├── .Rbuildignore ├── .github └── workflows │ └── rhub.yaml ├── .gitignore ├── DESCRIPTION ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── aft.R ├── gaussquad.R ├── multistate.R ├── pm2-3.R ├── random.R ├── read_gsm.R ├── tvc.coxph.R ├── vuniroot.R └── zzz.R ├── README.md ├── data ├── brcancer.rda ├── colon.rda ├── legendre.quadrature.rule.200.rda └── popmort.rda ├── inst ├── CITATION ├── aft.tex ├── competing_risks.R ├── equations.org ├── fig1-README.md.jpg ├── fig2-README.md.jpg ├── include │ ├── aft.h │ ├── c_optim.h │ ├── gsm.h │ └── splines.h ├── math.input ├── math.org ├── test.do ├── tutorial │ ├── Makefile │ └── timevar.org ├── tvc-cox.R ├── unitTests │ ├── runTests.R │ └── runit.Basic.R ├── working_code.R └── working_code.max ├── man ├── aft-class.Rd ├── aft.Rd ├── bhazard.Rd ├── brcancer.Rd ├── coef.Rd ├── colon.Rd ├── cox.tvc.Rd ├── eform.Rd ├── grad.Rd ├── gsm.Rd ├── gsm.control.Rd ├── gsm_design.Rd ├── incrVar.Rd ├── legendre.quadrature.rule.200.Rd ├── lines.Rd ├── markov_msm.Rd ├── markov_sde.Rd ├── nsx.Rd ├── nsxD.Rd ├── numDeltaMethod.Rd ├── plot-methods.Rd ├── popmort.Rd ├── predict-methods.Rd ├── predict.nsx.Rd ├── predictnl-methods.Rd ├── predictnl.Rd ├── pstpm2-class.Rd ├── residuals-methods.Rd ├── rstpm2-internal.Rd ├── simulate-methods.Rd ├── smoothpwc.Rd ├── stpm2-class.Rd ├── tvcCoxph-class.Rd ├── voptimize.Rd └── vuniroot.Rd ├── src ├── Makevars ├── RcppExports.cpp ├── aft.cpp ├── c_optim.cpp ├── cox_ph.cpp ├── gaussq2.f ├── gsm.cpp ├── laplace.f90 ├── multistate.cpp ├── package_init.c ├── pluginEstimate2.cpp ├── splines.cpp ├── test-nmmin.cpp ├── utils.cpp ├── vintegrate.cpp └── vuniroot.cpp ├── tests ├── testthat.R └── testthat │ ├── test_base.R │ ├── test_delayed.R │ ├── test_markov_msm.R │ ├── test_missing.R │ ├── test_vuniroot.R │ └── test_zeroModel.R └── vignettes ├── Introduction.Rnw ├── Makefile ├── SimpleGuide.Rnw ├── aft-weibull-20190816.pdf ├── aft-weibull-los-20190816.pdf ├── algorithm2e.sty ├── enumitem.sty 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