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
issue with non UTF-8 commented line in TraMineRextras.Rd
seqCompare to remove dependence on gtools that has become orphaned.
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.
seqindic.dyn() checked whether
fstat is a function by comparing
class with a string. Now uses
Issue with example in seqtabstocc.Rd.
Issue with non literal item name in seqsamm.Rd.
seqcta() organizes data for CTA analysis (Studer et al., ALCR 2018).
seqsammeha organize and retrieve data for SAMM analysis (Studer et al., Soc. Meth. 2018).
plot.SAMM() plot of
SAMM object returned by
seqsha() organizes data for SHA analysis (Rossignon et al., in Ritschard & Studer, 2018).
Updated description and some Rd files.
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.
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.
plot.dynin() issue with check of
seqindic.dyn() dynamic individual indicator values.
plot.dynin() plot method for
dynin objects produced
seqpolyads() degree of similarities between polyadic members
(contributed by Tim Liao)
polyads example data set.
seqplot.tentrop() default color now set using
colorspace with the
'Dark 3' palette.
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.
seqgranularity() two new methods
"last.valid" for sequences with missing values.
seqplot.rf() gains a new argument
seqgranularity() did not return a proper
stslist object when
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).
seqprecarity(), seqprecorr(), seqprecstart() deleted. These functions are now in TraMineR since v 2.0-13.
title is deprecated, use
type = 'survival', now supports the
conf.int argument of
plot.survfit to control the display of confidence intervals.
seqedplot(): An issue with the joint use of the
xlim arguments when calling
plot.survfit raised a warning since
seqprecstart() gain an argument
seqprecarity(): there is now a print method for the generated
seqprec object that prevents the printing of all its attributes.
border.effect argument. To avoid a border
effect, when method is
computed transition frequencies or probabilities
p are adjusted
p - p/
border.effect when any
p > 1 - .1/
seqtabstocc() gains an argument
method='TRATE' now works as expected.
seqprecstart(): errors due to bad handling of missing states.
plot.survfit with a
that has been suppressed (non documented in survival news);
seqprecorr(): New argument
tr.type to select the type of transition weights.
Two additional methods have been implemented, namely
(for rank-based transition weights) and
non-weighted transitions. Also new argument
stprec to allow
specifying rank values for
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
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.
seqsplot() now supports the
ncol argument for controlling the number of columns in the color legend.
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.
seqgen.missing() the number of left and right
elements to be turned into missings were inverted.
seqeordplot() suppressed. It is superseded by the
seqpcplot() of the TraMineR package.
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
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
seqsplot(): specific version of the TraMineR
to plotting survival curves of states in sequences.
seqrep.grp()) renamed argument names for consistency with TraMineR.
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.
seqtabstocc()): label synchronization issues.
TraMineR.check.depr.args() introduced in TraMineR v 2.0-8. So, depends now on version >= 2.0-8.
STS_to_SPELL(): Deleted. Converting to the
"SPELL" format is now a feature
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.
Replaced deprecated argument names in example of
Now imports from RColorBrewer, survival and cluster instead of depending on those packages.
Suppressed unused import from combinat.
TraMineRextras has been adapted to and requires now TraMineR 2.0-5.
TSE_to_STS(): The two last sequences were not converted and unexpected outcome in case of a single sequence.
plot.seqimplic(): adjusted argument names (main, with.legend, legend.pos, diss, ...) to conform to the TraMineR 2 naming convention.
with.missing=TRUE in a help example as
biofam.seq doesn't contain missing values and to conform to TraMineR 2.0-5+.
seqerulesdisc(): Renamed '
seqe' as '
eseq' in internal code to conform to TraMineR 2.0-5+.
Adjusted examples in help files (
seqentrans) to conform to TraMineR 2.0-5+.
ctplot() suppressed. It is superseded by the
seqpcplot() of the TraMineR package.
C++ routines are now registered.
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.
seqplot.rf(): Implements the Relative Frequency Sequence Plots
introduced in Fasang and Liao (2014)
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.
seqtabstocc(): frequencies of state co-occurrence patterns
seqgranularity(): new method
seqedplot(): replaced calls of TraMineR internal functions
TraMineR.legend with respectively
(should be transparent to the end user).
Fixed issue with calling Rinternals from within extern "C" in seqstart.cpp (request of B. Ripley)
NEWS is now in Rd format into inst/NEWS.Rd
FCE_to_TSE(): Events were not properly chronologically sorted.
TSE_to_STS(): produced inconsistent results when events were not chronologically
sorted by cases.
First release on CRAN
seqplot.tentrop.m(): new argument
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.
seqrep.grp() now also accept distance objects as
group.p has now a
seqedist(): fixed a mix between norm and interval arguments.
fixed build warning generated by calls of foreign functions.