coxed.gam.tvc: Predict expected durations using the GAM method with...
In coxed: Duration-Based Quantities of Interest for the Cox Proportional Hazards Model

Description Usage Arguments Details Value Author(s) References See Also Examples

This function is called by coxed and is not intended to be used by itself.

1 2	coxed.gam.tvc(cox.model, newdata = NULL, k = -1, coef = NULL, b.ind = NULL, warn = TRUE)

`cox.model`	The output from a Cox proportional hazards model estimated with the `coxph` function in the `survival` package or with the `cph` function in the `rms` package
`newdata`	An optional data frame in which to look for variables with which to predict. If omitted, the fitted values are used
`k`	The number of knots in the GAM smoother. The default is -1, which employs the `choose.k` function from the `mgcv` package to choose the number of knots
`coef`	A vector of new coefficients to replace the `coefficients` attribute of the `cox.model`. Used primarily for bootstrapping, to recalculate durations using new coefficients derived from a bootstrapped sample. If `NULL`, the original coefficients are employed
`b.ind`	A vector of observation numbers to pass to the estimation sample to construct the a bootstrapped sample with replacement
`warn`	If `TRUE`, displays warnings, and if `FALSE` suppresses them

This function employs the GAM method of generating expected durations described in Kropko and Harden (2018). See coxed.gam for details. This code replicates the code for cox.gam, but works with data whose structure allows time-varying covariates, and requires using the time2 argument of the Surv function. This function requires the data to be reported as cumulative durations. The GAM model is fit using the ending times for each interval and using only the non-censored observations. Expected durations are drawn from this GAM as with coxed.gam.

Returns a list containing the following components:

`exp.dur`	A vector of predicted mean durations for the estimation sample if `newdata` is omitted, or else for the specified new data.
`gam.model`	Output from the `gam` function in which the durations are fit against the exponentiated linear predictors from the Cox model.
`gam.data`	Fitted values and confidence intervals from the GAM model.

Jonathan Kropko <jkropko@virginia.edu> and Jeffrey J. Harden <jharden2@nd.edu>

Kropko, J. and Harden, J. J. (2018). Beyond the Hazard Ratio: Generating Expected Durations from the Cox Proportional Hazards Model. British Journal of Political Science https://doi.org/10.1017/S000712341700045X

gam, coxed, coxed.gam

bs.surv <- Surv(time = boxsteffensmeier$start, time2 = boxsteffensmeier$te,
     event = boxsteffensmeier$cut_hi)
bs.cox <- coxph(bs.surv ~ ec + dem + south + iv, data = boxsteffensmeier, method = "breslow")
summary(bs.cox)

ed <- coxed.gam.tvc(bs.cox)
ed$exp.dur