simulate.data: Simulate data for the cross-validated adaptive signature...

In svetlanache/rapids: What the Package Does (One Line, Title Case)

Simulate data for the cross-validated adaptive signature design/cross-validated risc scores design.

Description

The data is simulated assuming that the response to treatment is influenced by a subset of K unknown covariates (the sensitive covariates) through the following model:

logit(p_i)= mu+lambda*t_i+gamma_1*t_i*x_i1+...+gamma_K*t_i*x_iK,

where p_i is the probability of response to treatment for the i-th patient; mu is the intercept; lambda is the treatment main effect that all patients experience regardless of the values of the covariates; t_i is the treatment that the i-th patient receives (t_i = 0 for the control arm and t_i=1 for the treatment arm); x_i1,...,x_iK are the values for the K unknown sensitive covariates; gamma_1,...,gamma_K are treatment-covariate interaction effects for the K covariates. The model assumes that there is a subset of patients (the sensitive group) with a higher probability of response when treated with the new treatment, compared with the control treatment.

Usage

## S3 method for class 'data'
simulate(
  N = 1000,
  L = 100,
  K = 10,
  rho1 = 0,
  rho2 = 0,
  rho0 = 0,
  mu1 = 1,
  mu2 = 0,
  mu0 = 0,
  sigma1 = 0.5,
  sigma2 = 0.1,
  sigma0 = 0.5,
  perc.sp = 0.1,
  rr.nsp.treat = 0.25,
  rr.con = 0.25,
  rr.sp.treat = 0.6,
  runs = 1,
  seed = NULL
)

Arguments

N	Number of patients.
L	Overall number of covariates.
K	Number of sensitive covariates.
mu1, sigma1, rho1	Mean, sd and correlation for sensitive covariates in sensitive patients.
mu2, sigma2, rho2	Correlation parameter for sensitive covariates in non-sensitive patients.
mu0, sigma0, rho	Correlation parameter for non-sensitive covariates in all patients.
perc.sp	Percentage of sensitive patients.
rr.nsp.treat	Response rate on the treatment arm in non-sensitive patients.
rr.con	Response rate on the control arm.
rr.sp.treat	Response rate on the treatment arm in sensitive patients.
runs	Number of replicates to simulate.
seed	A seed for the random number generator.

Value

A list of 3 data frames: patients, covar, response.

patients: a data frame with one row per patient and the following columns: FID (family ID), IID (individual ID), sens.true (true sensitivity indicator), treat (1 for treatment and 0 for control), rr (probability of response for a binary outcome)

covar: covariate data for L covariates

response: simulated binary responses, one column per simulation (number of columns = runs)

Author(s)

Svetlana Cherlin, James Wason

See Also

analyse.simdata and cvrs.plot functions; print and plot methods.

Examples

N = 400
L = 100
K=10
rho1 = 0
rho2 = 0
rho0 = 0
mu1 = 1
mu2 = 0
mu0 = 0
sigma1 = 0.5
sigma2 = 0.1
sigma0=0.5
perc.sp = 0.1
rr.nsp.treat = 0.25
rr.con = 0.25
rr.sp.treat = 0.98
runs = 10
seed = 123

datalist = simulate.data (N , L , K, rho1, rho2, rho0, mu1, mu2, mu0, sigma1, sigma2, sigma0, perc.sp, rr.nsp.treat, rr.con, rr.sp.treat, runs, seed)

svetlanache/rapids documentation built on Sept. 15, 2023, 7 a.m.