[R-pkgs] survival3.1

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[R-pkgs] survival3.1

Terry Therneau
Version 3.x of the survival package is now available from CRAN.  This is a
major update whose primary goal is to make the analysis of multi-state
survival models as easy to do as simple Kaplan-Meier and Cox proportional
hazard fits. The primary changes are

    -- in Surv(time1, time2, status) the status variable can now be a
factor that specifies which state a subject has transitioned into.  From a
user's point of view this is the single key change.

    -- survfit() will then create multi-state Pr(state | time) curves,
i.e., the Aalen-Johansen estimate.  (Kaplan-Meier and cumulative incidence
are special cases of the AJ).  Printout and plotting are unchanged.

    -- coxph() will then create multi-state fits.  There is an easy
formula-like syntax for specifying shared coefficients or baseline hazards.

    -- all use standard data, i.e. the (time1, time2, status) format that
is common for time-dependent covariates; there is no need to create special
intermediate data sets.  (An id variable is necessary to specify which rows
go with whom.)

    -- robust variance estimates available throughout

Many other CRAN packages depend on survival, which drove a second goal of
"don't break it".  Part of the testing involved running the test suits of
all 679 reverse dependencies under the new version.

Terry Therneau
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