coxph.object {survival} R Documentation

Proportional Hazards Regression Object

Description

This class of objects is returned by the coxph class of functions to represent a fitted proportional hazards model. Objects of this class have methods for the functions print, summary, residuals, predict and survfit.

Arguments

 coefficients the vector of coefficients. If the model is over-determined there will be missing values in the vector corresponding to the redundant columns in the model matrix. var the variance matrix of the coefficients. Rows and columns corresponding to any missing coefficients are set to zero. naive.var this component will be present only if the robust option was true. If so, the var component will contain the robust estimate of variance, and this component will contain the ordinary estimate. loglik a vector of length 2 containing the log-likelihood with the initial values and with the final values of the coefficients. score value of the efficient score test, at the initial value of the coefficients. rscore the robust log-rank statistic, if a robust variance was requested. wald.test the Wald test of whether the final coefficients differ from the initial values. iter number of iterations used. linear.predictors the vector of linear predictors, one per subject. Note that this vector has been centered, see predict.coxph for more details. residuals the martingale residuals. means vector of values used as the reference for each covariate. For instance, a later call to predict(fit, type='risk') will give the hazard ratio between an observation and this reference. (For most covariates this will contain the mean.) n the number of observations used in the fit. nevent the number of events (usually deaths) used in the fit. concordance a vector of length 6, containing the number of pairs that are concordant, discordant, tied on x, tied on y, and tied on both, followed by the standard error of the concordance statistic. first the first derivative vector at the solution. weights the vector of case weights, if one was used. method the method used for handling tied survival times. na.action the na.action attribute, if any, that was returned by the na.action routine. timefix the value of the timefix option used in the fit cmap the coefficient map, present for multi-state coxph fits. There a column for each transition and a row for each coefficient, the value maps that transition/coefficient pair to a position in the coefficient vector. If a particular covariate is not used by the transition the matrix will contain a zero, if two transitions share a coefficient the matrix will contain repeats. stratum_map stratum mapping, present for multi-state coxph fits. The row labeled ‘(Baseline)’ identifies transitions that do or do not share a baseline stratum. Further rows correspond to strata() terms in the model, each of which may apply to some transitions and not others. ... The object will also contain the following, for documentation see the lm object: terms, assign, formula, call, and, optionally, x, y, and/or frame.

Components

The following components must be included in a legitimate coxph object.