
Version 0.6-0 (06-Apr-2011, Rev. 547)
=====================================

- The GUI supports edges with variables (although sum checking of
  outgoing edges is disabled then till values are assigned to the
  variables.)
  
- New function: substituteEps

- Changes in class graphMCP:
 
  - Attribute for node weights is called "nodeWeight".  

  - New mandatory edge attribute "epsilon".
  
- graph2latex has the new arguments "labelTikZ", "tikzEnv" and 
  "offset".

Version 0.5-0 (28-Mar-2011, Rev. 525)
=====================================

- We use weights instead of direct alpha allocation in the graphs.
  This causes major API changes:

  - gMCP and many other functions have an argument alpha with an
    default 0.05

  - getAlpha is now called getWeights since it returns the weights

  - graph2weights is removed since it is a special case of getWeights

- due to these changes above, graphs that have been saved to files
  will cause errors when loaded and processed

- getX/Y were renamed into getX/YCoordinates due to Rgraphviz
  conflicts.

- graph2latex has a new argument "nodeTikZ".

- new function bdiagNA for building block diagonal matrices with NA
  values outside the diagonal

- Backward compatibility for R 2.8.0 and rJava 0.6-3.

- CTRL+C interrupts only the last R command and does not close the
  whole R session.

- CRAN has disabled checks on arch="ppc", so MacOS builds are again
  available from CRAN.

- Bug report sends now also the result from traceback()

- A lot of bug fixes for corner and edge cases

- CITATION file

- Please note that full epsilon support is postponed for version 0.6-0

 61 files changed, 868 insertions(+), 482 deletions(-)


Version 0.4-0 (21-Mar-2011, Rev. 462)
=====================================

- Added code for graph based MCPs with partial knowledge of the
  correlation structure from Florian Klinglmueller, who is now
  coauthor.

- New dependencies in this code: gtools and multcomp (and therefore
  also mvtnorm)

- gMCP has a new optional parameter "correlation".

- The new vignette "correlated.pdf" shows the new features.

- graphGUI Parameter grid is now 0 by default. This restores the last
  used grid value.

- Fractions instead of decimal numbers are shown in more places.

- Alpha values can be entered as R expression, e.g. "0.05/7".

- When the test phase is started in the GUI, you are asked, whether
  you have (partial) knowledge about the correlations between the
  tests.

- Better support for more than one GUI window in the same R session.

- All help files open correctly on windows machines - even with 
  Java 5.0

 48 files changed, 278 insertions(+), 91 deletions(-)


Version 0.3-6 (15-Mar-2011, Rev. 410)
=====================================

- Mainly a bug-fix release, since the GUI was often not responding 
  in 0.3-5.

- C compiler is needed for building gMCP since the first C source file
  was added.

- When saving/loading graphs, reports or png/LaTeX files, the last
  directory is remembered.

- Adjusted p-values are now truncated and can not be bigger than one.

 36 files changed, 278 insertions(+), 495 deletions(-)


Version 0.3-5 (13-Mar-2011, Rev. 379)
=====================================

- Unfortunately after release it was noted that the GUI was not
  responding in 0.3-5.

- New dependencies: MASS for MASS::fractions and PolynomF for polynoms
  in epsilon.

- Saving and loading of graphs to/from files.

- Method graphGUI has a new optional argument "pvalues" for loading
  p-values.

- Trying to show fractions in the GUI instead of decimal numbers

- Line width of graphs can be adjusted (line width 2 is now default)

- Use of antialiasing for nicer graphics 

- Improvement of PNG exports

- Parameters for example graphs in GUI

- More RUnit tests

 40 files changed, 363 insertions(+), 406 deletions(-)


Version 0.3-4 (26-Nov-2010, Rev. 341)
=====================================

- New functions: graph2matrix and matrix2graph

- Adjaceny matrix is shown and can be edited.

 38 files changed, 152 insertions(+), 134 deletions(-)


Version 0.3-3 (15-Nov-2010, Rev. 318)
=====================================

- Be careful with epsilon edges (we never specified what exactly they
  are and how they should behave) and please wait for version 0.6
  which will handle them in a completely new way and will document it.
  Support for them is broken in this release.

- New example graph from Hommel et al. 2007.

- Inserted missing $ in LaTeX code output from graph2latex.

- Better automatic placement of edge labels.

- Options dialog in GUI.

- All doc files are accessible from the GUI menu.

- The GUI Locale object is always set to English - that way there is
  no decimal separator confusion etc.

- Edges with small weights are rendered better.

- Dialog that shows adjusted p-values with much better layout.

- New accompanying doc file: Description of Edges with Infinitesimal
  Small Epsilon Weights (unfinished). [Removed in 0.3-4]

- graph2latex has the same vertical orientation as the GUI.

- Option whether we want to still show already rejected nodes or not.

- Option whether graphs should be colored or not.

- Update in the GUI for confidence intervals to avoid a confused user.

- Removed function adjPValues from public API - adjusted p-values are
  now calculated in the gMCP call.

 33 files changed, 269 insertions(+), 282 deletions(-)


Version 0.3-2 (08-Oct-2010, Rev. 277)
=====================================

- Renaming of parameter in simConfint: "confintF" is now "confint"

- Updated confidence interval dialog (but still in development).

- Confidence intervals for t- and normal distribution can be
  calculated based on the p-values and point estimates in most cases.

- Reduced the package size.

- Further improved capabilities for bug reporting.

- We need rJava in version 0.8-3 or later.

- Vignette can be shown from inside the GUI.

- Function "setAlpha".

 36 files changed, 242 insertions(+), 110 deletions(-)


Version 0.3-1 (02-Oct-2010, Rev. 249)
=====================================

- The GUI has a menu bar.

- Improved capabilities for bug reporting. All information that is
  sent is also shown.

- Workaround for a problem with the graph package when a node has no
  out-going edges.

- Numbers are now accepted with "." and "," as decimal points

- A newly created edge is now by default an epsilon edge.

- Edges from one node to itself (loops) are not allowed any more.

- Start button is only enabled, if the graph has any nodes.

- Bug-fix regarding epsilon edges.

 25 files changed, 186 insertions(+), 113 deletions(-)


Version 0.3-0 (01-Oct-2010, Rev. 238)
=====================================

- Major API changes (mostly gsrmtp replaced by gMCP - but now the API
  should stay relatively stable).

- GraphGUI can now also be called directly on objects of class
  graphMCP, like graphGUI(rejectNode(graph, "H1")).

- Small GUI bug-fix for placing edge labels while in any other zoom
  level than 100%.

- Completely separated nodes (which only occur in sub-optimal testing
  procedures) are now handled correctly.

- If the graph has no nodeRenderInfo available when the GUI is called,
  the edges are placed in a circle.

- Deducer support if installed and loaded.

 42 files changed, 980 insertions(+), 930 deletions(-)


Version 0.2-4 (30-Sep-2010, Rev. 215)
=====================================

- After some alpha and beta releases on r-forge this is the first beta
  version on CRAN.

- We support: Graphs with epsilon edges, confidence intervals,
  adjusted p-values.
