`plot.MEDseq`

gains a number of new arguments:`soft`

allows soft cluster membership probabilities to be used for the`"d"`

,`"f"`

,`"Ht"`

,`"ms"`

,

&`"mt"`

`type`

plots (default:`soft=TRUE`

) + the`"i"`

&`"I"`

plots (default:`soft=FALSE`

), in a

manner akin to`WeightedCluster::fuzzyseqplot()`

: previously, all but the`"ms"`

plot used the

hard MAP partition and discarded the soft assignment information (i.e.`soft=FALSE`

, implicitly).`sortv`

allows overriding the`smeth`

arg. to instead order observations in certain plots

(where`seriated`

is one of`"observations"`

or`"both"`

) by the`"dbs"`

or`"asw"`

values;

additionally, and for consistency with`WeightedCluster::fuzzyseqplot()`

,

`sortv="membership"`

is provided for`soft=TRUE`

`type="I"`

plots.`weighted`

(`TRUE`

, by default) allows control over whether the weights (if any) are used;

relevant only for`"d"`

,`"f"`

,`"Ht"`

,`"i"`

,`"I"`

,`"ms"`

, &`"mt"`

`type`

plots.

- Exported
`MEDseq_clustnames`

&`MEDseq_nameclusts`

functions and added`SPS`

arg. to`plot.MEDseq`

,

`MEDseq_meantime`

,`MEDseq_stderr`

, & various/more`print`

/`summary`

methods: now certain plots &

outputs can be (or are by default) labelled with the central sequences in SPS format, as per the paper. `seriated`

options`"observations"`

&`"both"`

can now be used for`"i"`

type plots,

with related minor fixes for`"i"`

&`"I"`

type plots for weighted data with seriated observations.- Added
`predict`

,`fitted`

, &`residuals`

methods for`"MEDgating"`

objects, i.e.`x$gating`

. `MEDseq_meantime`

gains the arg.`wt.size`

(defaults to`FALSE`

).- Minor speed-ups to model-fitting for
`modtype="CU"`

.

- A warning message is now printed if the gating network’s MLR ever fails to converge, prompting users to

modify the`itmax`

arg. to`MEDseq_control`

: the 2^{nd}element of this arg. governs the maximum number of

MLR iterations — consequently, its default has been modified from`100`

to`1000`

, which is liable to slow

down internal calls to`nnet::multinom`

, but generally reduces the required number of EM iterations. - Changes to default colour palettes & plotting symbols for certain plot types:

`Suggests:`

package`viridisLite`

now only invoked if available. - Minor fixes to returned
`x$gating`

object, especially for`equalPro`

models

with a noise component and weighted models*without*any gating covariates at all. - Stronger checks to ensure
`weights`

arg. is explicitly supplied to`MEDseq_fit`

in cases where the`"stslist"`

object passed via`seqs`

has the`"weights"`

attribute. - Added error message to
`MEDseq_fit`

when the number of states exceeds 9,

to better inform of this bug which will be rectified in future updates. - Fixed bug preventing inclusion of higher-order terms in
`gating`

formulas when there are duplicates. - Minor fixes to
`get_MEDseq_results`

and how its optional args. are internally handled by`plot.MEDseq`

. - Stronger checks for variables in
`gating`

formula which are not found in`covars`

. `type="mean"`

option renamed to`type="central"`

in`plot.MEDseq`

.`type="ms"`

plots now work properly when`seriated="clusters"`

or`seriated="both"`

.- Removed some superfluous warnings for all but the
`"mt"`

`TraMineR`

type plots. - Fixed small bug in
`MEDseq_meantime`

when`MAP=FALSE`

. - Further robustifications to handle empty components.
- Minor fixes to
`print.MEDseq`

for models where DBS &/or ASW statistics weren’t computed. - Minor vignette edits and documentation clarifications.
- Updated citation info after online publication in
*JRSSA*.

- The
`"d"`

,`"f"`

,`"Ht"`

,`"i"`

, &`"I"`

plot types now properly account for sampling weights. - Layout and legend-placement has been improved for these same types of plots.
- Mimicking
`TraMineR`

further,`plot.MEDseq`

also gains the`type`

options`"ms"`

&`"mt"`

. - Minor speed-ups associated with the
`opti="medoid"`

setting. - Added ORCID iDs to DESCRIPTION.
- Minor CRAN compliance edits to the vignette.

- Corrected the parameter count penalty for the BIC, ICL, and AIC model selection criteria,

specifically, the count is now greater for the central sequence position estimates. - Hence,
`criterion="bic"`

is now the default for`MEDseq_control`

,`MEDseq_compare`

, and

`get_MEDseq_results`

(previously`"dbs"`

), with modifications to`print`

&`summary`

functions. - Non-noise components’ central sequence positions associated with precision parameters of zero

are now printed (`print.MEDseqtheta`

) & plotted (`plot.MEDseq(..., type="mean")`

) always:

the`preczero`

argument has thus been removed from both functions.

`MEDseq_meantime`

gains two new arguments (see documentation for more details):`weighted`

(default:`TRUE`

, old:`FALSE`

) allows the sampling weights to be used,

with or without the cluster assignment probabilities, in the computation of the weighted averages.`prop`

(default:`FALSE`

) divides the output when`norm=TRUE`

by the sequence length.

`MEDseq_control`

gains the arg.`random=TRUE`

, governing tie-breaking of estimated central sequence

positions: old behaviour (always choosing the first candidate state) recoverable via`random=FALSE`

.`plot.MEDseq`

arg.`quant.scale=FALSE`

replaces old arg.`log.scale`

: quantiles now used

to determine non-linear colour breakpoints when invoked with`type="precision"`

.- Sped-up
`init.z="kmedoids"`

initialisation via`pam`

for*unweighted*sequences, by using the

*highest available*value for the`pamonce`

option, based on the`cluster`

package’s version number. `init.z`

gains the options`"kmodes"`

&`"kmodes2"`

, though only for*unweighted*sequences:

both require the newly*suggested*`klaR (>= 0.6-13)`

package.`plot.MEDseq`

gains the arg.`smeth`

, governing the seriation method to be used (`"TSP"`

, by default).- For weighted sequences,
`init.z="kmedoids"`

is now itself initialised by Ward’s hierarchical clustering. - Significant speed-ups to computation of central sequences for all
`opti`

settings (esp.`"mode"`

). - Added
`SPS`

arg. (default=`FALSE`

) to`print.MEDtheta`

&`summary.MEDseq`

. `dbs`

gains the optional/experimental arg.`clusters`

- no change to default.

- Various fixes to the
`seriated`

arg. to`plot.MEDseq`

:- Arg. name changed from
`seriate`

to avoid conflict with function`seriation::seriate`

.

- Fixed
`seriated`

options`"clusters"`

/`"both"`

for models with no noise component.

`seriated="observations"`

(the default) now also works for`type="I"`

plots.

`seriated="clusters"`

now also works for`type="dbsvals"`

&`type="aswvals"`

plots.

- Arg. name changed from
`MEDseq_fit`

now always internally normalises the`weights`

to sum to the sample size.- Minor fixes to properly account for weighted sequences &/or duplicates when
`noise.gate=FALSE`

. - Minor fix to gathering of results to account for
`noise.gate=FALSE`

when`G=2`

. `MEDseq_stderr`

now respects the`algo`

,`opti`

, &`noise.gate`

settings of the original model.`MEDseq_compare`

now returns & prints`opti`

info where relevant.- Fixes to
`print`

&`summary`

methods for`MEDgating`

objects if`equalPro=TRUE`

. `MEDseq_fit`

now coerces`"character"`

covariates to`"factor"`

.- Minor fixes to
`print`

method for`MEDlambda`

objects also. - Additional minor edits to
`plot.MEDseq(..., type="gating")`

. `print.MEDseqCompare`

gains the args.`maxi`

&`rerank=FALSE`

.- Minor speed-ups for
`G=1`

models. - Added
`viridisLite (>= 0.2.0)`

to`Suggests:`

(for`plot.MEDseq(..., type="precision")`

). - Ensured
`matrixStats (>= 0.53.1)`

and`TraMineR (>= 1.6)`

in`Imports:`

. - Package startup message now checks if newer version of package is available from CRAN.
- Significant vignette edits.
- Updated maintainer e-mail address.
- Minor documentation, examples, and CRAN compliance edits.

- Maintenance release for compatibility with R 4.0.0 - minor edits.
`summary.MEDseq`

gains the printing-related arguments

`classification=TRUE`

,`parameters=FALSE`

, and`gating=FALSE`

.`x$params$lambda`

now inherits the`MEDlambda`

class,

with its own`print`

method as per`x$params$theta`

.`x$params$tau`

now has informative`dimnames`

.- Minor changes when supplying
`x.axis`

to`plot.MEDseq(..., type="gating")`

. - Documentation, vignette, examples, and references improvements.
- Added
`rmarkdown`

to`Suggests:`

. - Reformatted package startup message.

- Significant efficiency gains when ignoring duplicates in the presence of weights:
- before, unique cases were defined as unique sequence/covariates/weight combinations,

- now, cases with different weights that are otherwise duplicates are treated as duplicates.

- before, unique cases were defined as unique sequence/covariates/weight combinations,
`MEDseq_stderr`

is provided for computing the standard errors of the

coefficients for the covariates in the gating network via either the

weighted likelihood bootstrap or jackknife methods.- Small robustifications in the presence of empty components.
- Fixed
`get_MEDseq_results`

when`what="MAP"`

and non-noise models are chosen. - Fixed bug related to the colours used in the vignette plots.
- Odds ratios now returned (and printed) when calling
`summary`

on`x$gating`

. - Cosmetic fixes to
`plot.MEDseq`

when`type="clusters"`

for small sample sizes. - Other small cosmetic plotting & reference-formatting changes.
- Spell-checking of documentation and fixes to
`donttest`

examples.

- Speed-ups to E-step, especially for models with a noise component.
- Clarifications and improvements to documentation and examples.