| NEWS | R Documentation |
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
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.
plot.stslist() possible conflict between x names and arguments of order.
plot.stslist.rep() bad position of y-axis when !is.na(ylab)
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.
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.
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.
Suppressed dependence on cNORM because of license
incompatibility. (dissdomassoc uses now a proper
internal function in place of cNORM:::weighted.rank).
summary.ddomassoc() summary method that organizes outcome of dissdomassoc in table form.
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.
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.
Dependence on boot and RColorBrewer replaced by importFrom of functions boot and brewer.pal.
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.
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'.
seqlogp() error for state sequences with missing values.
New imports from psych and cNORM (for dissdomassoc)
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.
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.
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.
TraMineRextras added to the 'Suggests' list (to avoid NOTE on undeclared package in Rd xrefs.)
seqdef(): switched back from [grDevices] hcl.colors to [colorspace] qualitative_hcl to avoid dependence on R >=3.6 necessary for hcl.colors.
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.)
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.
Deleted unused OMVI2distance h and cpp files.
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.
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).
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.
print.stslist.freq() wrongly used width argument.
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)
seqlength(), seqST(), and seqsubsn() gain a with.missing argument to control how missing values should be treated.
seqST() normalization did not account for non-void missing values when present.
Fixed issue with \traminer in vignette.
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.
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.
eventseq.cpp: rchk message 'calling allocating function Rf_asChar with argument allocated using TMRNumberFormat'.
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.
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).
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.
Vignette: Error in formula for complexity index. Also, now DOI instead of link to JSS article.
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.
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".
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.
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.
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.
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.
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.
Documentation of seqformat() and seqecreate(): added examples of the handling of missings in conversion into TSE and SPELL format.
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.
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.
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)
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.
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.
Replaced default deprecated values of norm in
seqdistmc() and seqtree().
Fixed issues with examples in documentation page of
seqtree().
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().
Fixed an issue with an example in the documentation page of seqpcplot().
Fixed equation typing errors in seqrep() documentation.
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.
Changed character encoding from latin1 (ISO-8859-1) to UTF-8.
Normalized line endings: LF.
Removed the following unused functions: vidx(), seqmatsaltt(), seqmathenikoff().
Removed the functions deprecated in TraMineR 1.x: seqesetlength(), dissreg(), dissmfac().
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.
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.
Registration of native routines for R 3.4.x. See https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html.
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.
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.
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
bfspell: a small data set with 20 sequences in SPELL format.
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)
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.
updated disstreedisplay help page (tree argument).
updated seqdist help page (refseq argument and example).
updated CITATION file (new ref and fixed a doi argument).
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.
seqpcfilter(): convenience function to define the coloring
filter options to be passed as filter argument to seqpcplot().
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.
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.)
Two additional exported aliases to TraMineR internal functions:
TraMineRInternalSeqeage and TraMineRInternalLegend.
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.
exported alias functions allowing other packages to access TraMineR
internal functions (see ?TraMineRInternalLayout).
seqpcplot(): Suppressed unnecessary output argument. The
seqpcplot object is automatically retrieved when using the
assignment operator, e.g., p <- seqepcplot(...).
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.
Required packages RColorBrewer and boot now listed as "imports"
in DESCRIPTION and using import in NAMESPACE.
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.
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.
disstree2dot() and disstree2dotp() gain a new argument called title.outer.
If title.outer=TRUE, the title is printed in the outer margins.
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 updated with author and keyword fields.
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).
Added an internal function to fix an issue with an internal C level function when called from other packages.
Updated online help pages.
Updated list of references returned by citation("TraMineR").
seqpcplot(): parallel coordinate plot for sequence data.
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.
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)
Slightly modified JSS article vol. 40(4) added as a vignette on state sequence analysis.
added ex2 data sets to test and illustrate the handling of weights,
type help(ex2) for details.
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.
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.
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).
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.
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.
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.
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.
ex1 example data set: contains now an additional sequence 's7'
with only missing values.
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.
Added a startup message when loading the TraMineR library.
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).
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).
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.
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".
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.
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.
dissrep(): extracts a set of representative objects using a
dissimilarity matrix. This function is used by seqrep.
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.
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).
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).
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.
changes concern mainly the from="SPELL" and
from="SPS" options.
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.
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).
Plotting missing states with seqiplot() and seqfplot() functions.
Sum of transition rates with sequences of different lengths not equal to 1.
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).
dissreg() is renamed to dissmfac() for multi-factor dissimilarity analysis.
disstree(): great speed and memory improvements.
seqformat(): conversion to TSE format is now much faster.
seqdur()
seqST()
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")
CITATION file added.
seqST() caused an error when run with more than 12 states: bug fixed.
Fixed other minor bugs.
mvad example data set added
seqLLCP() instead of old seqLCP()
seqLLCS() instead of old seqLCS()
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 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.
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)
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.
seqgen(): generates a random sequence.