TODO

for every release
-----------------
* check all files are included in package build: help pages, PDF manual rebuilt, run update-docsrc.
* check Changelog, NEWS, DESCRIPTION file have correct dates and versions
* Run fast and slow tests
* Use winbuilder to run checks on R-devel, but this doesn't turn on --as-cran.
* Thus should compile a devel R locally! 
* R -d "valgrind --tool=memcheck --leak-check=full --track-origins=yes" --vanilla < ~/work/msm/devel/test.R.   
* PKG_CFLAGS=-g to get line numbers in valgrind  
* undefined behaviour sanitizer: gcc 4.9, and R-3.1.2 configured with flags on, installed locally at work. turn flags on for package building in .R/Makevars
* timing of tests


pci in comb with list() trans specific covs.
see tests/natalia_pci.r

in pearson output, display uncentred covariate values. 

informative error for character state/time, see ~/msm/tests/helpTylerPyleMSM.R

informative error if all q are zero 

vignette about using censor and viterbi for non HMMs to do prediction 


POSSIBLE MAJOR DEVELOPMENTS

MCMC estimation.  Done basic JAGS interface, but convergence
difficulties typical.  Stan might be better (esp for HMMs) but can't
do matrix exponentials in it.  Haven't tried inserting random effects
yet.
	 
Internationalisation.


SOME OTHER SUGGESTIONS: not all may be sensible.

Handle NA or NaN arg or params in ptnorm, pmenorm, pmeunif and their q fns, and qpexp

Return inf lik instead of halting when overflow occurs?  see tests/rory.r for test case where this doesn't help 

Predict HMM pars and init probs for given covariate values 

phase type constraints. yes/no for each phased state.  regular fixedpars/constraints apply to phase-constrained pars.
msm.rep.constraints and msm.form.params

ppass.msm with time dependent covs.  method in source comment.

sojourn.msm with time dependent covs - needs mean of piecewise exponential, not sure analytic.  Similarly for efpt.msm
  
force treatment contrasts in model matrix instead of warning?

more print statements for tracing.  print in lik.msm.  print parameter values before doing the likelihood, user accessible debug in C? 

A FAQ: discrete-time models, exact times, flexible models

OpenMP for parallel C code called from R, see Writing R Extensions.
Can't call R from parallel part, but using R math lib or lapack/expm OK?

Bureau survival plots

Truncated observations.

Steady state probabilities

Use S_alloc instead of Calloc as in Viterbi - no need to free. Can't use on.exit to free on interrupt unless pointer declared globally.

Time-inhomogeneous models with smoothly-varying intensities.  Product
integral method looks easy, e.g. for predictable covariates like age.
Alternatively, numerically integrate the Kolmogorov equations, as in
Titman (Biometrics 2011).  deSolve package could be used for this in C.
Difficult .Call type mechanism needed for using user-defined R functions
in C. See Writing R Extensions 5.11.1 for a possible starting point.
Or Rcpp.

make msm.check.model for censored states - detect model
   inconsistency. see previous errors.R

parallelsugar: An implementation of mclapply for Windows