Description Usage Arguments Value Examples

View source: R/CalcCoxCalibRSIntsP.R

For a given time point, calculate the probability of positive exposure value for multiple observations (participants). The function uses the results of proportional hazards grouped risk-set calibration model fit, and given covariates and collected data on the history of the binary exposure for each participant.

1 | ```
CalcCoxCalibRSIntsP(w, w.res, point, fit.cox.rs.ints, hz.times, Q, pts.for.ints)
``` |

`w` |
A matrix of time points when measurements on the binary covariate were obtained. |

`w.res` |
A matrix of measurement results of the binary covariate. Each measurement corresponds to the time points in |

`point` |
The time point at which the probabilities are estimated |

`fit.cox.rs.ints` |
The result of |

`hz.times` |
Times used for calculating the baseline hazard function from PH calibration model |

`Q` |
Matrix of covariates for the PH calibration model |

`pts.for.ints` |
Points defining the intervals for grouping risk-sets (first one has to be zero). Should be sorted from zero up |

A vector of estimated probabilities of positive exposure status at time `point`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
set.seed(17)
sim.data <- ICcalib:::SimCoxIntervalCensCox(n.sample = 100, lambda = 0.1,
alpha = 0.25, beta0 = 0,
gamma.q = c(log(0.75), log(2.5)),
gamma.z = log(1.5), mu = 0.2,
n.points = 2)
# The baseline hazard for the calibration model is calculated in observation times
cox.hz.times <- sort(unique(sim.data$obs.tm))
# Fit proprtional hazards calibration model
fit.cox.rs.ints <- FitCalibCoxRSInts(w = sim.data$w, w.res = sim.data$w.res,
Q = sim.data$Q, hz.times = cox.hz.times,
n.int = 5, order = 2, pts.for.ints = seq(0,4,1),
tm = sim.data$obs.tm, event = sim.data$delta)
# Calculate the conditional probabilities of binary covariate=1 at time one
probs <- CalcCoxCalibRSIntsP(w = sim.data$w, w.res = sim.data$w.res, point = 1,
fit.cox.rs.ints = fit.cox.rs.ints,
pts.for.ints = seq(0,4,1), Q = sim.data$Q,
hz.times = cox.hz.times)
summary(probs)
``` |

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