User-visible changes only. For internal changes, see Github commits.

Subject-level weights supported for likelihood calculation with new

`msm()`

argument`subject.weights`

.Tidying methods added for

`msm`

objects and most of msm’s output functions (`prevalence.msm`

,`qmatrix.msm`

and related functions, and`totlos.msm`

and related functions). These methods convert the output to a tidy data frame (tibble), in the manner of the broom package.To use these methods, just call

`tidy(x)`

, where`x`

is the result of calling, e.g.`msm`

,`prevalence.msm`

, or`qmatrix.msm`

.Hence the msm package now imports the

`generics`

and`tibble`

packages.Subjects with one observation are no longer dropped in HMMs, since they provide information about the distribution of the outcome given the hidden state.

`ppass.msm`

now supports`pci`

models and other time-inhomogeneous models. Thanks to Jon Fintzi for working on this.New function

`hmodel2list`

to extract HMM constructor function calls from fitted HMMs. Thanks to Will Hulme for working on this.Objects returned by

`totlos.msm`

,`efpt.msm`

and`envisits.msm`

now have class`"msm.estbystate"`

Objects returned by

`prevalence.msm`

now have class`"msm.prevalence"`

Fix of bugs for models containing a covariate named

`"baseline"`

or`"Baseline"`

.

Fix of a bug in the Viterbi algorithm for the calculation of the fitted state at the initial time for each subject.

Bug fix for

`pmatrix.piecewise.msm`

given just intensity matrices instead of a fitted model.Auto-generated initial values set to a small positive number rather than zero when there are no observed data for a particular permitted transition. This fixes consistency checks (e.g. for

`qconstraint`

) in this situation.Fix when covariates come into the data as one-column matrices instead of vectors.

Modernised to use roxygen, and pkgdown website created at https://chjackson.github.io/msm

Some internal functions (e.g.

`deriv.msm`

) that clash with base S3 generics renamed

`rpexp`

is now more efficient. Thanks to Mark Clements. Note that the values simulated by`rpexp`

,`sim.msm`

and`simmulti.msm`

for a specific seed will now be different in models where the intensities are piecewise constant.Bug fix: in HMMs with partially known initial states specified through

`obstrue`

and`censor`

,`initprobs`

is now accounted for.Bug fix for bootstrapping with character subject IDs.

`crudeinits.msm`

handled when state is a factor.Fix for

`hranges`

on multiple parameters.`obstrue`

handled in forward-backward algorithm (`viterbi.msm`

).

- … and earlier versions: see inst/NEWS in the source for changes.