simDAG 0.5.1

New Features

• Added the node_polr() function to allow generation of data from an ordered logistic or probit regression.

Enhancements

• Added support for all 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!
• Removed the allow_ties argument from sim_discrete_event() (ties are now handled automatically in a more efficient manner, without the need for user intervention).

simDAG 0.5.0

New Features

• Added the 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.
• Added the rtexp() function to allow sampling from left-truncated exponential distributions.
• Added the rsample() function as a convenient wrapper around sample(), as suggested by Ed Hagen (@grasshoppermouse).
• Added the node_aalen() function to allow data to be generated according to an Aalen additive hazards model with time-constant betas and baseline hazard.
• Added the as_tidy_dagitty.DAG() method, which allows direct conversion of DAG to tidy_dagitty objects used to create plots in the ggdag package.

Enhancements

• Added the remove_if and break_if arguments to the sim_discrete_time() function, to allow users some options that potentially make the simulation much faster.
• Allow function input to the data_format argument of the sim_n_datasets() function to avoid potentially weird bugs in parallel processing.
• There was a slight change to 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.
• Made the 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.
• Added the 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.
• Allow DAG.node definitions in the values argument of the do() function, to make changing existing DAGs easier.

Bug Fixes

• Fixed a bug where using n_sim=1 in sim_from_dag() lead to a false error with some child node types.
• Function calls on the 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

• Small changes to include the new sim_discrete_event() everywhere.
• Added a new vignette introducing the sim_discrete_event() function.

simDAG 0.4.1

New Features

• Added the 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.
• Added the as.dagitty.DAG() function to allow direct conversion of DAG objects to dagitty objects.

Bug Fixes

• Previously, the 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).
• Fixed a bug that occurred when calling node() or node_td() inside a function with objects passed to parents or formula.

Documentation

• Added explanations for how to simulate data for Cox models with time-varying covariates and Aalen additive hazards models with time-varying covariates to the cookbook vignette.

simDAG 0.4.0

New Features

• Added the 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

• Added the kind argument to node_identity() to allow different kinds of input to the formula argument.
• Added the include_networks argument to dag2matrix() and as.igraph(), due to the new networks-based simulation features.
• Added the 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

• Fixed a minor bug that occurred when using node + DAG (in this order).
• Fixed a faulty error message produced when using formula with just one predictor in nodes that do not need an intercept.
• Fixed a faulty error message when using a string of a formula with node_identity() in sim_discrete_time().

Documentation

• Added a new vignette to describe the new networks-based simulation features.
• Updated existing documentation pages to include networks-based simulation features.

simDAG 0.3.2

Documentation

• Added a vignette of the Journal of Statistical Software paper (provisionally accepted)
• Changed all citation information accordingly

simDAG 0.3.1

Enhancements

• Added the remove_vars argument to the sim2data() function, to allow users to exclude certain variables from the output if desired.

Bug Fixes

• Fixed a bug where sim_n_datasets() would fail with n_cores > 1 whenever nested custom functions were used in nodes.

Documentation

• The previous node_custom documentation page has been turned into a vignette (which it should have been from the start).

simDAG 0.3.0

New Features

• Support for random effects and random slopes (mixed model syntax) has been added to the formula interface of node() and node_td() when using nodes of type "gaussian", "binomial" or "poisson".
• Added seven new node types: node_aftreg(), node_ahreg(), node_poreg(), node_ypreg(), node_ehreg(), node_zeroinfl() and node_mixture().

Enhancements

• Added the 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.
• Added the include_td_nodes and include_root_nodes arguments to as.igraph.DAG().
• Changed the default of n_cores in the sim_n_datasets() function to 1 from parallel::detectCores()
• Function input to the cens_dist argument in the node_cox() function is now allowed.
• The argument 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

• Fixed a bug that occurred when a user-specified root node function returned a data.frame-like object with more than one column.
• Fixed a bug when printing the structural equation of a poisson node, in which the exp() call did not show up when the node was defined using the formula argument.

Documentation

• Added new “cookbook” vignette to showcase more possible use cases of the package.
• Visual update of the DAGs shown in the vignette figures.

simDAG 0.2.2

Bug Fixes

• When specifying a node as both a root or child node and as a time-dependent node, it is no longer counted twice in print.DAG()
• Fix small error in tests due to changes in data.table

simDAG 0.2.1

Enhancements

• External variables may now be used in the formula interface using eval() calls.
• Added the remove_not_at_risk argument to the sim2data() function.
• Change default of t0_sort_dag in sim_discrete_time() from TRUE to FALSE for more consistency with sim_from_dag().

Bug Fixes

• Using sim2data() with time-dependent nodes of type node_competing_events() no longer results in an unwarranted error message.
• Using the column name "time" in the time argument of long2start_stop() now works properly.

New Features

• Added the 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

• Added more examples in the formula vignette.

simDAG 0.2.0

Enhancements

• Added the output argument to the rbernoulli() function to allow different output formats.
• Change default of sort_dag in sim_from_dag() from TRUE to FALSE.
• Moved the functionality of the coerce2factor and coerce2numeric arguments in rcategorical(), node_multinomial() and node_binomial() to the output argument for a more consistent syntax and easier usage.
• It is now allowed to directly supply functions to the type argument in node() and node_td().
• Passing optional arguments to the layout function in plot.DAG() is now supported.

Bug Fixes

• The node_fill argument of the plot.DAG() function is no longer being ignored if mark_td_nodes was set to TRUE.

New Features

• Added a new enhanced formula interface, which allows users to directly type out the underlying structural equations for many node types. This replaces the old 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

• Added a new vignette explaining in detail how the new enhanced formula interface for the node() function works.

simDAG 0.1.2

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 crew

Enhancements

• Print underlying structural equations in summary.DAG() and summary.DAG.node()
• Added the overlap argument to both long2start_stop() and sim2data() to directly create start-stop data with overlapping durations, as needed for some statistical models
• Added the target_event and keep_only_first arguments to sim2data() and related functions, to allow direct transformation into model-ready dataset
• Made the long2start_stop() function more computationally efficient

Bug Fixes

• Fixed a small bug in input checks of the node_time_to_event() function, which printed an error when not all arguments to prob_fun were supplied, even when these arguments had default values
• Fixed bug in print.DAG.node() which occurred when a time-to-event node with no parents was supplied
• Fixed a bug in sim2data() 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.
• Fixed a bug that resulted in errors when interaction terms were being supplied through formula objects of child nodes

New Features

• Added the as.igraph.DAG() method which extends the generic function as.igraph() to conveniently parse DAG objects to igraph objects
• Added as.data.table.simDT() and as.data.frame.simDT() for user convenience

Documentation

• Documentation pages of most nodes now include formal descriptions of the data generation mechanism
• Re-wrote the documentation page for custom node definition

simDAG 0.1.1

Enhancements

• node() and node_td() now support character vectors in the ‘name’ argument, allowing easy creation of multiple nodes with the same definition

Bug Fixes

• There was a bug in the 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.
• There was a small bug in 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

• Added the sim_n_datasets() function to generate multiple datasets from a single dag object, possibly using multicore processing

Documentation

• Minor changes to documentation pages
• Minor changes to vignettes

simDAG 0.1.0

• This is the first release of this package