NEWS file of the TraMineRextras package

Changes in version 0.7.8 [2024-08-17]

New function

• dissCompare() comparison of two groups of data represented by a pairwise dissimilarity matrix.

Bug fixes

• seqCompare() caused an error when only one group occurs in one of the sets. Now returns NA for such sets.

• internal seq.comp() renamed as seqxcomp().

• missing package anchors for Rd link targets.

Changes in version 0.6.7 [2024-01-08]

Changes in existing functions

• 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

• seqimplic.Rd: lack of description for argument ylim.

• seqpolyads(): time reported when core > 1 was not reliable

• convert.g(): error when path=NULL.

• convert.g() adapted to changes in ImageMagick.

Changes in version 0.6.6 [2023-03-07]

New function

• 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

• seqsplot(), argument axes is deprecated and replaced by xaxis. Argument yaxis can now also be one of "all" or "left".

• seqsplot(), ylab can be a vector of labels by group level.

• seqsplot() supports arguments of legend among the ... list.

• 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.

• seqsplot(), seqplot.tentrop(), seqplot.tentrop.m(), seqedplot(), plot.dynin(), and plot.stslist.surv(): default value of main is "auto" and NULL suppresses the titles as expected.

• seplot.entrop.m() now in namespace.

• seqedplot() argument names and behavior made conformable with those of TraMineR:::seqplot

Changes in version 0.6.5 [2022-10-09]

Changes in existing functions

• seqplot.rf() argument plus.one renamed grp.meth

Bug fixes

• seqplot.rf() which.plot = "diss.to.med" did not work.

• seqplot.rf() issue with unwanted ":" in plot title.

• sorti() possible conflict between column names of seqdata and arguments passed to order.

• issue with non UTF-8 commented line in TraMineRextras.Rd

Misc.

• Replaced permute(.) with sample(.) in seqCompare to remove dependence on gtools that has become orphaned.

Changes in version 0.6.4 [2022-06-13]

Changes in existing functions

• 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

• seqindic.dyn() checked whether fstat is a function by comparing class with a string. Now uses inherits.

• Issue with example in seqtabstocc.Rd.

• Issue with non literal item name in seqsamm.Rd.

Changes in version 0.6.3 [2022-01-19]

New functions

• seqcta() organizes data for CTA analysis (Studer et al., ALCR 2018).

• seqsamm(), seqsammseq() and seqsammeha organize and retrieve data for SAMM analysis (Studer et al., Soc. Meth. 2018).

• plot.SAMM() plot of SAMM object returned by seqsamm.

• seqsha() organizes data for SHA analysis (Rossignon et al., in Ritschard & Studer, 2018).

Misc.

• Updated description and some Rd files.

Changes in version 0.6.2 [2021-06-23]

Changes in existing functions

• seqindic.dyn() gains two arguments: wstep to control the spacing between successive windows and endmiss.as.void to control whether sequences end at first ending missing value or at the first void.

• plot.dynin() (plot method for objects produced by seqindic.dyn) can now plot series of summary values that end with missing values.

• plot.dynin() conf can now be logical or the confidence probability, TRUE being equivalent to 0.95.

• TSE_to_STS() now checks that tmin > 0.

• seqplot.rf() returns (invisibly) group memberships.

Bug fixes

• plot.dynin() issue with check of fstat.

Changes in version 0.6.1 [2021-01-20]

New functions

• seqindic.dyn() dynamic individual indicator values.

• plot.dynin() plot method for dynin objects produced by seqindic.dyn.

• seqpolyads() degree of similarities between polyadic members (contributed by Tim Liao)

• polyads example data set.

Changes in existing functions

• seqplot.tentrop() default color now set using qualitative_hcl from colorspace with the 'Dark 3' palette.

Changes in version 0.6.0 [2020-04-24]

New functions

• seqCompare() BIC and Likelihood ratio test (LRT) for comparing two sets of sequences.

• seqLRT() LRT for comparing two sets of sequences.

• seqBIC() BIC for comparing sequence data.

Changes in existing functions

• seqgranularity() two new methods "first.valid" and "last.valid" for sequences with missing values.

• seqplot.rf() gains a new argument which.plot.

Bug fixes

• seqgranularity() did not return a proper stslist object when method="mostfreq".

Changes in version 0.4.7 [2020-03-02]

Bug fixes

• seqedplot(): issue with color selection when only one event.

• seqedplot(): Now calls plot.survfit with by default conf.int=FALSE instead of "none" (advised by Terry Therneau).

Misc.

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

Changes in version 0.4.6 [2019-09-06]

Changes in existing functions

• seqedplot(): argument title is deprecated, use main instead.

• seqedplot(): when type = 'survival', now supports the conf.int argument of plot.survfit to control the display of confidence intervals.

Bug fixes

• 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 version 0.4.5 [2019-05-06]

Changes in existing functions

• seqprecarity() and seqprecstart() gain an argument with.missing.

• seqprecarity(): there is now a print method for the generated seqprec object that prevents the printing of all its attributes.

• 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.

• seqtabstocc() gains an argument with.missing.

Bug fixes

• seqprecorr(): method='TRATE' now works as expected.

• seqprecarity(), seqprecorr(), and seqprecstart(): errors due to bad handling of missing states.

• seqedplot() called plot.survfit with a firstx argument that has been suppressed (non documented in survival news); now uses xlim instead.

Changes in version 0.4.4 [2018-12-14]

Changes in existing functions

• plot.stslist.surv(): new xlab argument.

• seqprecarity(), seqprecorr(), and seqprecstart(): Important code cleaning.

• 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

• 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.

• seqsplot(): color synchronization failed when one of the states selected was unobserved in one of the groups.

• seqprecorr(): identification of non-comparable states did not work as expected.

• seqprecstart(): did not work as expected when equiv class included incomparable states.

Changes in version 0.4.3 [2018-08-22]

Changes in existing functions

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

• 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.

• seqrep.grp(): an error is raised when one of the groups has less than two cases.

Bug fixes

• Function seqgen.missing() the number of left and right elements to be turned into missings were inverted.

Misc

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

Changes in version 0.4.2 [2018-02-01]

New functions

• seqprecarity(): computes the sequence precarity index from a provided partial state order. The index is a corrected complexity index. See documentation page.

• seqprecorr(): determines the correction factor used by seqprecarity().

• seqprecstart(): determines the starting precarity level of the sequence from the partial state order.

• seqsurv(): fits survival curves for states in state sequences. There is a plot method for objects returned by seqsurv().

• seqsplot(): specific version of the TraMineR seqplot() function to plotting survival curves of states in sequences.

Changes in existing functions

• seqrep.grp()) renamed argument names for consistency with TraMineR.

• 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

• seqtabstocc()): label synchronization issues.

Misc

• Uses function TraMineR.check.depr.args() introduced in TraMineR v 2.0-8. So, depends now on version >= 2.0-8.

Changes in version 0.4.1 [2017-08-16]

Changes in existing functions

• STS_to_SPELL(): Deleted. Converting to the "SPELL" format is now a feature of seqformat() in TraMineR 2.0-6+.

• seqrep.grp(): Added argument with.missing to allow computing the default distances (when diss = NULL) for sequences with missing values.

Misc

• Replaced deprecated argument names in example of seqrep.grp().

• Now imports from RColorBrewer, survival and cluster instead of depending on those packages.

• Suppressed unused import from combinat.

• init.c file.

Changes in version 0.4.0 [2017-05-13]

Note

• TraMineRextras has been adapted to and requires now TraMineR 2.0-5.

Bug Fixes

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

Changes in existing functions

• seqplot.rf(), seqplot.tentrop(), seqrep.grp(), dissvar.grp(), plot.seqimplic(): adjusted argument names (main, with.legend, legend.pos, diss, ...) to conform to the TraMineR 2 naming convention.

Misc

• 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+.

• seqeformat(), seqentrans(), seqerulesdisc(): Renamed 'seqe' as 'eseq' in internal code to conform to TraMineR 2.0-5+.

• Adjusted examples in help files (sortv, seqtabstocc, seqrep.grp, seqplot.tentrop, seqplot.fr, seqimplic, seqgranularity, seqgen.missing, seqedplot, seqentrans) to conform to TraMineR 2.0-5+.

Changes in version 0.2.6 [2017-03-01]

Misc

• Function ctplot() suppressed. It is superseded by the function seqpcplot() of the TraMineR package.

• C++ routines are now registered.

Changes in version 0.2.5 [2016-11-10]

New functions

• 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 version 0.2.4 [2015-07-23]

New functions

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

Misc

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

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

Changes in version 0.2.3 [2015-01-27]

New functions

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

Changes in existing functions

• seqgranularity(): new method "mostfreq"

• 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 version 0.2.2 [2013-10-30]

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

Changes in version 0.2.1 [2013-03-15]

General

• NEWS is now in Rd format into inst/NEWS.Rd

Bug Fixes

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

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

Changes in version 0.2 [2012-12-06]

General

• First release on CRAN

Changes in existing functions

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

• 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.

• dissvar.grp() and seqrep.grp() now also accept distance objects as mdis argument.

• group.p has now a weights argument.

Bug Fixes

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

• fixed build warning generated by calls of foreign functions.