Parameters of fitted two-phase models, in mixture model parameterisation.

## Usage

```
phasemeans.msm(
x,
covariates = "mean",
ci = c("none", "normal", "bootstrap"),
cl = 0.95,
B = 1000,
cores = NULL
)
```

## Arguments

- x
A fitted multi-state model, as returned by

`msm`

.- covariates
Covariate values, see

`qmatrix.msm`

.- ci
If

`"none"`

(the default) no confidence intervals are calculated. Otherwise`"normal"`

, or`"boot"`

as described by`qmatrix.msm`

.- cl
Width of the symmetric confidence interval, relative to 1.

- B
Number of bootstrap replicates, or number of normal simulations from the distribution of the MLEs.

- cores
Number of cores to use for bootstrapping using parallel processing. See

`boot.msm`

for more details.

## Value

Matrix with one row for each state that has a two-phase
distribution, and three columns: the short-stay mean, long-stay mean and
long-stay probability. These are functions of the transition intensities of
the expanded hidden Markov model, defined in `d2phase`

.

## Author

C. H. Jackson chris.jackson@mrc-bsu.cam.ac.uk