NEWS.md
In simDAG: Simulate Data from a DAG and Associated Node Information

simDAG 0.1.0

This is the first release of this package

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 0.1.2

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 0.2.0

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 0.2.1

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 0.2.2

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 0.3.0

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