This function returns predictions for an object of class “`pch`

”, usually the result of a call
to `pchreg`

.

1 2 3 |

`object` |
a “ |

`type` |
a character string (just the first letter can be used) indicating the type of prediction. See ‘Details’. |

`newdata` |
optional data frame in which to look for variables with which to predict. It must include all the covariates that enter the model and, if |

`p` |
vector of quantiles, to be specified if |

`sim.method` |
a character string (just the first letter can be used) indicating the simulation method if |

`...` |
for future methods. |

If `type = "distr"`

(the default), this function returns a data frame with columns `(haz, Haz, Surv, f)`

containing the fitted values of the hazard function, the cumulative hazard, the survival function, and
the probability density function, respectively.

If `type = "quantile"`

, a data frame with the fitted quantiles (corresponding to the supplied
values of `p`

) is returned.

If `type = "sim"`

, new data are simulated from the fitted model. Two methods are available:
with `sim.method = "quantile"`

, data are simulated by applying the estimated quantile function
to a vector of random uniform numbers; if `sim.method = "sample"`

, the quantile function is only used to identify the time interval, and the data are resampled from the observed values in the interval.
The second method only works properly if there is a large number of breaks. However, it is less sensitive to
model misspecification and facilitates sampling from distributions with a probability mass or non compact support.

If the data are censored, some high quantiles may not be estimated: beyond the last observable quantile,
all types of predictions (including `type = "sim"`

with `sim.method = "sample"`

) are
computed assuming that the hazard remains constant after the last interval.

Predictions are computed at `newdata`

, if supplied. In the current implementation, `newdata`

must include all the variables that are needed for the prediction. Note that if `type = "distr"`

,
new values of the responde variable are also required.

If `type = "distr"`

, a 4-columns data frame with columns `(haz, Haz, Surv, f)`

.
If `type = "quantile"`

, a named data frame with a column for each value of `p`

.
If `type = "sim"`

, a vector of simulated data.

The presence of `NA`

values will always cause the prediction to be `NA`

.

Paolo Frumento <paolo.frumento@ki.se>

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | ```
# using simulated data
##### EXAMPLE 1 - Continuous distribution ############################
n <- 1000
x <- runif(n)
time <- rnorm(n, 1 + x, 1 + x)
cens <- rnorm(n,2,2)
y <- pmin(time,cens) # censored variable
d <- (time <= cens) # indicator of the event
model <- pchreg(Surv(y,d) ~ x, breaks = 20)
# predicting hazard, cumulative hazard, survival, density
pred <- predict(model, type = "distr")
plot(pred$Surv, 1 - pnorm(y, 1 + x, 1 + x)); abline(0,1)
# true vs fitted survival
# predicting quartiles
predQ <- predict(model, type = "quantile", p = c(0.25,0.5,0.75))
plot(x,time)
points(x, qnorm(0.5, 1 + x, 1 + x), col = "red") # true median
points(x, predQ$p0.5, col = "green") # fitted median
# simulating new data
tsim1 <- predict(model, type = "sim", sim.method = "quantile")
tsim2 <- predict(model, type = "sim", sim.method = "sample")
qt <- quantile(time, (1:9)/10) # deciles of t
q1 <- quantile(tsim1, (1:9)/10) # deciles of tsim1
q2 <- quantile(tsim2, (1:9)/10) # deciles of tsim2
par(mfrow = c(1,2))
plot(qt,q1, main = "sim.method = 'quantile'"); abline(0,1)
plot(qt,q2, main = "sim.method = 'sample'"); abline(0,1)
# prediction with newdata
predict(model, type = "distr", newdata = data.frame(y = 0, x = 0.5)) # need y!
predict(model, type = "quantile", p = 0.5, newdata = data.frame(x = 0.5))
predict(model, type = "sim", sim.method = "sample", newdata = data.frame(x = c(0,1)))
##### EXAMPLE 2 - non-compact support ############################
# to simulate, sim.method = "sample" is recommended ##############
n <- 1000
t <- c(rnorm(n,-5), rnorm(n,5))
model <- pchreg(Surv(t) ~ 1, breaks = 30)
tsim1 <- predict(model, type = "sim", sim.method = "quantile")
tsim2 <- predict(model, type = "sim", sim.method = "sample")
par(mfrow = c(1,3))
hist(t, main = "true distribution")
hist(tsim1, main = "sim.method = 'quantile'") # the empty spaces are 'filled'
hist(tsim2, main = "sim.method = 'sample'") # perfect!
``` |

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