Description Usage Arguments Value Examples

Data Simulation Function

1 2 | ```
sim_SCR_data(data_size, ncol_gene_mat, feat_m, feat_d, mu_cen, cov,
lam_m = 1/15, lam_d = 1/20, norm_vcov = c(1, 0.5, 0.5, 1))
``` |

`data_size` |
an integer giving the simulated sample size |

`ncol_gene_mat` |
an integer giving the simulated number of genomic covariates |

`feat_m` |
a function that transforms the genomic features into the signal for the metastasis
process. This function should a matrix of dimensions |

`feat_d` |
a function that transforms the genomic features into the signal for the death
process. This function should a matrix of dimensions |

`mu_cen` |
mean of the exponential censoring process |

`cov` |
the correlation between the genomic covariates |

`lam_m` |
baseline hazard constant for metastasis process. Default is |

`lam_d` |
baseline hazard constant for death process. Default is |

`norm_vcov` |
vector of length 4 of correlation between errors between the two processes on
the normal scale before being complementary-log-log-transformed. Default is |

a `data.frame`

with columns:

`XR`

: time to recurrence / death / censoring`XD`

: time to death / censoring`DeltaR`

: Indicator of censoring (0), recurrence (1), or death (2) for this earliest time`XR`

`DeltaD`

: Indicator of censoring (0) or death (1)`XPFS`

: time to recurrence / death / censoring (=`XR`

)`DeltaPFS`

: Indicator of censoring (0) or recurrence or death, whichever came first (1)`Z_1,...,Z_P`

: genomic variables

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
feat_m_fun <- function(X){
sin(X[,1]+X[,2]^2)-1
}
feat_d_fun <- function(X){
(X[,4]-X[,5])^2/8
}
mydata <- sim_SCR_data(data_size = 400, ncol_gene_mat = 20, feat_m = feat_m_fun,
feat_d = feat_d_fun, mu_cen = 30, cov=0.5)
head(mydata)
## how many experience both events
mean(mydata[,"DeltaR"]==1 & mydata[,"DeltaD"]==1)
## how many only recur
mean(mydata[,"DeltaR"]==1 & mydata[,"DeltaD"]==0)
## how many only die
mean(mydata[,"DeltaR"]==2 & mydata[,"DeltaD"]==1)
## how many are censored
mean(mydata[,"DeltaR"]==0 & mydata[,"DeltaD"]==0)
``` |

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