NEWS file for the TraMineR package

Changes in version 2.2-11 [2024-12-08]

Changes in existing functions

• dissrep(): when all distances are zero, the number nb of cases in the neighborhood of the representative is set as the sum of weights (was zero in previous versions)

Bug fixes

• dissrep() error when seqdata is a single sequence.

• seqecreate() (and tmrsequenceseveral cpp function): segfault error when intEvent is NULL. (Fix required by Brian Ripley)

Changes in version 2.2-10 [2024-05-20]

New functions

• dissmergegroups() merges groups so as to minimize loss of partition quality.

• seqhasmiss() count and identification of sequences with missings.

Changes in existing functions

• seqdist() new argument opt.args to test non-documented arguments at development stage.

• seqdef() now raises an error when it finds negative or NA weights.

• seqprecstart() includes derived state.order and state.equiv as attributes of returned object.

Bug fixes

• seqcost() method="INDELSLOG" returned NA costs for token 0 when alphabet is numeric.

• print.stslist(, format="SPS") error with some version of R.

• plot.stslist.statd(type="dH") error when xtstep > 1.

• plot.stslist.statd(type="Ht") argument main was ignored.

• plot.stslist.statd(type="Ht") displayed useless x-label "Index" when xlab=NULL.

• seqdHplot() and seqplot(,type="dH") use col.entr instead of col to control color of overlayed entropy because of name conflict.

• seqidegrad() and seqinsecurity: unexpected results when order of undesirableness degrees provided with stprec differed from alphabet order.

• seqdomassoc() error when only two domains.

• noRemap issues.

Changes in version 2.2-9 [2024-01-08]

Changes in existing functions

• All TraMineR plot functions: improved support of graphical parameters. (E.g., las and cex.axis can now be used to control the display of tick labels.)

• seqdist() transforms kweights into vector rep(kweights,ncol(seqdata)) when it is scalar.

• seqdist() raises a warning when the vector kweights is shorter than the number of columns in seqdata.

Bug fixes

• seqdef(): lack of separation between found tokens not listed in the alphabet.

• seqdist(): error when all DSS have length 1 and method is one of OMspell, NMSMST, and SVRspell.

• seqdist(): error when all DSS are identical with length 1 and method is OMstran.

• seqdist() with method="OMstran": returned distance matrix was not labeled with sequence rownames.

• Issues with lost braces in .Rd files (NOTE in CRAN check)

Changes in version 2.2-8 [2023-09-18]

New functions

• disstree.get.rules() character string vector of the classification rules of a disstree as R commands.

• disstree.assign() determines the index of the rules that apply to the provided profiles.

Changes in exiting functions

• seqST() When number phi of subsequences is NaN, it is set as .Machine$double.xmax to compute turbulence and a warning is raised.

• seqplot() and seqplotMD(): when type="f", the yaxis argument can now also be "pct" or "left.pct".

• seqrep() and dissrep(): returned object gains attributes Rep.group with the representative to which each object is assigned, and idx.rep a list with indexes of all occurrences of each representative.

• seqtreedisplay() and seqtree2dot(): argument axes is deprecated and replaced by xaxis to be conformable with seqplot.

• disstreedisplay() and seqtreedisplay() now raise an error when the file filename of the image cannot be created.

• disstreeleaf() gains an argument collapse to control separator within classes of categories.

Bug fixes

• seqfplot() and seqplot(type="f"): option yaxis="pct" did no longer work after update to v 2.2-7.

• disstreedisplay() and seqtreedisplay() did not find the GraphViz path.

• disstreedisplay() and seqtreedisplay() uselessly printed TRUE when filename was not NULL.

Changes in version 2.2-7 [2023-03-31]

New functions

• seqplotMD() plot of multidomain/multichannel sequences by domain and group.

• seqdomassoc() pairwise state association between domains.

Changes in exiting functions

• dissrf() and seqrf() sortv="mds" is now the default and sortv=NULL selects the original seqdata order.

• seqrfplot() (seqplot(..., type="rf", ...)) with option sortv="mds" (new default in seqrf) the MDS sorting is done on the whole seqdata instead of independently for each group.

• seqMD(): with.missing can now be NULL (new default), in which case the with.missing value of each domain is set as TRUE when the domain has missings and as FALSE otherwise.

• seqMD(): new logical argument fill.with.miss, which offers the option to fill the shorter sequences with missings in case of non-matching lengths across domains.

• seqplot() and all the seqxxplot() family functions: ylab can be a vector of labels by group level.

• seqplot() and all the seqxxplot() family functions support arguments of legend among the ... list.

• "[.stslist" raises a warning when row subsetting condition has NAs.

Bug fixes

• seqrf(): options sortv="from.start" and sortv="from.end" did not work as expected.

• seqMD(): error when sequences had different lengths.

• foreign c function wcorr called with character string naming while package calls R_forceSymbols. (Fix asked for by K. Hornik).

Misc.

• Statement "SystemRequirements: C++11" dropped from DESCRIPTION as requested by CRAN check

• Using new CITATION commands.

Changes in version 2.2-6 [2022-11-29]

Changes in existing functions

• seqplot() and all the seqxxplot() family functions: default value for the main argument is now "auto" and NULL removes all titles as it should.

• seqplot() and all the seqxxplot() family functions: argument axes is deprecated and replaced by xaxis. Argument yaxis can now also be one of "all" or "left".

• plot() methods for objects returned by seqdef, seqstatd, seqtab, seqmodst, seqmeant, and seqrf now display the ylab closer from the y-axis when yaxis=FALSE.

• plot() method for object returned by seqrep now displays the ylab closer from the y-axis when stats=FALSE.

Bug fixes

• summary.dissrf(): five number statistics ignored weights (reported by Marcel Raab)

• seqstatl(): non-integer state value were not recognized.

• plot() methods for objects returned by seqdef, seqstatd, seqtab, seqmodst, seqmeant, seqrf, and seqrep ignored the cex.lab argument.

• issues with prototypes in init.c

• removed unused code with deprecated sprintf in eventdictionary.cpp

Misc.

• Replaced seqdistmc with seqMD in examples of dissdomassoc.

Changes in version 2.2-5 [2022-08-30]

New functions

• dissrf() medoids of relative frequency (RF) groups

• seqrf() medoid sequences of RF groups

• plot.seqrf() plot method for medoid sequences of RF groups

• seqrfplot() alias for seqplot(...,type="rf",...)

• print and summary methods for dissrf and seqrf objects

• seqfposend() position of end of spell in given state

Changes in existing functions

• seqplot() new value "rf" (RF plots) for argument type.

• seqtab() result gains an attribute idxf with indexes of first found frequent sequences.

• seqdistmc() renamed seqMD to better reflect that the function can return various outcomes related to multidomain (MD) sequences, not just distances based on the MCSA trick. Old name maintained as an alias for backward compatibility.

• plot.stslist() now raises an explicit error for bad ytlab value.

Bug fixes

• plot.stslist() possible conflict between x names and arguments of order.

• plot.stslist.rep() bad position of y-axis when !is.na(ylab)

Misc.

• Proper wtd.cor, wtd.mean, wtd.var, wtd.fivenum, and wtd.boxplot internal functions to avoid issues with dependence on packages weights, Hmisc, and ENmisc. (Code in TraMineR-weights.R and TraMineR-wtd-stats.R.)

• Function TraMineR.checkupdates has been removed.

Changes in version 2.2-4 [2022-06-08]

New functions

• seqdHplot() alias for seqplot(...,type="dH",...)

• seqlength.align() sets lengths of sequences of multiple domains as the shortest length among the domains.

• seqmaintokens() returns indexes of more frequent tokens.

Changes in existing functions

• plot.stslist.statd() new type "dH" that overlays entropy line on the chronogram. In addition, new arguments col, lwd, and ylim allow controlling aspect of entropy line.

• seqplot() new type "dH".

• seqformat(), seqdef(), seqdecomp(), seqconc(), seqstatl() now support tibble input data.

• seqformat() accepts a tibble as pdata table.

• seqformat() accepts a character string vector as input data.

• seqdistmc(): option what="sm" becomes what="cost". Deprecated "sm" value maintained for backward compatibility.

• plot.stslist.rep() gains two arguments seq.alt to specify the domain in which representatives are displayed and info to control whether coverage info should be displayed.

Misc.

• Suppressed dependence on cNORM because of license incompatibility. (dissdomassoc uses now a proper internal function in place of cNORM:::weighted.rank).

Changes in version 2.2-3 [2022-01-19]

New functions

• summary.ddomassoc() summary method that organizes outcome of dissdomassoc in table form.

Changes in existing functions

• dissdomassoc() now returns also p-values of computed correlations.

• plot.subseqelistchisq() (plot of outcome of seqecmpgroup) gains attribute with.legend.

• plot.stslist.modst() new attribute info to control whether frequency of sequence of modal state should be displayed.

• plot.ststlist.meant() now uses an internal function to draw error bars to avoid issues with dependence on Hmisc.

• plot.ststlist.meant() new arguments bar.labels, cex.barlab, and offset.barlab to display and control bar labels.

• seqmtplot() (seqplot(..,type="mt", ..)) adapted for handling bar labels with groups. See details in seqplot help page.

• seqformat() with from="SPELL", provides info about number of sequences truncated, empty sequences because of spell occurring before birth year, and empty because of missing start time. A new attribute issues contains the indexes of sequences with issues.

• seqdef() now prints, when applicable, the number of empty sequences and lists the first 9 empty sequences only.

• seqdistmc() gains an argument ch.sep to control the separator symbol for building state names of the expanded alphabet.

• seqdistmc() rows and columns of the returned distance matrix and the mc sequences are now labelled with rownames of the first channel. Rows and columns of the returned mc substitution cost matrix are labelled with the expanded alphabet.

• seqdistmc() columns of the returned expanded sequence object now labelled with column names of longest domain.

• seqdistmc() indel can now be "auto" (new default) to automatically set indel values. In addition, state dependent indels are now supported.

• seqdistmc() with.missing can now be a vector to provide different values for each channel.

• seqdistmc() now also supports "INDELS" and "INDELSLOG" values for the sm argument.

• seqcost() removed "->" at end of row/column labels of matrix sm.

Bug fixes

• seqdiff() negative values in cmprange caused an error.

• seqdiff() changed deprecated norm=TRUE into norm='auto' in default seqdist.args value.

• seqecreate() NAs introduced by coercion with character id.

Misc.

• Dependence on boot and RColorBrewer replaced by importFrom of functions boot and brewer.pal.

Changes in version 2.2-2 [2021-06-03]

New functions

• seqidegrad() degradation index (replaces seqprecorr() that becomes obsolete). Class seqprecorr now named seqidegrad and associated print method renamed accordingly.

• seqibad() badness index.

• seqinsecurity() insecurity index.

• dissdomassoc() computes measures proposed in Piccarreta (SMR 2017) to assess the degree of association between domains.

Changes in existing functions

• seqdist() can now compute distances between two subsets of sequences. The subsets are defined by providing a list with two subsets of sequence indexes as refseq argument.

• seqdist() dimnames of the objects returned by seqdist are now all set from the rownames of the provided sequence object.

• seqdist() method="DHD" now supports sm="INDELS" and sm="INDELSLOG".

• seqcost() time.varying=TRUE works with "INDELS" and "INDELSLOG".

• seqdistmc() gains a what argument to choose what value will be returned: distances, costs, or combined state sequences.

• seqintegration() renamed seqintegr()

• seqindic() the possible indic list gains elements 'degrad' for degradation index, 'bad' for badness index, 'insec' for insecurity index, and the type 2 forms 'meand2', 'dustd2', 'turb2', and 'turb2n' taking non-visited states into account. In addition, indic accepts now also value 'ranked' that is equivalent to c('degrad','bad','prec','insec').

• seqindic() value 'inpos' of indic renamed 'integr', 'volat' now in the 'complexity' group.

• seqindic() changes in order of indicators in the returned table.

• seqformat() with from='SPELL' and process=TRUE now issues a warning message when the max of the end column exceeds limit.

• seqlegend() gains an argument boxes to control how colors are displayed. In addition, now supports any argument of function legend and, e.g. x (or x and y) can be used instead of position.

• seqstatf() gains the with.missing argument.

• seqlogp() gains the with.missing argument. In addition, the overall state distribution can now be used as starting point by setting begin='global.freq'.

Bug fixes

• seqlogp() error for state sequences with missing values.

Misc.

• New imports from psych and cNORM (for dissdomassoc)

Changes in version 2.2-1 [2020-10-24]

New functions

• seqivardur() computes the variance of spell durations for each individual sequence. Either the variance of the observed spells or by considering also the 0-time spent in non-visited states. The associated print method can print the mean, standard deviation, variance, and max variance.

Changes in existing functions

• seqST() gains an argument type to select the type of duration variance used.

• seqindic() the possible indicator list gains elements 'recu' for recurrence index, 'nvolat' for normative volatility, 'meand' for mean spell duration, 'dustd' for standard deviation of the duration. The indic argument accepts now also values 'basic', 'diversity', 'complexity', and 'binary' that each selects a subset of indicators.

• seqprecstart() the normalized stprec has now a minimum 0.

• seqdist() the check of allowed number of unique sequences now depends on refseq and used thresholds are sqrt(.Machine$integer.max) when refseq==NULL, and .Machine$integer.max otherwise. In addition, a new argument permits to skip the test.

Bug Fixes

• seqdur() returned sometimes bad values for the duration of the last spell of sequences of unequal lengths when with.missing=TRUE.

• seqdur() unexpected outcome for sequences with missing values when with.missing=FALSE. Now correctly ignores missing values.

• seqdplot() and plot.stslist.statd() ignored the xlab argument.

• seqconc(), seqdecomp(), seqformat(), and the print method for stslist objects produced in some circumstances output without the row names of the input data.

• seqsubsn() error for sequences with missing values when with.missing=FALSE. Now correctly ignores missing values.

Misc.

• TraMineRextras added to the 'Suggests' list (to avoid NOTE on undeclared package in Rd xrefs.)

Changes in version 2.2-0.1 [2020-04-29]

Misc.

• seqdef(): switched back from [grDevices] hcl.colors to [colorspace] qualitative_hcl to avoid dependence on R >=3.6 necessary for hcl.colors.

Changes in version 2.2-0 [2020-04-22]

Changes in existing functions

• seqdist(), argument indel can now be "auto" (new default) in which case a suitable indel value is generated for the provided sm.

• seqdist() now uses the rbind stslist method to add refseq to the set of sequences when it is a state sequence object. (Transparent to the user.)

• seqdist() now gives a zero weight to the refseq when specified as a state sequence object.

• seqdist() refseq including refseq as a state sequence object can be used with all methods (did not work with OMstran, CHI2, and EUCLID).

• seqdist() vector indel now supported by OMspell and OMslen (in addition to OM and OMstran).

• seqdist(), normalization now also possible for OMspell, OMslen, OMstran, OMloc, and TWED.

• seqdef() now uses hcl.colors (grDevices) instead of qualitative_hcl (colorspace) to set default colors when n>13. (Transparent to the user.)

Bug fixes

• rbind.stslist() bad handling of missing states.

• seqdist(), argument sm did not recognize values "INDELS" and "INDELSLOG".

• seqdist() raised warnings when method='OMslen' because of a vector of conditions in an if test.

• seqdist() ignored the weighted value when computing substitution costs with the sm method.

• seqdist() for OMstran ignored the weighted value when computing probability-based indels (i.e. with transindel="prob").

• seqdist() TWED wrongly depended on the indel value. Now indel serves only in the improbable case of empty sequences.

• seqdist() maxlength and gmean normalization generated negative distances in some circumstances. Fixed by setting the maximum length as max length x max indel.

Misc.

• Deleted unused OMVI2distance h and cpp files.

Changes in version 2.0-15 [2020-03-18]

New functions

• seqintegration() index of integrative potential of C. Brzinsky-Fay.

• seqivolatility() index of objective volatility of C. Brzinsky-Fay.

• print.seqipos() print method for objects returned by seqipos().

• is.stslist() checks that the object is a proper stslist object.

• rbind.stslist() rbind method for state sequence objects.

Changes in existing functions

• seqdef() now provides a default color palette (using colorspace) when number of states exceeds 12.

• alphabet() gains an argument with.missing.

• seqipos() gains an argument index to select between three types of indicators: share of positive states, volatility, or integrative potential for the positive state.

• seqipos() returned object has an attribute sbinary with the derived binary sequences.

• seqindic() possible values for argument indic include now the indicators of objective volatility and integrative potential both for the provided sequences and the positive-negative sequences derived from them.

• seqdist(): OMloc, OMslen, OMspell, and OMstran now also apply to sequences of different lengths.

• seqdist(): with.missing=TRUE now supported by all methods.

• seqdist() raises a warning when there are empty sequences except for OMloc where an error is raised.

• seqcost(): with.missing forced as FALSE (as in seqdist) when there are no non-void missings in the sequences.

• seqprecorr(): new methods "FREQ+", "TRATE+", "TRATEDSS+", "RANK+" that adjust the returned penalty for the mean transition weight.

• seqprecorr(), a same state value is assigned to equivalent states when counting transitions and computing transition probabilities (methods FREQ, TRATE, TRATEDSS).

Bug fixes

• Print methods for seqprec and seqprecorr objects did not work.

• print.stslist() did not print ending missing values when format='SPS'.

• print.stslist(), when format='SPS', additional parameters for controlling the format were ignored.

• seqformat() did not account for the right argument when to='SPS'.

• seqdist() with method=CHI2. Fixed issue with unexpected warnings when over an interval all sequences stay in the same state.

• seqdist() raised an error for some methods when the unused argument indel was a vector.

• seqdist(), argument sm: values 'CONSTANT' and 'TRATE' were only accepted for method='OM' and 'HAM'. Now can be used with all methods that require the sm argument.

• seqplot() raised an error when deprecated tlim argument was used. Now a warning.

• [] subsetting of stslist objects with negative column indexes produced unexpected results.

Changes in version 2.0-14 [2020-01-13]

Bug Fixes:

• print.stslist.freq() wrongly used width argument.

Changes in version 2.0-13 [2019-11-19]

New functions

• seqindic() returns a table with per sequence values of selected indicators.

• seqipos() proportion of positive spells/states per sequence.

• seqprecarity() precarity index (previously in TraMineRextras)

• seqprecorr() correction factor for precarity index (previously in TraMineRextras)

• seqprecstart() state precarity level for precarity index (previously in TraMineRextras)

Changes in existing functions:

• seqlength(), seqST(), and seqsubsn() gain a with.missing argument to control how missing values should be treated.

Bug Fixes:

• seqST() normalization did not account for non-void missing values when present.

Misc.:

• Fixed issue with \traminer in vignette.

Changes in version 2.0-12 [2019-06-21]

Changes in existing functions:

• seqdef() now raises an error when argument alphabet contains duplicate elements.

• alphabet() in its assign form now raises an error when the assigned vector contains duplicate elements.

• seqdist() gains a new argument global.pdotj to control the marginal distribution to be used for the 'CHI2' distance.

• seqdist(), 'CHI2' and 'EUCLID' distances are now, when norm='auto', normalized by the maximal distance, which for 'CHI2' depends on the marginal state distribution.

• seqici(), seqient(), and seqST() gain a new argument silent to control whether messages about running operations should be displayed.

• seqST(): suppression of useless messages when norm=TRUE.

Misc.:

• Suppressed unused argument weighted from internal OMstran function.

• Help page for seqdist: description of the weighted argument adjusted to reflect that it applies only to the "CHI2" distance.

• Updated links to Swiss Household Panel in actcal and biofam help pages.

Changes in version 2.0-11.1 [2019-03-22]

Bug Fixes:

• eventseq.cpp: rchk message 'calling allocating function Rf_asChar with argument allocated using TMRNumberFormat'.

Changes in version 2.0-11 [2019-03-18]

Changes in existing functions:

• seqdef(). Speed improvement suggested by Jouni Helske. Transparent for the user.

• seqdist(). An error is raised when the number of unique sequences exceeds the maximal allowed.

• plot.ststlist.statd(). Now checks the type argument and returns the values plotted.

Bug Fixes:

• seqtab(), seqxtract(), checkcost(), SPELL_to_STS(). Issues with length > 1 in coercion to logical.

• Warning about potential stack imbalanced PROTECT in relation with TMRNumberFormat in the C++ code (eventseq.cpp).

Changes in version 2.0-10 [2018-11-18]

Bug Fixes:

• seqdist(): when refseq was passed as a state sequence object wrong results were sometimes returned.

• seqdist(): CHI2 and EUCLID distances were computed using counts instead of proportions.

• seqdist(): CHI2 and EUCLID bad behavior in presence of missings.

• Vignette: Fixed issue with updated fancyvrb.sty.

Misc.:

• Vignette: Error in formula for complexity index. Also, now DOI instead of link to JSS article.

Changes in version 2.0-9 [2018-08-20]

Changes in existing functions:

• seqplot() now supports the ncol argument for controlling the number of columns in the color legend.

• seqdef(): new argument tick.last to set the tick.last attribute of the state sequence object. Default is tick.last = FALSE to preserve the previous behavior.

• plot.stslist(), plot.stslist.freq(), plot.stslist.statd(), plot.stslist.modst(), plot.stslist.rep() (i.e. also seqplot with type "i", "I", "f", "d", "Ht", "ms", or "r"), and plot.seqdiff(): 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.

• seqformat():

  • For from = "SPELL" and process = FALSE, pdata = "auto" is now equivalent to NULL instead of raising an error. Also, using argument pvar with pdata = NULL now raises a warning instead of an error and pvar is simply ignored.

  • For from = "SPELL" an error is raised when columns referred to by begin and end are of class "Date". Integer values are expected.

  • When from = "SPELL" or to = "SPELL", an error is raised when the birth year column of pdata is of class "Date". Integer values are expected.

• seqplot(): for type = "r" (seqrplot), an error is raised when a group has less than two cases.

Bug fixes:

• seqformat(): An unneeded warning was raised when data was a matrix with a single string element.

• seqdef(): Bad handling of missing argument when informat = "SPS" or "SPELL".

Changes in version 2.0-8 [2018-01-26]

Changes in existing functions:

• seqcost(): argument miss.cost.fixed is now NULL by default and will be set as FALSE when method = "INDELS" or "INDELSLOG", and as TRUE otherwise.

• seqpcplot(): new logical weighted argument to control whether weights should be used or not.

Bug fixes:

• seqrplot() and seqplot(..., type="r", ...): the method and other related arguments for computing the diss matrix when the later was not provided was not recognized.

• seqplot(): Fixed some unused argument issues.

Misc:

• Vignette: Suppressed the loading of two unused LaTeX packages (subfigure and afterpage) that prevented the vignette to be built under OSX.

• Declaring use of C++11 for log1p: SystemRequirements: C++11 declaration in DESCRIPTION and math.h header in NMSdistance.cpp

• Internal function checkargs() renamed as TraMineR.check.depr.args() and made public for use in TraMineRextras.

Changes in version 2.0-7 [2017-08-15]

Changes in existing functions:

• alphabet(): the get form now also applies to event sequences. In addition, an error is now raised when the argument is not a state sequence object, an event sequence object, or a probabilistic suffix tree (see the PST package for the latter).

• seqdecomp(): the miss argument can now also be a vector, e.g. miss = c("*", "%")

• seqformat() has a new right argument to be used with to = 'SPELL'. The default right = 'DEL' suppresses the end spells of missing values. Set right = NA to keep the end spells of missing values.

• seqdef() now raises an error message when void is not a character different from left, gaps, and right.

• seqtrate() gains a new argument count. When count = TRUE, the function returns counts of transitions instead of transition probabilities.

Bug fixes

• seqpcplot(): Due to a change in the R tapply function, option ltype="non-embeddable" did no longer work.

• seqefsub() with non-null str.subseq argument: multiple partial matches between events in str.subseq and the alphabet of events of the eseq event sequence object crashed the R session. Fixed by a change in the internal seqecreatesub function.

• seqformat(): to="TSE" and to="SPELL" produced errors or unexpected results in presence of missing and/or void states. Now, when to = "SPELL", the missing and void codes are both converted to NA before conversion while they are kept as is when to = "TSE".

• seqetm() produced an error in presence of void elements.

• An error occurred in the internal implicativestat function when a same condition subsequence was present in all subsequences.

Misc:

• Documentation of seqformat() and seqecreate(): added examples of the handling of missings in conversion into TSE and SPELL format.

Changes in version 2.0-6 [2017-06-17]

Changes in existing functions:

• seqformat():

  • Redesigned version of the function with a new extensible, robust and documented implementation.

  • Rewritten documentation with argument types, default values, scopes and detailed explanations.

  • Added and generalized conversion to "SPELL" from TraMineRextras; added a with.missing argument specifically for this conversion.

  • Added the possibility to pass directly the unique individual IDs (row names) of the input sequences with id when converting to "TSE".

  • Clarified the meaning of the id argument and changed its position in the list of arguments to reflect this.

  • Changed the default value of the id, begin, end, and status arguments (now "SPELL" oriented).

  • Renamed compressed argument as compress to avoid confusion (here it applies to the output, not to input data).

  • Renamed nr argument as missing to avoid confusion (here it specifies the code to consider as missing values in input data, which is not the TraMineR internal code for missing values in state sequence objects).

  • Adapted function calls to match the renamed argument names (compressed, nr) and the new input type checking (ie. single strings are deprecated).

  • See the updated documentation of seqformat() for details.

• SPS_to_STS(): renamed nr argument as missing to match seqformat() argument names renaming.

Bug fixes:

• seqformat():

  • From "SPELL" to "TSE": output IDs were incorrect.

  • From "SPELL" to "STS": states not appearing in the data were dropped from the output column levels.

Misc:

• Added new internal helper functions:

  • msg.warn0(): same as the existing msg.warn() but without white space insertion.

  • is.positive.integers(): check if an object is a vector of positive integers.

  • is.a.character(): check if an object is a (unique) character.

  • is.a.string(): check if an object is a string.

  • is.strings(): check if an object is a vector of strings.

  • is.index(): check if an object is a positive integer or a string.

  • is.indexes(): check if an object is a vector of positive integers or strings.

  • checkindex(): check if an object is a valid data frame or matrix index; otherwise, an error is raised and an information message is displayed.

  • checkindexes(): check if an object is a vector of valid data frame or matrix indexes; otherwise, an error is raised and an information message is displayed.

• Grouped internal is.xxx helper functions into a single TraMineR-is_helpers.R file.

• Generalized msg.warn() / msg.warn0() and msg() / msg0() code.

• Internal C/C++ function tmrWeightedInertiaDist() made public as the R function TraMineRInternalWeightedInertiaDist(). (Used by package Weightedcluster)

Changes in version 2.0-5 [2017-05-13]

Note:

• This is a major update of the CRAN version of TraMineR.

• Check also changes in versions 1.9-14, 2.0-0, 2.0-1, 2.0-2, 2.0-3, and 2.0-4 that have not been released on the CRAN.

Bug fixes:

• seqtrate(): now accepts a sequence object (seqdata argument) containing only one sequence.

• seqdist(): now accepts a reference sequence object (refseq argument) containing missing values while the main sequence object (seqdata argument) doesn't.

Misc:

• Replaced default deprecated values of norm in seqdistmc() and seqtree().

• Fixed issues with examples in documentation page of seqtree().

Changes in unreleased version 2.0-4 [2017-04-13]

Changes in existing functions:

• Renamed several argument names to increase consistency within TraMineR and between TraMineR and R. The aim is also to have a common naming convention within TraMineR. A new internal function (checkargs())is used to guarantee backward compatibility. If the old argument name is used instead of the new one, a warning message with an explanation is displayed and the execution continues. If the new and old argument names are used together, an error message is displayed and the execution stops. The following functions have at least one renamed argument: dissrep(), disstree(), disstree2dot(), disstree2dotp(), disstreedisplay(), is.eseq(), is.seqelist(), seqdiff(), seqeconstraint(), seqecontain(), seqecreate(), seqefsub(), seqeid(), seqelength(), seqelength<-, seqetm(), seqeweight(), seqeweight<-, seqlegend(), seqpcplot(), seqplot(), seqrep(), seqtab(), seqtrate(), seqtree(), seqtree2dot(), seqtreedisplay(), seqeisweighted(), plot.seqalign(), plot.seqdiff(), plot.stslist(), plot.stslist.freq(), plot.stslist.meant(), plot.stslist.modst(), plot.stslist.rep(), plot.stslist.statd(), plot.subseqelistchisq().
  See the help page of each of these functions for the mapping between old and new argument names.

• Renamed function: is.seqe() was renamed as is.eseq().

Misc:

• Fixed an issue with an example in the documentation page of seqpcplot().

• Fixed equation typing errors in seqrep() documentation.

Version 2.0-3 [2017-04-06] (Unreleased version)

Misc:

• In src/tmrsequence.cpp from TraMineR 1.8-13:

  • Fixed two memory errors detected by Valgrind.

  • Fixed a PROTECT error.

• Fixed issues with examples in documentation pages of dissmfacw, disstree, seqtree, and plot.stslist.meant.

Version 2.0-2 [2017-03-28] (Unreleased version)

Misc:

• Changed character encoding from latin1 (ISO-8859-1) to UTF-8.

• Normalized line endings: LF.

Version 2.0-1 [2017-03-27] (Unreleased version)

Misc:

• Removed the following unused functions: vidx(), seqmatsaltt(), seqmathenikoff().

• Removed the functions deprecated in TraMineR 1.x: seqesetlength(), dissreg(), dissmfac().

Version 2.0-0 [2017-03-27] (Unreleased version)

New function:

• seqcost(): Evolution of seqsubm() that offers different ways (CONSTANT, TRATE, INDELS, INDELSLOG, FUTURE, FEATURES) to determine indel and substitution costs (see the documentation of seqcost() for details). Unlike seqsubm(), seqcost() returns both the indel and the substitution costs.

Changes in existing functions:

• seqdist():

  • New major version with many new features and a new extensible, robust and documented implementation (R code).

  • New methods: localized OM (OMloc), spell length sensitive OM (OMslen), OM of spells (OMspell), OM of sequences of transitions (OMstran), Time Warp Edit Distance (TWED), Number of Matching Subsequences (NMS), Number of Matching Subsequences weighted by the Minimum Shared Time (NMSMST), Subsequence Vectorial Representation (SVRspell), Euclidean distance (EUCLID), Chi-squared distance (CHI2).

  • New arguments: kweights, tpow, expcost, context, link, h, nu, transindel, otto, previous, add.column, breaks, step, overlap, weighted, prox.

  • sm: value "CONSTANT" has been removed for DHD as it doesn't make sense and the values "INDELS" and "INDELSLOG" have been added (see seqcost() documentation).

  • norm: value TRUE is replaced by "auto" and FALSE by "none".

  • See the updated documentation of seqdist() for details.

• seqsubm(): This is now an alias for seqcost(...)$sm.

Version 1.8-14 [2017-03-20] (Unreleased version)

Misc:

• Registration of native routines for R 3.4.x. See https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html.

Version 1.8-13

Misc:

• Changes in C-code for the seqefsub function: replaced call to function round by a call to fround to comply with forthcoming changes in R 3.4.0 (request of Brian D. Ripley). The change is transparent for the user.

Version 1.8-12

Changes in existing functions:

• seqST(): new argument norm to ask for a normalized turbulence index.

• seqformat(): The transformation now stops with an error message when the columns referenced with the begin and end argument contain a non integer value.

Bug fixes:

• plot.stslist(): an unnecessary warning occurred when a vector of labels was passed as ytlab argument.

• seqdef(): now accepts to create a state sequence object with an alphabet that has only one element. Fixed an error that occurred when there was only one state

New data examples:

• bfspell: a small data set with 20 sequences in SPELL format.

Misc:

• updated seqformat help page: now includes an example of a transformation from SPELL to STS.

• fixed bad use of extern "C" {} in TraMineR.h (done by B. Ripley, CRAN version 1.8-11.1)

Version 1.8-11

Changes in existing functions:

• seqmeant(): New serr argument. When serr=TRUE, seqmeant computes the variance and standard deviation of the total times spent in the different states, and the standard error of the mean total times.

• seqmtplot(): When serr=TRUE, error bars are displayed in the mean time plot.

• seqdist():

  • New error message when sm=NA with method "OM".

  • New error message when refseq is a state sequence object with an alphabet assigned to it different from that of seqdata.

Misc:

• updated disstreedisplay help page (tree argument).

• updated seqdist help page (refseq argument and example).

• updated CITATION file (new ref and fixed a doi argument).

Version 1.8-10

Misc:

• Updated help pages: seqeconstraint, seqtree, distree2dot.

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

• One additional exported alias to a TraMineR internal function: TraMineRInternalSeqgbar.

Version 1.8-9

New function:

• seqpcfilter(): convenience function to define the coloring filter options to be passed as filter argument to seqpcplot().

Changes in existing functions:

• seqpm(): New sep argument to allow searching for string patterns when states are not labelled with single characters.

• seqpcplot():

  • New argument seed to control the jittering.

  • The filter argument can now simply be a scalar, in which case the minfreq filter is applied with this numeric value as threshold. See also the new function seqpcfilter().

  • New argument missing to control whether and how to display missing values.

Bug fixes:

• seqformat(): fixed error occurring when converting from STS to TSE with a tevent matrix containing empty strings (i.e. "")

• dissmfacw(): reported F values now obtained by dividing the within discrepancy in the denominator by (n-m), where n is the sample size and m the total number of predictors (contrasts for categorical factors). Up to here (n-m-1) was mistakenly used (Reported by Vicente Ponsoda.)

Misc:

• Two additional exported aliases to TraMineR internal functions: TraMineRInternalSeqeage and TraMineRInternalLegend.

Version 1.8-8

Bug fixes:

• seqecreate(): an error is thrown when events are not grouped by id in inputted TSE data. (Reported by Nicolas Jay). This requirement is now specified in seqecreate help page.

Misc:

• exported alias functions allowing other packages to access TraMineR internal functions (see ?TraMineRInternalLayout).

Version 1.8-7

Changes in existing functions:

• seqpcplot(): Suppressed unnecessary output argument. The seqpcplot object is automatically retrieved when using the assignment operator, e.g., p <- seqepcplot(...).

Bug fixes:

• seqformat(): When converting from STS to TSE, an error was raised if the tevent matrix had empty strings (i.e. ""). Now, this is considered as no event.

• seqpcplot(): Fixed error that appeared at the use of "_end" events.

• seqpcplot(): An error occurred when plotting a state sequence object (of class stslist) with a numeric cnames attribute.

Misc:

• Required packages RColorBrewer and boot now listed as "imports" in DESCRIPTION and using import in NAMESPACE.

Version 1.8-6

Changes in existing functions:

• seqformat(): new nr argument to specify the missing state symbol in SPS input.

• disstreeleaf(): new logical label argument to specify whether the leaf membership should be labelled with the classification rules.

Bug fixes:

• seqtreedisplay() and disstreedisplay(): GraphViz installer no longer adds GraphViz to the PATH environment variable. Therefore the two functions have been adapted to search for GraphViz. In case GraphViz would not be found, you can specify the GraphViz installation directory with the new gvpath argument.

• disstree() and seqtree(): removed the warning when R equals 0 or 1 (no permutations).

• seqformat(): fixed a problem with missing states when converting from SPS to STS (see Changes in function above.)

• seqpcplot(): fixed issues with which argument of plot.seqpcplot.

• seqpcplot(): fixed issues with arguments xlab and title.

• seqpcplot(): replaced a warning message by an error message at failures in finding plot positions for sequences. The error message advices to modify the (currently hidden) maxit argument. Additionally, automatically generated subtitles are now hidden when the argument title is used.

• as.character.seqelist(), print.seqelist(): fixed an issue with time display in event sequences which was in scientific notation for numbers with more than 2 digits. The function now uses the R format function and thus accounts for global formatting options such as options(digits=) and/or options(scipen=).

• seqtrate(): fixed error with sequence objects having only two columns.

New functionalities:

• disstree2dot() and disstree2dotp() gain a new argument called title.outer. If title.outer=TRUE, the title is printed in the outer margins.

Version 1.8-5

Bug fixes:

• seqefsub(): reported support did not properly account for weights.

• seqtreedisplay(): corrected a bug when using representative sequences and a dist object was passed to the dist.matrix argument (reported by Emanuela Struffolino).

• seqLLCS() and seqLLCP(): added a check on the argument. Both sequences should belong to state sequence objects with a common alphabet.

• seqpcplot(): small change in default lower ylim.

Help pages:

• help pages updated with author and keyword fields.

Version 1.8-4

Bug fixes:

• seqrep(), dissrep(), seqrplot(): wrong (unweighted) "na" values were returned; also quality measures "MD" (mean distance to representative) and "V" (discrepancy) were not computed properly when more than one representative selected (since version 1.8-2).

User invisible changes:

• Added an internal function to fix an issue with an internal C level function when called from other packages.

Version 1.8-3

Information pages:

• Updated online help pages.

• Updated list of references returned by citation("TraMineR").

New functionalities:

• seqpcplot(): parallel coordinate plot for sequence data.

Changes in existing functions:

• seqdss(): adding long state labels to returned sequence object.

• seqplot(): new option type = "pc".

• seqplot(), seqdplot(), seqiplot(), seqfplot(), seqmsplot(), seqrplot(): if density and/or angle are used to produce shading lines instead of solid colors, the legend is plotted using the same parameters and thus corresponds to the colors/shades used in the plot.

• seqplot(): if group argument is a factor, the plots are now ordered the same way as the factor levels.

• seqplot(), plot.stslist(): if sortv is a factor, the sequences are now sorted according to the order of the factor levels.

• seqmodst() and plot.stslist.modst(): changed name of attribute occurences of object returned by seqmodst to occurrences. Made resulting changes in plot.stslsit.modst.

Bug fixes:

• seqdef(): When selecting subsets of sequence objects using rownames instead of row indexes, the corresponding weights were not selected. Fixed by setting (row)names of weight vector as the sequence rownames. (Alexis Gabadinho)

Version 1.8-2

Vignettes:

• Slightly modified JSS article vol. 40(4) added as a vignette on state sequence analysis.

Misc:

• added ex2 data sets to test and illustrate the handling of weights, type help(ex2) for details.

New functionalities:

• New faster interface between C code and R.

• seqalign() and associated print and plot methods to see computation details about the alignment of two state sequences.

Changes in existing functions:

• seqtree(), disstree(): speed improvements.

• seqtm(): gives a warning when state names or state labels contain a comma.

• seqdef(): changed the display of alphabet, state labels and long labels when creating a state sequence object.

• seqistatd() and seqmeant(): added prop argument to calculate proportions of time spent in each state instead of absolute values.

• seqplot() and aliases: group now also accepts as argument a list of variables/vectors and produces a plot for each combination of the values of the variables in the list.

• dissrep(), seqrep(), seqrplot(): now accounts for weights when present.

• seqtrate(), seqsubm(): added two arguments:

  • lag: compute transition rates from t to t+lag, set to one by default.

  • with.missing: If TRUE, compute transition rates to and from missing values.

• seqtreedisplay(): now overwrites previous file if filename is not NULL. Tree quality measures displayed with R code.

• checktriangleineq(): internal function to check triangle inequality is now in C, which allows checking much bigger distance matrices.

• seqIplot(), seqiplot() and seqplot() with type "I" or "i": the sortv argument now also accepts a sorting method, namely one of "from.start" or "from.end". See the help page ?plot.stslist for explanation.

• seqeconstraint() and other seqe... functions for event sequences: support of subsequences can now be determined by means of any of Joshi's 5 counting methods (see the ref manual page). The method should be specified with seqeconstraint().

• seqeapplaysub(): when method=NULL is specified (now the default), the count method assigned to the event sequence object is used. With method="count" CDIST_O (number of distinct occurrences) is used as previously.

• seqrep(): attribute Index of the returned object is now a vector instead of an object of class dissrep.

Bug fixes:

• seqtreedisplay(): was changing current directory when an error occurred in the plotting function.

• dissrep(), seqrep(): error when nrep cannot be reached (reported by M. Studer)

• seqefsub(): when using strsubseq argument, countMethod of seqeconstraint was not taken into account (Reported by Reto Bürgin).

• seqeconstraint(): added consistency checks to avoid misuses (Reported by Reto Bürgin).

• print.seqelist() and as.character.seqelist(): generated segfault when converting long event sequences to character (Reported by Pierre Molinier).

• seqsubm(): Very small rounding errors (1e-16) were sometimes leading to non symmetric substitution cost matrix (Reported by Alexandre Pollien).

Version 1.8-1

Misc:

• updated references in the citation file and manual pages to point to the newly published article in the Journal of Statistical Software

• other references update in the manual pages.

Version 1.8

New functionalities:

• seqtreedisplay(): drawing a sequence regression tree.

• seqtree(): creating a sequence regression tree from a dissimilarity matrix.

• seqrecode(): recoding state sequences objects (i.e., merging states).

• weights are now supported by all dissimilarity analysis functions.

• weights can be assigned to event sequence objects and are supported by all related functions.

• seqdef(): xtstep option added to set step between displayed tick-marks and labels on the x-axis of state sequence plots.

• seqplot(): xtstep option added to state sequence plots.

Bug fixes:

• seqformat(): fixed problems with fillblanks argument when converting from SPELL to STS.

• seqdist() and seqdistmc(): method="HAM" did not account for the provided substitution cost matrix; it used 1 for all substitution costs (Reported by Florian Hertel).

• seqdist(): fixed a (possible) memory leak.

• seqdss(), seqdur(): fixed bad handling of missing values in several cases:

  • sequences finishing with missing values,

  • sequences made of only one distinct state and missing values.

• seqiplot(), seqIplot(), seqfplot(): changed the automatic setting of the x-axis length, to ensure identical lengths of the x-axis when the maximal sequence length differs between groups (reported by M. Studer).

• seqplot() and aliases: fixed error with xaxis argument.

• seqtransn(): the returned normalized number of transitions for sequences of length 1 was NaN (value of transn.norm=0/seqlength-1). Now set to 0.

• seqici(): returns now correctly 0 instead of NaN for sequences of length 1.

Changes in existing functions:

• seqient(): new option base for choosing the base of the logarithm used to compute the entropy.

• seqdist(): enhanced check of substitution cost matrix.

  • The function can now be cleanly interrupted by the user.

  • Timing information now uses the processor time (instead of the elapsed time).

• seqformat() when converting from "SPELL":

  • new error message when a start time is lower than 1 and/or an end time is smaller than the start time.

  • warning message when start time of episode 1 is missing (sequence creation is skipped)

  • warning message when start/end time of an episode is missing (episode is skipped and filled with NA's)

• disstree() and dissassoc() have been entirely redesigned; objects created with the old function are no longer supported.

• seqdss() and seqdur(): the number of columns of the returned object is now set to the maximum DSS length rather than to the length of the original state sequence object.

Misc:

• ex1 example data set: contains now an additional sequence 's7' with only missing values.

Version 1.6-2

Bug fixes:

• seqdef(): now checks whether all states encountered in the input data are present in an optional user provided alphabet (state argument)

• seqefsub(): The support of a subsequence with a total support of 1 was set to 0 (hence, this only applies if the minimum support is 1.) This is now corrected (Reported by Anna Hera).

• Corrected compilation problems under SOLARIS (Reported by Prof Brian Ripley).

• seqformat(): when converting from SPELL to STS, the fillblank argument was not used.

Version 1.6-1

New functionalities:

• Added a startup message when loading the TraMineR library.

Changes in existing functions:

• seqtab() and seqfplot(): tlim argument now allows to return any selected frequent sequences, in the same way as the tlim argument used in plot.stslist() and seqiplot() (Requested by G. Ritschard). For example, tlim=3:6 returns the third, fourth, fifth and sixth most frequent sequences in the set. Default for tlim is now 1:10 instead of 10.

• seqsubsn(): added detection of missing state in the sequences and computation of number of subsequences by adding missing state to the alphabet.

• seqST(): added detection of missing state in the sequences and computation of turbulence by adding missing state to the alphabet (Requested by G. Ritschard).

• seqrplot now accepts ‘half’ matrices (dist objects) as produced by seqdist with the full.matrix=FALSE option (Requested by L. Lesnard).

• seqiplot() and plot.stslist(): new ytlab option allowing to display sequence labels on the Y-axis in sequence index plots (if set to "id", the sequence ids are displayed). An additional ylas option sets the orientation of the labels (Requested by Andrew ?? and P. Jeuniaux).

• seqsubm():

  • When method="TRATE", the substitution costs are now based on the value of cval: SC(i,j) = cval -P(i,j) - P(j,i) where P(i,j) is the transition rate from state i to j.

  • added a new transition argument to use only transition from "previous" or "next" state instead of the default "both" when time.varying = TRUE.

  • Now, by default cval equals 2, unless transition is set to both and time.varying is TRUE in which case cval equals 4.

• plot.stslist.meant(), seqmtplot(), plot.stslist.freq(), seqfplot(), plot.stslist.modst(), seqmsplot(): added display of weighted n instead of n in axis label if weighted=TRUE.

• seqdplot(): disabled plot of a legend for missing state if with.missing=FALSE (Requested by M. Studer and G. Ritschard).

• seqplot(), plot.stslist(), plot.stslist.statd(), plot.stslist.modst(), plot.stslist.freq(), plot.stslist.meant(): when weighted=TRUE, weighted n displayed in the axis label rounded to 2 digits (Requested by M. Studer).

Bug fixes:

• plot.stslist.modst(), seqmsplot(): fixed bad display of missing states if with.missing=TRUE.

• seqmeant(): added color for missing state to color palette when using with.missing=TRUE.

• dissrep(), seqrep(), seqrplot(): fixed bad coverage statistics when tsim set to other than default value of 0.10 (Reported by G. Ritschard).

• seqdist(): Bad handling of missing values in DHD distance (wrong default substitution costs with missing values, set to one instead of four).

• seqdist(): Fixed an error in seqdist when using refseq with missing values (Reported by an anonymous user).

Version 1.6

New functionalities:

• seqIplot() and seqplot(..., type="I"): sequence index plot displaying all sequences with no space (space=0) and no border (border=NA) by default.

• stlab(): retrieving or setting the long state labels of a sequence object.

• seqici(): computes the complexity index, a composite measure of sequence complexity.

• seqtransn(): computes the number of transitions in a sequence.

Bug fixes:

• seqrplot() and plot.stslist.rep(): missing states are now correctly plotted (reported by G. Ritschard).

• dissrep() (called by seqrplot() and plot.stslist.rep()): when using coverage threshold, does no longer select one too many representatives.

• seqdplot() / plot.stslist.statd(): fixed bad coloring of missing states (reported by M. Studer).

• seqstatd() and print.stslist.statd(): fixed error when printing seqstatd output and length of the longest short state label was >2. (reported by G. Ritschard).

• seqdss(): (with default with.missing=FALSE value) DSS with identical successive states resulted when there were missing values between two identical states. For example, before: DSS of "A-A-*-A-*-A" was "A-A-A" and now "A".

Changes in existing functions:

• summary.stslist(): added information in the output of the summary method for state sequence objects.

• seqdist(), seqdistmc(), seqdss(), seqdur(), seqient(), seqistatd(), seqmpos(), seqnum(), seqsubm(): with.miss argument replaced by with.missing (obsolete with.miss argument still works for backward compatibility)

• seqmeant(): added with.missing argument to account for missing states.

• seqdef():

  • new warning when one or several sequences contain only missing values.

  • when no weights are provided:

    • weights attribute of the returned sequence object is now set to NULL instead to a vector of 1's;

    • the "[>] sum of weights" message is suppressed;

  • new Version attribute with the number of the TraMineR version used for creating the sequence object;

  • message "[>] missing values in input file" changed to "[>] found missing values ('...') in sequence data" and displayed only if missing values are found in the input data.

• seqIplot(), seqiplot(), seqplot(..., type="I"), seqplot(..., type="i") and plot.stslist(): new weighted argument. If set as TRUE sequence bar widths are set proportional to weights.

• seqiplot() and plot.stslist(): when the sequence object contains less than 10 sequences and tlim=NULL, only the actual sequences are plotted without additional ‘void sequences’.

• seqmodst(): added weighted and with.missing arguments.

• seqtab() and seqstatd(): attribute nbseq of the returned object is now the sum of weights (if weighted=TRUE and the sequence object has weights) instead of the number of sequences.

• seqfplot() / plot.stslist.freq() and seqdplot() / plot.stslist.statd(): when weights are used, i.e. when the weighted=TRUE argument is passed and the sequence object has weights,

  • the ‘n=...’ in the y axis legend now gives the sum of weights instead of the number of sequences;

  • ‘weighted’ is specified in the y axis legend;

• seqfplot() and plot.stslist.freq(): more precise positioning of the 0 of the y axis;

• seqrplot() and plot.stslist.rep():

  • new stats option. If set to FALSE, statistics are not plotted;

  • label of the yaxis changed.

• dissrep(): name of the main argument changed from dist.matrix to diss as in other diss... functions.

Version 1.4-1

Bug fixes:

• seqecreate(): Problems with handling simultaneous events when creating event sequences with data not previously sorted on id, timestamp and event.

• seqrep() with "density" criterion: neighborhood diameter is now correctly set to trep*dmax instead of trep.

New functionalities:

• dissrep(): extracts a set of representative objects using a dissimilarity matrix. This function is used by seqrep.

Changes in existing functions:

• seqrep():

  • much faster extraction of the representative set;

  • default criterion is now "density" instead of "frequency";

  • trep now sets a coverage threshold for the representative set rather than a size threshold for the candidate list;

  • in the output object, name of the attribute containing statistics for the representative set changed from Quality to Statistics and that of the attribute containing the overall quality measure changed from rindex to Quality.

• seqplot(): now checks that the length of the vector given as group argument matches the number of sequences.

• plot.stslist(): now checks that the length of the vector given as sortv argument matches the number of sequences.

• seqformat(): dramatic speed improvement in conversion from SPELL data.

Version 1.4

New functionalities:

• TraMineR.checkupdates(): check for TraMineR updates.

• seqdistmc(): computes multichannel distances.

• seqmeant(): computes mean duration in each state.

• seqmodst(): returns the sequence of modal states.

• seqmsplot(): for plotting the sequence of modal states. This function is a shortcut for seqplot with type="ms", see below.

• seqrep(): extracts a set of representative sequences.

• seqrplot(): for producing representative sequence plots. This function is a shortcut for seqplot with type="r", see below.

• seqHtplot(): for producing Entropy Index plots. This function is a shortcut for seqplot with type="Ht", see below.

• seqlogp(): Computing logarithm of sequence probabilities.

• seqdef(): new weights= option for providing a vector of weights.

• seqstatd(), seqtrate(), seqlogp() and seqtab(): new option weighted=TRUE for using the weights when computing the statistics.

• seqtrate() and seqsubm(): new time.varying argument for computing position dependant transition rates or costs.

• seqdist(): two additional methods are now available for computing distances, namely "HAM" (Hamming distance) and "DHD" (Dynamic Hamming Distance).

• Output produced by seqstatd(), seqtab(), seqmeant(), seqmodst(), and seqrep() can now be plotted with their plot() dedicated methods (see new classes and methods below).

Important changes:

• seqplot(): is now the generic function for plotting state sequence objects with type argument. Available types are "d" for state distribution plots, "f" for sequence frequency plots, "Ht" for entropy index plots, "i" for sequence index plots, "ms" for modal state sequence plots, "mt" for meant time plots, "r" for representative plots. This function replaces the previous generic plot.stslist() function.

• plot.stslist(): now produces only a sequence index plot (see new classes and methods below).

Changes in existing functions:

• seqfplot():

  • new ⁠yaxis⁠ option: with yaxis="cum" (default) cumulated percentages are displayed, while with yaxis="pct" individual sequence percentages are shown.

  • pbarw=TRUE is now the default for the pbarw argument.

• seqtab(): the format argument that specifies the format of the sequences displayed as rownames is now set by default to the short SPS format, e.g. TR/9-EM/63.

• seqiplot(): sequence indexes are now displayed by default on the y axis. This can be disabled with yaxis=FALSE.

Fixed minor bugs in seqformat():

• changes concern mainly the from="SPELL" and from="SPS" options.

New classes and methods:

• new class stslist.statd for objects produced by the seqstatd() function and methods for printing and plotting such objects.

• new class stslist.freq for objects produced by seqtab() function and methods for printing and plotting such objects.

• new class stslist.meant for objects produced by seqmeant() function and methods for printing and plotting such objects.

• new class stslist.modst for objects produced by seqmodst() function and methods for printing and plotting such objects.

Version 1.2-1

Changes in function arguments:

• seqdef(): new id argument for setting the rownames of the sequence object.

• disscenter(): new medoid.index argument to get the indexes of all medoids (rather than only the first one).

Minor bugs fixed:

• Plotting missing states with seqiplot() and seqfplot() functions.

• Sum of transition rates with sequences of different lengths not equal to 1.

Version 1.2

Changes regarding plotting functions:

• New generic function plot.stlist() with option type= for plotting state sequence objects of class ststlist created by the seqdef() function. Old functions seqdplot(), seqfplot(), seqiplot(), seqmtplot() work as in the previous version but by calling plot.stslist with the appropriate type= option (types are 'd', 'f', 'i' and 'mt'). However, the order of the functions' arguments may have changed and this may cause problems if the names of the arguments were not explicitly specified in your scripts (which is inadvisable anyway).

Changes in the dissimilarity and discrepancy analysis diss module:

• dissreg() is renamed to dissmfac() for multi-factor dissimilarity analysis.

• disstree(): great speed and memory improvements.

Speed and memory improvements:

• seqformat(): conversion to TSE format is now much faster.

• seqdur()

• seqST()

Changes in the computation of distances between sequences:

• seqdist() now checks if substitution costs respect the triangle inequality. When this is the case it ensures that the resulting dissimilarity matrix also respects the triangle inequality.

• New options for selecting the distance normalization method.

• New reversed LCP, i.e. longest common suffix method. (method="RLCP")

Various changes:

• CITATION file added.

• seqST() caused an error when run with more than 12 states: bug fixed.

• Fixed other minor bugs.

Version 1.1

New example data

• mvad example data set added

Name changes of functions

• seqLLCP() instead of old seqLCP()

• seqLLCS() instead of old seqLCS()

New module

New diss module for analysing a dissimilarity matrix (such as the one returned by seqdist)

• dissassoc(): Computes association with a factor;

• dissreg(): Regression analysis of a dissimilarity matrix;

• disstree(): Tree analysis of a dissimilarity matrix;

• dissvar(): Computes a pseudo-variance from a dissimilarity matrix.

Changes in graphic functions

Changes in the graphics functions (seqiplot, seqfplot, seqdplot, ...):

• New group option allowing to draw several plots for the levels of a factor within a single command;

• TraMineR now uses layout for controlling the position of the plots and the legend in the graphic area. This is not compatible with par(mfrow=...). To use the standard par(mfrow=...) method, one must set the use.layout=FALSE option in the plot functions;

• seqmtplot(): new function that plots the mean time spent in each state;

• Option withborder=FALSE is now obsolete and replaced by the standard border=NA option.

Changes in event sequence (seqe) module:

• New plot for exhibiting discriminant subsequences (seqecmpgroup).

• Overall syntax have been reviewed and is now much simpler.

• seqefsub now allows to search for user specified subsequences (seqefsub).

• Event subsequence lists now have specific plot and print method (seqefsub, seqecmpgroup)

• seqecreate now accepts state sequences and performs automatic conversion (seqecreate)

• Time constraints are now implemented separately and are stored with the results (seqeconstraint)

Changes in the seqformat() function:

• New options for importing SPELL formatted data.

• The STS internal and the output in STS, SPS or DSS formats are now by default in extended format (a matrix with one state per column) instead of compressed format (a character string). Use the compressed=TRUE option to get an output in the compressed format (sequences as character strings).

• "SPS1" and "SPS2" formats are now replaced by the generic "SPS" format with options SPS.in and SPS.out for defining the separator and surrounding characters used for specifying the state/duration couples.

Other new functions:

• seqgen(): generates a random sequence.