High-Performance Open-Source Archive
New features
node_cox(). This also makes it possible to perform
discrete-event simulations using sim_discrete_event() with
variables that have continuous time-dependent baseline hazards, by using
the model argument.Enhancements
all_levels argument to the
rcategorical() function to allow users to keep all levels,
even when some never occur in the generated data.dag_from_data() function, additional
arguments are now supported.Bug Fixes
dag_from_data()
with categorical parents in nodes based on generalized linear models and
negative binomial regression models.Documentation
Bug Fixes
simr package. Nothing else changed.New Features
node_polr() function to allow generation of
data from an ordered logistic or probit regression.Enhancements
rsurv package based time-to-event
nodes in the model argument of
node_next_time() nodes in discrete-event simulation. Many
thanks to Fábio N. Demarqui (@fndemarqui) for making this
possible!allow_ties argument from
sim_discrete_event() (ties are now handled automatically in
a more efficient manner, without the need for user intervention).New Features
sim_discrete_event() function, which allows
users to perform discrete-event simulations to generate complex
longitudinal data in continuous time. This function is usually much
faster than comparable sim_discrete_time() calls, although
at the cost of some flexibility.rtexp() function to allow sampling from
left-truncated exponential distributions.rsample() function as a convenient wrapper
around sample(), as suggested by Ed Hagen (@grasshoppermouse).node_aalen() function to allow data to be
generated according to an Aalen additive hazards model with
time-constant betas and baseline hazard.as_tidy_dagitty.DAG() method, which allows
direct conversion of DAG to tidy_dagitty
objects used to create plots in the ggdag package.Enhancements
remove_if and break_if arguments
to the sim_discrete_time() function, to allow users some
options that potentially make the simulation much faster.data_format argument of the
sim_n_datasets() function to avoid potentially weird bugs
in parallel processing.node_binomial(), which
increases performance if return_probs=TRUE is used
(avoiding a needless rbernoulli() call). The results of
simulations with a DAG containing a node with both
type="binomial" and return_probs=TRUE might
therefore differ on the same random number generator seed as compared to
previous versions.node_cox() function faster, added the
left argument to it to allow left-truncation and changed
the default of cens_dist to NULL. These
changes likely result in different data being generated as compared to
previous versions, even with the same random number generator seed.formula argument to
node_time_to_event() to allow users to easily calculate
event probabilities from binomial regression models without having to
specify a prob_fun.DAG.node definitions in the values
argument of the do() function, to make changing existing
DAGs easier.Bug Fixes
n_sim=1 in
sim_from_dag() lead to a false error with some child node
types.intercept part of enhanced
formulas are now supported correctly. Previously,
formulas like ~ log(0.1) + 2*A would have
resulted in a false error.Documentation
sim_discrete_event()
everywhere.sim_discrete_event() function.New Features
link argument to
node_gaussian(), node_binomial(),
node_poisson(), node_negative_binomial() and
node_zeroinfl() to allow different link functions when
generating data from these nodes.as.dagitty.DAG() function to allow direct
conversion of DAG objects to dagitty
objects.Bug Fixes
sim_n_datasets() function used
stats::runif(1) as a default for the seed
argument. Because seeds are coerced to integers in
set.seed(), this essentially meant the seed
argument was always set to 0 (unless changed by the user), which was not
intended. We changed the default to be NULL, which is
equivalent to not setting a seed. This might change results
obtained using previous versions. To get the same result as in previous
versions, use seed=0 or
seed=stats::runif(1).node() or
node_td() inside a function with objects passed to
parents or formula.Documentation
New Features
network(), network_td() and
net() functions to allow simulations with network based
dependencies among individuals. This includes static and dynamic
networks in regular DAGs and discrete-time
simulations.Enhancements
kind argument to node_identity()
to allow different kinds of input to the formula
argument.include_networks argument to
dag2matrix() and as.igraph(), due to the new
networks-based simulation features.unif argument to
node_time_to_event() to allow users to generate multiple
time-to-event nodes at once that are basically using the same “seed”
value for the random number generator.Bug Fixes
node + DAG
(in this order).formula with just one predictor in nodes that do not need
an intercept.formula with node_identity() in
sim_discrete_time().Documentation
Documentation
Enhancements
remove_vars argument to the
sim2data() function, to allow users to exclude certain
variables from the output if desired.Bug Fixes
sim_n_datasets() would fail with
n_cores > 1 whenever nested custom functions were used
in nodes.Documentation
node_custom documentation page has been
turned into a vignette (which it should have been from the start).New Features
formula interface of
node() and node_td() when using nodes of type
"gaussian", "binomial" or
"poisson".node_aftreg(),
node_ahreg(), node_poreg(),
node_ypreg(), node_ehreg(),
node_zeroinfl() and node_mixture().Enhancements
reference argument to
rbernoulli() and rcategorical() to make it
easier to specify the reference category when coding the output as a
factor variable.+.DAG now checks whether the DAG would
become cyclic when adding a node() and returns an error if
it does.include_td_nodes and
include_root_nodes arguments to
as.igraph.DAG().n_cores in the
sim_n_datasets() function to 1 from
parallel::detectCores()cens_dist argument in the
node_cox() function is now allowed.as_two_cols was added to the
node_cox() function to allow users to return only the
time-to-event as a single column if no censoring is applied.Bug Fixes
data.frame-like object with more than one
column.exp() call did not show up when the node was
defined using the formula argument.Documentation
Bug Fixes
print.DAG()data.tableEnhancements
eval() calls.remove_not_at_risk argument to the
sim2data() function.t0_sort_dag in
sim_discrete_time() from TRUE to
FALSE for more consistency with
sim_from_dag().Bug Fixes
sim2data() with time-dependent nodes of type
node_competing_events() no longer results in an unwarranted
error message."time" in the time
argument of long2start_stop() now works properly.New Features
node_identity() function to allow users to
directly calculate nodes as an R expression of other nodes without the
need to define a new function.Documentation
Enhancements
output argument to the
rbernoulli() function to allow different output
formats.sort_dag in
sim_from_dag() from TRUE to
FALSE.coerce2factor and
coerce2numeric arguments in rcategorical(),
node_multinomial() and node_binomial() to the
output argument for a more consistent syntax and easier
usage.type argument in node() and
node_td().layout function in
plot.DAG() is now supported.Bug Fixes
node_fill argument of the plot.DAG()
function is no longer being ignored if mark_td_nodes was
set to TRUE.New Features
formula argument. Standard
formulas (without betas and intercepts) are still supported, but no
longer mentioned in the documentation and will be deprecated in future
versions.Documentation
node() function works.General
simDAG no longer lists data.table under
“Depends” in the description file. It is instead listed under “Imports”
as recommended by the data.table crewEnhancements
summary.DAG()
and summary.DAG.node()overlap argument to both
long2start_stop() and sim2data() to directly
create start-stop data with overlapping durations, as needed for some
statistical modelstarget_event and keep_only_first
arguments to sim2data() and related functions, to allow
direct transformation into model-ready datasetlong2start_stop() function more
computationally efficientBug Fixes
node_time_to_event() function, which printed an error when
not all arguments to prob_fun were supplied, even when
these arguments had default valuesprint.DAG.node() which occurred when a
time-to-event node with no parents was suppliedsim2data() which lead to inconsistent
results when event_duration=0 was used in one or more nodes
of type “time_to_event” or “competing_events”. This made me realize that
event durations smaller than 1 make no sense. They are now no longer
allowed and the default of the node types has been changed
accordingly.formula objects of child nodesNew Features
as.igraph.DAG() method which extends the
generic function as.igraph() to conveniently parse
DAG objects to igraph objectsas.data.table.simDT() and
as.data.frame.simDT() for user convenienceDocumentation
Enhancements
node() and node_td() now support character
vectors in the ‘name’ argument, allowing easy creation of multiple nodes
with the same definitionBug Fixes
node_time_to_event() function
that lead to the immunity_duration parameter being used
incorrectly. Since events were still recorded correctly, this was only
apparent when using save_states="all". Works correctly
now.dag2matrix() if the dag object
contained only root nodes. In this case, a logical matrix was returned.
Now it returns the correct numeric matrix.New Features
sim_n_datasets() function to generate
multiple datasets from a single dag object, possibly using multicore
processingDocumentation
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