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pomp to-do list

For pomp:

  • replace melt with data.table::melt?

  • YAML interface

  • "Getting Started" vignette:

    • finish discussion of smoothing and hindcasting
    • include discussion of forecasting

  • ARMA benchmarking (a la spatPomp)?

  • make mcap into a generic, provide a method for data frames and a plotting method

  • overriding C snippets should overwrite/delete old C snippets, keep one C snippet file

  • options(pomp_cdir) should take effect at run time and not at initial compile time as currently

  • pomp_fun should be able to take symbols

  • in pfilter, perhaps filter trajectory (one sample from the smoothing distribution) should go into states slot (??)

  • rewrite to use rmultinom, which is now part of the R API (?)

  • more demanding tests of enkf and eakf

  • iterated EnKF

  • better scheme for indicating derivatives and maps in C snippets

  • support for asymmetric MCMC proposals

  • spy methods for derived objects

  • for log-barycentric transformations, check that parameters are contiguous

  • manual pages on the organization of the package

    • diagnostic tools
    • auxiliary functions
    • plotting methods
    • parallelization tools
    • extending the package

  • make R-level functions for various distributions and transformations

    • BetaBinom
    • BetaNegBinom

  • remove need to specify paramnames when log,logit,barycentric partrans is given? HOW?

  • demonstration of Fisher information via pfilter on slice designs?

  • new userdata function to get void *?

  • easier interface for lists of probes in probe

  • documentation on mifList, pmcmcList, etc.?

  • methods to change data (obs<-)?

    • perhaps recognized data variables, states, covariates in calls to pomp are replaced?

  • MCMC proposals as pomp slots?

  • probes as pomp slots?

  • what does a generic pomp_fun interface look like?

  • should parameter transformations allow renaming of variables?

    • would require attention to rw_sd, e.g.

  • streamline the R snippets so that ... is unnecessary?

    • probably not worth the trouble, since C snippets are so much faster

  • add include argument to pomp?

  • graceful stopping for optimizers (at least for nloptr)

  • trap errors for LAPACK

  • one-point SCQL function for possible use in fitting initial conditions

  • partial rejection control for pfilter?

  • adaptive particle numbers in pfilter (?)

  • plugin for adaptive tau leaping algorithm.

  • plugin for compartmental models

Documentation

  • FAQ needs update with new issues from @MarieAugerMethe:
    • prediction vs smoothing
  • documentation for existing issues with "todo" label

Helper packages

  • parallel mif-farm and multi-start optimization helpers
  • number of processors stored in bake, stew, freeze outputs
  • parallel likelihood profiling tool (with MCAP)

Examples

  • SDE examples
  • LPA beetle examples
  • budmoth examples
  • variants on SIR: SEIR, SIRS, ...
  • more toy models
  • more/better examples
    • need examples of objective function methods
    • pmcmc examples