
# simDAG 1.0.1

Bug Fixes

* Temporary fix for a bug caused by changes in `lme4`, which in turn caused a bug in the `simr` package. Installing `simr` from github already fixes the issue, so this update was made solely to retain `simDAG` on CRAN. 

# simDAG 1.0.0

New features

* Allow arbitrary baseline hazard functions in `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

* Added the `all_levels` argument to the `rcategorical()` function to allow users to keep all levels, even when some never occur in the generated data.
* When defining custom node generation functions for custom nodes required for the `dag_from_data()` function, additional arguments are now supported.

Bug Fixes

* Fixed a bug that occurred when using `dag_from_data()` with categorical parents in nodes based on generalized linear models and negative binomial regression models.

Documentation

* Added the official citation information for the newly published Journal of Statistical Software paper.

# simDAG 0.5.2

Bug Fixes

* This update was only done to fix failing tests on CRAN due to an update in the `simr` package. Nothing else changed.

# 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 `DAG`s 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 `formula`s are now supported correctly. Previously, `formula`s 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 `DAG`s 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
