NEWS

LaMa 2.1.3 (2026-08-25)

pseudo_res(mod) computes pseudo-residuals from the model object alone: the likelihood function is evaluated again with its densities replaced by their CDFs, after checking that this is valid; several data streams give one set of residuals each
scores(mod) computes the score contribution of each observation for models using forward(), e.g. for robust (sandwich) standard errors; it takes the model from report() or the RTMB object, respects map, and the likelihood function does not need to change
report() also stores obj (the same object, not a copy), so MCreport() can be called on the model object from report() or qreml()

pseudo_res(): missing observations give NA in all variants (before 0 with normal = FALSE, -Inf for non-randomised discrete residuals)
pseudo_res(): parameters given per observation (matrix or vector of length nObs) work with missing observations
forward(): with track-specific delta or Gamma, the AD version matched them to the wrong tracks if the track IDs were not sorted (e.g. "ID1", ..., "ID10")
forward(): tracks of length one failed with AD
logspace = TRUE is now exact (delta is no longer modified) and also stable without AD
one-state models are correct with logspace = TRUE and report their quantities
forward_p() works if tod does not contain all values 1, ..., L
forward_g() works without AD for two observations
stateprobs_g(forecast = TRUE) with trackID used the transition matrix of the previous time point, which also affected pseudo_res() for inhomogeneous models with tracks
stateprobs() passes forecast on for time-varying Gamma
viterbi() and stateprobs() work for tracks of length one
stateprobs(forecast = TRUE): the first row of each track is delta, not the filtered probabilities given x_1, so pseudo_res() is correct for the first observation

forward(), forward_g() and forward_p() share one implementation (one C++ and one R version for AD); forward_p() no longer expands Gamma for the computation
tracks need to be contiguous, otherwise forward() gives an informative error
without AD, forward() gives an error for NA in allprobs
the TapeConfig performance tip is shown only once per session
viterbi(), stateprobs() and their _g and _p versions use the inputs of forward() and one C++ implementation each, so Gamma is no longer expanded; as in forward(), tracks need to be contiguous
forward_p() reports Gamma with its L slices and type "periodic"
forward(), viterbi() and stateprobs() have an argument tod for periodic models, so they handle all model types; forward_g(), forward_p(), viterbi_g(), viterbi_p(), stateprobs_g() and stateprobs_p() are deprecated and give a message
viterbi() and stateprobs() also take the model object as first argument, e.g. viterbi(mod) instead of viterbi(mod = mod)
tpm_g() and generator_g() are deprecated in favour of tpm(beta, Z) and generator(beta, Z), which also accept a single covariate vector Z; the sparse argument of tpm_g() is gone

vignettes 1-3 have been updated to work with automatic differentiation
tpm(), forward(), stateprobs(), viterbi() can now be used with inhomogeneous models: call their inhomogeneous counterparts internally
function MCreport() has been added for sampling
- from the distribution of the MLE (fixed effects only models)
- from the joint post. distribution of parameters and random effects (random effects models)

some functions have been renamed, e.g. stationary_cont() -> stationary_ct() (old versions still exist)
some internal cleanup