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NEWS
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### 0.10.10 (15 May 2020)
* Remove dependencies on `RBGL` and `Rgraphviz`
### 0.10.5 (6 January 2016)
* Update `plot.HydeNetwork` to accommodate changes in `DiagrammeR`.
### 0.10.4 (1 April 2016)
* Added methods for survreg models. The predicted value returned is the predicted
survival time.
* Made changes to unit tests to accommodate new version of `testthat`
* Replaced dependency on `ArgumentCheck` to `checkmate`
* Code formatting changes.
### 0.10.3 (18 January 2016)
* Added dependency to `pixiedust` to allow better parsing of term names. This
also resulted in removing the dependency on `broom` (which is alright, because
`pixiedust` depends on `broom`.
### 0.10.2 (13 November 2015)
* Expanded options for specifying policy matrices (per Issue #95)
### 0.10.1 (30 October 2015)
* Corrected a serious bug in how character values were handled in the
`data` argument of `compileDecisionModel`.
* Adds `factorFormula` to assist in writing formulae that make use
of factor levels instead of their numeric codes.
* Deterministic nodes are now represented as diamonds by default.
### 0.10.0 (26 Sept 2015)
* Implements the `factorLevels` element in network objects
and arguments in `setNode`. See Issue #81
* Changes to `plot.HydeNetwork` relevant to changes in
`DiagrammeR` 0.8.0. Note that the column names in custom node
data frames no longer contain `node_id` but use `nodes`
instead. However, the `HydeNet` function arguments have no
changed names, in order to maintain compatibility with 0.9.0.
Future versions may allow for either `node_id` or `nodes` to
be used. In custom edge data frames, `edge_from` and `edge_to`
are changed to `from` and `to`, respectively.
### 0.9.3 (24 Sept 2015)
* Minor bug fix related to creating policy matrices with nodes that
don't have a 'nodeFitter' specified.
### 0.9.2 (11 Sept 2015)
* Fixed a bug in `compileJagsModel` and `compileDecisionModel` that prevented `cpt`
objects from being passed to JAGS models correctly.
* Added `nodeData` argument to `setNode`.
* Added unit tests.
### 0.9.1 (6 July 2015)
* Conversion of argument checks to using the `ArgumentCheck` package
* Connections are closed in `compileDecisionModel`. This allows decision networks to be
compiled for absurdly large policy matrices (> 1000 policies)
### 0.9.0 (2 July 2015)
* Added imports from `utils` and `stats` to comply with new CRAN policies.
* Adds the functionality to allow all `nodeType` specifications to properly build in
`writeJagsModel`. (See Issue #72)
* Incremented to version 0.9.0 for CRAN release.
### 0.8.11 (26 June 2015)
* Fixed a bug preventing `cpt` arrays from being passed to `jags.model` in
`compileDecisionModel`
* Fixed a bug preventing bernoulli values from being passed to `cpt` arrays in the JAGS models.
### 0.8.10 (19 June 2015)
* Streamlined the generation of the `factorRef` element of the compiled Hyde Networks.
This also allows all data frames in all nodes to be included to generate a complete list
of factors throughout the network (previously, it only generated references for factors
in the overall `data` element, not the `nodeData` elements.
### 0.8.9 (16 June 2015)
* Incorporated minor changes for compatibility with DiagrammeR 0.7
* Minor bug fix to `mergeCustomNodes` to prevent loss of custom settings
* Minor changes to `HydeNetPlots` vignette
* Minor changes to `GettingStartedWithHydeNet` vignette.
* Removed `ObtainingPosteriorDistributions` vignette.
* Added `VignetteBuilder` option to the description file. For now, when reinstalling the
package, use the command `devtools::install_local([directory])`. If you try to build the
vignettes with the package, a strange error occurs that prevents the installation. This
error is related to the `WorkingWithHydeNetObjects` vignette, but I can't reproduce the
error outside of the build command.
### 0.8.8 (5 June 2015)
* `setNodeModel` and `writeJagsFormula` methods are complete.
* `writeJagsModel` now accommodates `cpt` objects
* `compileJagsNetwork` retrieves `cpt` objects to include in the
`data` argument, allowing JAGS to compile without the user having to
remember to assign the `cpt` object to the data.
### 0.8.7 (29 May 2015)
* `cpt` function is added to assist in developing multidimensional conditional
probability tables. `cpt` and `cptInput` are generics with methods for `list`
and `formula`. Their structure is undergoing some growing pains right now,
so expect more changes in the future.
* Improvements to `setNode` validation.
* Improvements to efficiency of `compileDecisionModel`.
* Consolidated all data documentation into a single file.
* `HydeNetwork` chooses `cpt` as the fitter for variables where the node is
a factor and all parents are factors.
* Added `modelToNode.cpt`. This is untested as of yet and may be buggy. Final
changes are pending the finalization of the `cpt` objects.
### 0.8.6 (15 May 2015)
* An additional function called `nodeFromFormula` is used to generate most likely
node names from terms in model formulas that are used in functions and other
transformations. For instance, when a formula has `factor(x)`, only the `x`
is used in node names. (Solves Issue #31)
* A new, unexported function called `matchVars` is used to reduce terms in
model formulas to just the node name. (Solves Issue #26)
* An additional argument is used in `writeJagsModel` and `modelToNode` that is
required by an unexported function `matchVars`.
* Changed behavior of `setNode` to retain current settings for decision and
utility nodes (Issue #53)
* Added a message to indicate that character strings defining parameters
in `setNode` are not validated (Issue #24).
* Updated `BlackJack` network object to be consistent with the object defined in
the Decision Nodes vignette.
* Now Imports on `broom (>= 0.3.7)`. This makes sure that the multinom tidiers
are available.
### 0.8.5 (7 May 2015)
* Moved `gRbase` from Depends: to Imports:
* Repaired a bug in `plot.HydeNetwork` that prevented plotting without defaults
* Updated the `HydeNetPlots` vignette to accommodate new plotting features.
### 0.8.4 (3 May 2015)
* Revamped plotting utilities to make use of the DiagrammeR package. This makes
the full range of GraphViz available for use.
### 0.8.3 (2 May 2015)
* Implemented policy matrices into `compileDecisionModel` and fixed all the
bugs that popped up in doing so.
* Changed the name of the Black Jack training data from `bjdata` to
`BlackJackTrain`. Added documentation for it.
* Completed Documentation.
### 0.8.2 (1 May 2015)
* Adds functionality to customize plot defaults.
* Adds functionality to customize nodes in plots.
* Added the `BlackJack` data object, which contains a `HydeNetwork` object
simulating a game of black jack.
* Included a vignette showing off the use of plotting methods.
### 0.8.1 (25 April 2015)
* Fixes Issue #10 dealing with utility nodes not being properly initialized
and set.
### 0.8.0 (24 April 2015)
* Added a new dependency on package `dplyr` and `magrittr`. This was done to
make `dplyr` available for joining MCMC matrices returned by `coda.samples`.
* Modified `compileJagsModel` to accommodate compiling multiple JAGS models when
a policy/decision matrix is provided.
* Added the function `HydePosterior`, which generates posterior distributions
of all of the JAGS models compiled by `HydePosterior`.
* Added a print function for the output of `HydePosterior`
* Added a function to bind all of the MCMC output from `HydePosterior` into
a single data frame.
* Addressed a bug in `compileJagsModel` that affected observed data values.
(Issue #36 on GitHub).
* Addressed a bug in `modelToNode` that printed the node name in the first
parameter, causing `compileJagsModel` to fail. (Issue #35 on GitHub).
### 0.7.2 (10 April 2015)
* The primary additions to this developmental change are the addition of
decision nodes. Each node now has a new descriptor (found in
`network$nodeDecision`. It is a logical value indicating if the node should
be considered a decision node.
* The behavior of decision nodes is exactly like all other nodes in every
respect _until_ you call the `compileDecisionNetwork` function.
`compileDecisionNetwork` evaluates all of the decision nodes, builds a table
of all combinations of decision options, and systematically runs
`compileJagsModel` for each row of that table to create a JAGS model for
each combination of decisions.
* Decision nodes can be defined in `setNode`, but for convenience, a new
function is introduced (`setDecisionNodes`) to allow multiple nodes to be
defined as decision nodes in one call. This is intended for use when a list
of models is used to define a network.
* Various bugs have been corrected that were uncovered while testing conditional
logic nodes (this is not a formal feature of HydeNet, but can be done. A
vignette describing their use will be built later)
* Additional bugs have been corrected while uncovered during the testing of
decision node features.