                CHANGES IN TraMineRextras VERSION 0.7.8 [2024-08-17]
                
New function:
    o   dissCompare() comparison of two groups of data represented by 
        a pairwise dissimilarity matrix.
        
Bug fixes
    o   seqCompare() caused an error when only one group occurs in 
        one of the sets. Now returns NA for such sets.
    o   internal seq.comp() renamed as seqxcomp().
    o   missing package anchors for Rd link targets. 
                           
                
                CHANGES IN TraMineRextras VERSION 0.6.7 [2024-01-08]

Changes in existing functions:
    o   All TraMineRextras plot functions: improved support of 
        graphical parameters. (E.g., las and cex.axis can 
        now be used to control the display of tick labels.)
        
Bug fixes:
    o   seqimplic.Rd: lack of description for argument 'ylim'.
    o   seqpolyads(): time reported when core > 1 was not reliable.
    o   convert.g(): error when path=NULL.
    o   convert.g() adapted to changes in ImageMagick.
    

                CHANGES IN TraMineRextras VERSION 0.6.6 [2023-03-07]

New functions:
    o   dissindic() case indicators to select observations that are typical, atypical, 
	    illustrative of or counterexample of a statistical association between trajectories 
		and a covariate/typology.

Changes in existing functions:
    o   seqsplot(), argument `axes` is deprecated and replaced by `xaxis`.
        Argument `yaxis` can now also be one of "all" or "left".
    o   seqsplot(), ylab can be a vector of labels by group level.
    o   seqsplot() supports arguments of legend among the ... list.
    o   plot.stslist.surv(), plot method for objects returned by seqsurv displays
        the ylab closer from the y-axis when yaxis=FALSE. It also recognizes the `cex.lab` argument.
    o   seqsplot(), seqplot.tentrop(), seqplot.tentrop.m(), seqedplot(), plot.dynin(),
        and plot.stslist.surv(): default value of main is now "auto" and NULL suppresses
        the titles as expected.
    o   seqplot.tentrop.m() now in namespace.
    o   seqedplot()} argument names and behavior made conformable with those of TraMineR:::seqplot.

Misc.:
    o   Depends on TraMineR >= 2.2-5 (link to `seqrf` in `seqplot.rf` help page)


                CHANGES IN TraMineRextras VERSION 0.6.5 [2022-10-09]

Changes in existing functions:
    o   seqplot.rf() argument 'plus.one' renamed 'grp.meth'

Bug fixes:
    o   seqplot.rf() which.plot = "diss.to.med" did not work.
    o   seqplot.rf() issue with unwanted ":" in plot title.
    o   sorti() possible conflict between column names of seqdata and arguments passed to order.
    o   issue with non UTF-8 commented line in TraMineRextras.Rd

Misc.:
    o   Replaced `permute(.)` with `sample(.)` in `seqCompare` to remove dependence
        on gtools that has become orphaned.


                CHANGES IN TraMineRextras VERSION 0.6.4 [2022-06-13]

Changes in existing functions:
    o   seqplot.rf() gains a new argument 'plus.one' to control which
        group sizes to increase when number of sequences is not a multiple of number of groups.

Bug fixes:
    o   seqindic.dyn() checked whether fstat is a function by comparing class with a string. Now uses inherits.
    o   Issue with example in seqtabstocc.Rd.
    o   Issue with non literal item name in seqsamm.Rd.


                CHANGES IN TraMineRextras VERSION 0.6.3 [2022-01-19]

New functions:
    o   seqcta() organizes data for CTA analysis (Studer et al., ALCR 2018).
    o   seqsamm(), seqsammseq(), seqsammeha() organize and retrieve data for SAMM analysis (Studer et al., Soc. Meth. 2018).
    o   plot.SAMM() plot of SAMM object returned by seqsamm.
    o   seqsha() organizes data for SHA analysis (Rossignon et al., in Ritschard & Studer, 2018).

Misc.:
    o   Updated description and some Rd files.


                CHANGES IN TraMineRextras VERSION 0.6.2 [2021-06-23]

Changes in existing functions:
    o   seqindic.dyn() gains two arguments: 'wstep' to control
        spacing between successive windows and
        'endmiss.as.void' to control whether sequences end at
        first ending missing value or at the first void.
    o   plot.dynin() (plot method for objects produced by
        seqindic.dyn) can now plot series of summary values
        that end with missing values.
    o   plot.dynin()} 'conf' can now be logical or the confidence
        probability, TRUE being equivalent to 0.95.
    o   TSE_to_STS() now checks that tmin > 0.
    o   seqplot.rf() now returns (invisibly) group memberships.

Bug fixes:
    o   plot.dynin() issue with check of fstat.


                CHANGES IN TraMineRextras VERSION 0.6.1 [2021-01-20]

New functions:
    o   seqindic.dyn() dynamic individual indicator values.
    o   plot.dynin() plot method for dynin objects produced
        by seqindic.dyn.
    o   seqpolyads() degree of similarities between polyadic members
        (contributed by Tim Liao)
    o   polyads example data set

Changes in existing functions:
    o   seqplot.tentrop() default color now set using
        qualitative_hcl from colorspace with the 'Dark 3' palette.


                CHANGES IN TraMineRextras VERSION 0.6.0 [2020-04-08]

New functions
    o   seqCompare() BIC and Likelihood ratio test (LRT) for comparing
        two sets of sequences.
    o   seqLRT() LRT for comparing two sets of sequences.
    o   seqBIC() BIC for comparing sequence data.

Changes in existing functions
    o   seqgranularity(): two new methods "first.valid" and
        "last.valid" for sequences with missing values.
    o   seqplot-rf() gains a new argument 'which.plot'.

Bug fixes
    o   seqgranularity() did not return a proper stslist object
        when \code{method="mostfreq"}.


                CHANGES IN TraMineRextras VERSION 0.4.7 [2020-03-02]

Bug fixes
    o   seqedplot(): Issue with color selection when only one event.
    o   seqedplot(): Now calls plot.survfit with by default
        conf.int=FALSE instead of "none" (advised by Terry Therneau).

Misc.
    o   seqprecarity(), seqprecorr(), seqprecstart() deleted. These
        functions are in TraMineR since v 2.0-13.


                CHANGES IN TraMineRextras VERSION 0.4.6 [2019-05-06]

Changes in existing functions
    o   seqedplot(): argument 'title' is deprecated, use 'main' instead.
    o   seqedplot(): when type = 'survival', now supports the 'conf.int'
        argument of plot.survfit to control the display of confidence
        intervals.

Bug fixes
    o   seqedplot(): An issue with the joint use of the 'xmax' and
        'xlim' arguments when calling plot.survfit raised a warning
        since Survival v3.0.


                CHANGES IN TraMineRextras VERSION 0.4.5 [2019-05-06]

Changes in existing functions
    o   seqprecarity() and seqprecstart() gain a argument 'with.missing'.
    o   seqprecarity()}: there is now a print method for the generated
        'seqprec' object that prevents the printing of all its attributes.
    o   seqprecorr(): new 'border.effect' argument. To avoid a border
        effect, when method is 'FREQ', 'TRATEDSS', or 'TRATE', the
        computed transition frequencies or probabilities p are adjusted
        as p - p/border.effect when any p > 1 - .1/border.effect.
    o   seqtabstocc() gains an argument 'with.missing'.

Bug fixes
    o   seqprecorr(): method='TRATE' now works as expected.
    o   seqprecarity(), seqprecorr(), and seqprecstart(): errors due
        to bad handling of missing states.
    o   seqedplot() called plot.survfit with a firstx argument
        that has been suppressed (non documented in survival news);
        now uses xlim instead.


                CHANGES IN TraMineRextras VERSION 0.4.4 [2018-12-14]

Changes in existing functions
    o   plot.stslist.surv(): new 'xlab' argument.
    o   seqprecarity(), seqprecorr(), and seqprecstart(): Important
        code cleaning.
    o   seqprecarity(), seqprecorr(): New argument 'method' that
        replaces 'tr.type' to select the type of transition weights.
        Two additional methods have been implemented, namely 'RANK'
        (for rank-based transition weights) and 'ONE' for
        non-weighted transitions. Also new argument 'stprec' to allow
        specifying rank values for method='RANK'.

Bug fixes
    o   seqsurv(): levels of spell$states were not ordered conformably
        with the alphabet of the state sequence object, which
        caused plot.ststlist.surv() to use wrong colors for the
        survival curves when 'per.state=FALSE'.
    o   seqsplot(): color synchronization failed when one of
        the states selected was unobserved in one of the groups.
    o   seqprecorr(): identification of non-comparable states did
        not work as expected.
    o   seqprecstart(): did not work as expected when equiv class
        included incomparable states.


                CHANGES IN TraMineRextras VERSION 0.4.3 [2018-08-22]

Changes in existing functions
    o   seqsplot() now supports the 'ncol' argument for controlling
        the number of columns in the color legend.
    o   plot.stslist.surv(), seqplot.tentrop(), seqplot.tentrop.m(),
        plot.seqimplic(), print.seqimplic(): new argument 'tick.last'
        that when set as TRUE allows to enforce a tick mark at
        the last position on the time x-axis. Has no effect when
        the last position is 1 + a multiple of xtstep.
        Default is to use the 'tick.last' attribute of the state
        sequence object.
    o   seqrep.grp() an error is raised when one of the groups has less than two cases.

Bug fixes
    o   seqgen.missing(): the number of left and right
        elements to be turned into missings were inverted.

Misc
    o   Function seqeordplot() suppressed. It is superseded by the
        function seqpcplot() of the TraMineR package.


                CHANGES IN TraMineRextras VERSION 0.4.2 [2018-02-01]

New functions
    o   seqprecarity(): computes the sequence precarity index from
        a provided partial state order. The index is a
        corrected complexity index. See documentation page.
    o   seqprecorr(): determines the correction factor used by
        seqprecarity().
    o   seqprecstart(): determines the starting precarity level
        of the sequence from the partial state order.
    o   seqsurv(): fits survival curves for states in state sequences.
        There is a plot method for objects returned by seqsurv().
    o   seqsplot(): specific version of the TraMineR seqplot() function
        to plotting survival curves of states in sequences.

Changes in existing functions
    o   seqrep.grp() renamed argument names for consistency with TraMineR.
    o   seqrep.grp(): when 'diss=NULL', the dissimilarity matrix is now
        computed by calling seqdist with the 'method' and possibly
        related parameters specified among the '...' arguments.
        An error is raised when 'diss=NULL' and no 'method' is provided.

Bug fixes
    o   seqtabstocc(): label synchronization issue.

Misc
    o   Uses function \code{TraMineR.check.depr.args()} introduced
        in TraMineR v 2.0-8. So, depends now on version >= 2.0-8.


                CHANGES IN TraMineRextras VERSION 0.4.1 [2017-08-16]

Changes in existing functions
    o   STS_to_SPELL(): Deleted. Converting to the "SPELL" format is now a
        feature of seqformat() in TraMineR 2.0-6+.
    o   seqrep.grp(): Added argument 'with.missing' to allow computing
        the default distances (when diss = NULL) for sequences with
        missing values.

Misc
    o   Replaced deprecated argument names in example of seqrep.grp().
    o   Now imports from RColorBrewer, survival, and cluster instead of
        depending on those packages.
    o   Suppressed unused import from combinat.
    o   ini.c file.


                CHANGES IN TraMineRextras VERSION 0.4.0 [2017-05-13]

Note
    o   TraMineRextras has been adapted to and requires now TraMineR 2.0-5+.

Bug Fixes
    o   TSE_to_STS(): The two last sequences were not converted and
        unexpected outcome in case of a single sequence.

Changes in existing functions
    o   seqplot.rf(), seqplot.tentrop(), seqrep.grp(), dissvar.grp(),
        plot.seqimplic(): adjusted argument names (e.g., main, with.legend,
        legend.pos, diss, ...) to conform to the TraMineR 2 naming convention.

Misc
    o   seqrep.grp(): Removed 'with.missing=TRUE' in a help example as biofam.seq
        doesn't contain missing values and to conform to TraMineR 2.0-5+.
    o   seqeformat(), seqentrans(), seqerulesdisc(): Renamed 'seqe' to 'eseq'
        in internal code to conform to TraMineR 2.0-5+.
    o   Adjusted examples in help files to conform to TraMineR 2.0-5+.


                CHANGES IN TraMineRextras VERSION 0.2.6 [2017-03-01]

Misc

    o   Function ctplot() suppressed. It is superseded by the
        function seqpcplot() of the TraMineR package.
    o   C++ routines are now registered.


                CHANGES IN TraMineRextras VERSION 0.2.5 [2016-11-10]

New functions

    o   seqimplic(): Identifies position wise typical states
        of groups of sequences when compared with all the others. There
        are also plot and print methods for the outcome of the function.


                CHANGES IN TraMineRextras VERSION 0.2.4 [2015-07-23]

New functions

    o   seqplot.rf(): Implements the Relative Frequency Sequence Plots
        introduced in Fasang and Liao (2014).

Misc

    o   revised help page for seqemlt() (distance of Rousset et al. 2012)

    o   Added required basic packages to the import statements to
        comply with R v3.3 requirements.


                CHANGES IN TraMineRextras VERSION 0.2.3 [2015-01-27]

New functions

    o   seqtabstocc(): frequencies of state co-occurrence patterns

Changes in existing functions

    o   seqgranularity(): new method "mostfreq"

    o   seqedplot(): replaced calls of TraMineR internal functions seqeage
        and TraMineR.legend with respectively
        TraMineRInternalSeqeage and TraMineRInternalLegend
        (should be transparent to the end user).


                CHANGES IN TraMineRextras VERSION 0.2.2 [2013-10-30]

    o   Fixed issue with calling Rinternals from within extern "C" {}
        in seqstart.cpp (request of B. Ripley)


                CHANGES IN TraMineRextras VERSION 0.2.1 [2013-03-15]

General

    o   NEWS now uses basic formatting rules and is saved as inst/NEWS

Bug Fixes

    o   FCE_to_TSE(): Events were not properly chronologically sorted.

    o   TSE_to_STS(): produced inconsistent results when events were
        not chronologically sorted by cases.


                CHANGES IN TraMineRextras VERSION 0.2 [2012-12-06]

General:

    o   First release on CRAN

Changes in existing functions:

    o   seqplot.tentrop() and seqplot.tentrop.m(): new argument 'cex.legend'
        for controlling legend scaling factor.

    o   seqentrans(): new option 'avg.occ'; when set as TRUE the table is
        completed with average number of occurrences of the subsequences
        in each sequence. The latter differs from the support for
        counting methods other than COBJ. Requires TraMineR 1.8-5 or higher.

    o   dissvar.grp() and seqrep.grp() now also accept distance object as
        'mdis' argument.

    o   group.p has now a 'weights' argument.

Bug Fixes

    o   seqedist(): fixed a mix between norm and interval arguments.

    o   fixed build warning generated by calls of foreign functions.

