plot.ceg
new plotting functions using igraph
plotting.make_stages_col
which help computing
stages colors for sevt
and ceg
plotting.sample_from
now returns a data.frame of factors. prob
earns a new argument conditional_on
, that
makes easier to compute conditional probabilities. confint.sevt
, implement a method for confidence intervals
for the parameters of a model of class sevt
. lr_test
new function, implementing likelihood-ratio
test.search_best
and search_greedy
.cid
function that implements context intervention discrepancy.sevt
and DAG representations.as_sevt.bn.fit
.find_stage
.summary.sevt
for objects without ctables
. path_probability
and prob
for sevt objects with not
ordered $prob
.fix color assignment consistency between plot.sevt
and barplot.sevt
This version introduces major changes, in functions capabilities
and in functions naming.
These changes are almost surely breaking any previous code
using older versions of the package.
In particular, all functions named *.sevt
but class methods are now
called differently.
Moreover, various improvements and functionalities are added
to better deal with unobserved situations and to improve
computations.
Additional model selection methods based on clustering are
now available.
COMPLETE CHANGELOG:
fit
parameter from full
, indep
.
Now full
and indep
always fit the model while
sevt
is just the basic constructor of the sevt
class.full
and indep
by default unobserved situations are joined
using join_unobserved
, and probabilities are fitted only after
the unobserved situations are joined, improving speed. Moreover, the
name of the unobserved stages are stored as name_unobserved
in the
staged tree object.new_label
to improve speed.plot.sevt
allows now to set edges color with
col_edges
.plot.sevt
and barplot.sevt
it
is possible to specify stages that should be ignored
and not plotted via the ignore
argument, by default the
name_unobserved
stages are ignored.plot.sevt
adds variables names by default (var_names
argument).compare_stages
: because of changes in plot.sevt
we need to specify that the root is always considered identical.stndnaming
accepts now uniq
, prefix
and
ignore
arguments, which control how stage names are generated and
if some stage names should be left untouched (default: the name_unobserved
stages). stages_bj
(previously bj.sevt
) distance is now passed with a
character and no longer as a function.stages_hclust
and
stages_kmeans
, to learn stage structure using hierarchical or
k-means clustering.scope
and ignore
parameters that allow to specify among which variables
run the algorithm and which stages should be left untouched
(default: the name_unobserved
stages). 1:length(x)
with the suggested seq_along
in all code.stages_bj
and stages_hclust
are compatibles.as.sevt
, only implemented one method
for bn.fit
class from bnlearn packageinclusions_stages
and provide better output. summary
, stages were wrongly matched to probabilitiesbarplot_stages
to draw barplots of the
floret probabilities. Implemented relative tests.plot.sevt
.order
can be passed to staged_ev_tree.bn.fit
join_zero
alias for join_zero_counts
indep
, probabilities should not be of class table
(it was triggering a bug in summary)subtree
, now removing unused probabilities
(it was triggering a bug in summary) get_stage
and get_path
and relative testsxor
is renamed as noisy_xor
noisy_xor
NaN
log-probabilities in predict.sevt
summary.sevt
function addedsubtree.sevt
works now for fitted objectsinclusion.stages
functionpredict.sevt
now returns conditional probabilities P(C|X)predict.sevt
works also if newdata
does not include the classcompare.sevt
works with three different methods.join_stages
throws error with bad stages.lambda = 0
does not induce errors in logLik
, join_stages
and thus in the model selection algorithms. nvar.sevt
bug ceg.sevt
varnames.sevt
and nvar.sevt
fit.sevt
is replaced by sevt.fit
(following the lm.fit
naming).
fit.sevt
is still available but marked as (DEPRECATED) in doc.compare.sevt
is updated with info on the capabilities.First released version of the package
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