_eff |
Simulated number of evaluable subjects, which is the resulting number of subjects with or without considering minimum follow-up time and/or minimum post-exposure follow-up time |
N_effexp_p |
Simulated proportion of exposed subjects with or without considering minimum follow-up time and/or minimum post-exposure follow-up time |
bhat |
Simulated value of regression coefficient (log hazard ratio) |
HR |
Simulated value of hazard ratio |
d |
Simulated number of events in total |
d_c |
Simulated number of events in control group |
d_exp |
Simulated number of events in exposed group |
mst_c |
Simulated median survival time in control group |
mst_exp |
Simulated median survival time in exposed group |
pow |
Simulated statistical power from the Cox regression model on data with time-dependent exposure |
Author(s)
Danyi Xiong, Teeranan Pokaprakarn, Hiroto Udagawa, Nusrat Rabbee
Maintainer: Nusrat Rabbee <rabbee@berkeley.edu>
Examples
# We recommend setting nSim to at least 500. It is set to 10 in the example to
# reduce run time for CRAN submission.
# Run 10 simulations. Each time simulate a dataset of 600 subjects
ret <- getpower.method2(nSim=10, N=600, duration=24, scenario="test",
lambda12=1.3, lambda23=0.04, lambda13=0.03, HR=NULL,exp.prop=0.2, rateC=0.05,
min.futime=4, min.postexp.futime=4,output.fn="database.csv", simu.plot=FALSE)