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jgellar / pcox

Penalized Cox regression models
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Status Update #8

Closed jgellar closed 9 years ago

jgellar commented 9 years ago

We could use this as a To Do list, moving items from the bottom section to the top one as appropriate.

Current capabilities:

  1. Overall structure
    • Converts smooth objects to coxph.penalty terms
    • Maximize the PPL using AIC, AICc, or EPIC optimization
  2. Acceptable types of terms:
    • Handles scalar predictors: linear and nonlinear effects
    • Handles baseline functional predictors: linear and nonlinear effects using lf(), af(), and lf.vd()
  3. Time-varying terms:
    • Concurrent functional terms: $\beta Z_i(t)$
    • Historical terms
    • Time-varying effects of all term types
  4. Naming of terms in the coxph formula: right now it is smooth1, smooth2, etc.
  5. Methods
    • coef.pcox()
    • predict.pcox()
  6. Mechanism for methods for baseline functional predictors needs to be different: don't have tt functions to handle it. Can we develop something similar?

    Functionality to add/change:

  7. Unequally spaced (and non-integer) grids: NEEDS FURTHER TESTING
  8. Random effects (frailty terms) - already implemented using frailty()?
  9. Interactions:
    • Scalar-scalar
    • Scalar-function
    • Function-function
  10. Re-parameterizations of historical functional terms: NEEDS FURTHER TESTING
    • Partial domain histories (limits)
    • Domain alignment: original (s), "lagged" (s-t), or domain-standardized (u?)
    • Linear interactions with time (for u domain only): gets complicated because it results in multiple functional terms
  11. ML/REML optimization (ML supposedly more robust - per Terry Therneau)
  12. Current version of getL() is getL3 (uses "masks")... is this the most efficient algorithm?
  13. Methods
    • plot.pcox()
    • print.pcox()
    • summary.pcox()
  14. Basic package-development issues:
    • License/version?
    • Variable-naming consistency
    • Consistency across functions
    • Dependencies handled correctly?
    • ::: and copying other code (from survival and refund)
jgellar commented 9 years ago

Most of these are old, so I'm closing it and moving relevant items to #30