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NEWS
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## =========
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.
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(), seqplot(,type="dH"), seqplotMD(,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
## =========
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 and
of length 1 when 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)
## =========
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 existing 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 sometimes
not find the GraphViz path.
- disstreedisplay() and seqtreedisplay() uselessly printed
TRUE when filename was not NULL.
## =========
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 existing 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: ylab can
be a vector of labels by group level.
- seqplot() and all the seqxxplot family support
arguments of legend among the ... list.
- "[.stslist" raises a warning when row subsetting
condition has \code{NA}s.
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.
## =========
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 behaves
as expected, i.e., removes all titles.
- seqplot()} and all the \code{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 \code{sprintf}
in eventdictionary.cpp
Misc.:
- replaced seqdistmc with seqMD in examples of dissdomassoc.
## =========
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 first spell in given state
Changes in existing functions
- seqplot() new value \code{"rf"} (RF plots) for argument type.
- seqtab(): result gains an attribute idxf with indexes
of first found most 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() 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.
## =========
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 function:
- 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).
## =========
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 the
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
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 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 argument can now be "auto" (new default)
to automatically set indel values. In addition, state
dependent indels are now supported.
- seqdistmc()} \code{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.
## =========
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 indicator 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 index order 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)
## =========
Version 2.2-1 [2020-10-24]
New functions:
- seqivardur() computes the variance of spell durations
for each individual sequence. Either the variance of observed
non null 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 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 'Suggests' list (to avoid NOTE on
undeclared package in Rd xrefs.)
## =========
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.
## =========
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 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, OMslen,
and OMstran (previously only by OM).
- 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 cpp and h files
## =========
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.
## =========
Version 2.0-14 [2020-01-13]
Bug Fixes:
- print.stslist.freq() wrongly used 'width' argument
## =========
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.
## =========
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.
## =========
Version 2.0-11.1 [2019-03-22]
Bug Fixes:
- eventseq.cpp: rchk message 'calling allocating function
Rf_asChar with argument allocated using TMRNumberFormat'.
## =========
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).
## =========
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 \code{fancyvrb.sty}.
Misc:
- Vignette: Error in formula for complexity index.
Also, now DOI instead of link to JSS article.
## =========
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 enforces 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.
- 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".
- 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".
## =========
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.
## =========
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 \code{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.
## =========
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" (previously in 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 meaning of '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 \code{tmrWeightedInertiaDist()} made public as the R
function TraMineRInternalWeightedInertiaDist(). (Used by package Weightedcluster).
## =========
Version 2.0-5 [2017-05-13] (Stable version)
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') containing only one sequence.
- seqdist(): now accepts a reference sequence object ('refseq') containing
missing values while the main sequence object ('seqdata') doesn't.
Misc:
- Replaced default deprecated values of 'norm' in
seqdistmc() and seqtree().
- Fixed issues with examples in documentation page of
seqtree().
## =========
Version 2.0-4 [2017-04-13] (Unreleased version)
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 now an alias for seqcost(...)$sm.
## =========
Version 1.9-14 [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:
- pcfilter(): 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 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.