
Version 0.7-1 (22-11-2011, Rev. 1001)
=====================================

- The GUI will (optionally) look for a newer version of 
  gMCP on CRAN.
  
- New function "subGraph" for the creation of subgraphs.

- User defined power functions.
  
Version 0.7-0 (26-Aug-2011, Rev. 964)
=====================================

- Package "graph" is no longer a dependency.
  Class definition of graphMCP has changed and is no
  longer a subclass of graphNEL. The function
  gMCP:::updateGraphToNewClassDefinition(object)
  is provided to update old serialized (saved) objects.
  The GUI will use this function on its own if necessary.

- Also not longer a dependency: gtools, xtable, MCPAN

- New dependency: lattice graphics for power simulations

- Due to S4-methods and the optional "graph" package a lot
  of renaming has taken place:
  addEdge -> setEdge, edgeData -> edgeAttr, 
  nodeData -> nodeAttr, nodes -> getNodes 

- Power simulation code from our third author
  Bjoern Bornkamp.

- New example graphs:

  - general and simple Successive Graphs
  - fixedSequence
  - Fallback Procedure
  - Truncated Holm (special case)
  - BauerEtAl2001
  - HuqueAloshEtBhore2011
  - BretzEtAl2009a/b/c

- Renaming of older example graphs to simpler names.

- CI dialog is modal.

- LaTeX-Code can be shown in Dialog and does not have 
  to be saved in a file.

- PValues can be attached to graphMCP objects as an 
  attribute "pvalues".
  
- Function graphGUI has a new parameter:
  experimentalFeatures=FALSE
  Set this to TRUE for experimental features like the following: 

- Power analysis in GUI.

- Code for adaptive procedures (marked as experimental).

 85 files changed, 2152 insertions(+), 1663 deletions(-)
  
    
Version 0.6-6 (04-Jul-2011, Rev. 860)
=====================================

- Fixed a bug in the GUI that deleted often p-values.

- Adjusted p-values are calculated also in the parametric case.

- Graphs without epsilon edges can be processed by a
  much faster procedure written in C.
  
- matrix2graph & graph2matrix deal better with variable edges.

- Hopefully setDividerLocation works now always correct, i.e. 
  the graph panel will always use 2/3 of the screen.
  
- Fractions like (1-a)/(1+b) are now shown with the 
  correct layout in the GUI.

- Speed up due to reduced Java/R communication.
  (More results are now cached in a Hashtable.)
  
 48 files changed, 559 insertions(+), 279 deletions(-)
  

Version 0.6-5 (26-May-2011, Rev. 825)
=====================================

- New dependency: CommonJavaJars
  This package contains now all the third party libraries.

- New example graphs:
  - Two versions of improved fallback procedures

- Improved placeNodes dialog.

- JavaGD plot is shown in CI dialog.

- Fixed bug with directory separators on Windows.

- Initialize the Java VM only if it is not initialized already.

 46 files changed, 157 insertions(+), 48 deletions(-)


Version 0.6-4 (11-May-2011, Rev. 782)
=====================================

- Fixed bug with saving and loading on Windows.

- Fixed bug with two graphs that could not be loaded.

- Fixed bug that the GUI expected a valid graph object on 
  start up.
  
- If an edge weights is 0 after variable replacement, 
  the edge is removed.
  
- Updated documentation that the graph package is not
  available any more on CRAN. 

- Layout of graph can be changed automatically from the GUI.

 22 files changed, 130 insertions(+), 38 deletions(-)

  
Version 0.6-3 (09-May-2011, Rev. 767)
=====================================

- New dependency: JavaGD, MCPAN

- Example graphs have been renamed (Please look at ?exampleGraph).

- Greek small letters are allowed as variables
  - enter them as e.g. "\epsilon", "\iota", "\phi" in the GUI.
  - use edgeData "variableWeight" to set them in R
    (see graph2FromBretzEtAl2009 as an example).
  - epsilon has to be entered as "\epsilon" instead of "e"

- Below the graphPanel is now a new panel with 
  graph description and graph analysis. 

- Function placeNodes is now exported with new parameters:
  nrow, ncol and force
  
- We use package highlight for the manuals.

- New example graphs:
   
  - Graphs from Hung and Wang (2010) and 
    Bretz et al. (2011)

- All example graphs have a description and
  graph attributes "description" are shown in the GUI.

- First data files: hydroquinone and simvastatin

- simConfint also returns the point estimates as second column.

- Improved compatibility for R 2.8.

- New HTML file References.html accessible from the GUI.
 
- Unified loading of graphs.

- New function: joinGraphs

- It looks like JavaGD is not available for Solaris?
  Anyone out there using this OS with gMCP?

75 files changed, 1398 insertions(+), 1117 deletions(-)


Version 0.6-2 (24-Apr-2011, Rev. 679)
=====================================

- New dependency: xtable 

- Indefinite ProgressPanel is shown while calculating.

- Calculations can be interrupted and canceled.

- Improved / updated gMCP-LaTeX-Report now in the GUI.

- New function: graphAnalysis

- Fixed a major bug which prevented saving/loading in the GUI.

- Mnemonic keys for the menu.

- Buttons for loading estimates / sd from R in CI-dialog.

- Improved zoom with TeXItem edge labels.

- Menu entry for loading p-values.

- Fixed visualization bug: 
  Panel with p-values was sometimes out of sync.

- Fixed bug: Edges with very small values were set to 0.

- Fixed visualization bug: 
  Adjacency table was not updated when edge was deleted.
  
- GUI deals a lot better with rounding errors.  

 58 files changed, 1072 insertions(+), 596 deletions(-)


Version 0.6-1 (09-Apr-2011, Rev. 589)
=====================================

- We use the library JLaTeXMath for edge labeling.

- Eye candy (for example the edge labels have now a border and 
  are always drawn at the end).
  
- The settings for correlation are moved to the p-value panel.

- The value for epsilon is optionally either asked every time
  or the value from the option panel is used.

- Changed the order of the buttons in the main button panel.

- GUI is remembering the last 4 used R objects / files. 

- Since r-forge has rJava problems at the moment and does
  not provide gMCP builds, we pushed 0.6-1 early to CRAN. 

 43 files changed, 666 insertions(+), 248 deletions(-)


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.)
  
- gMCP has new arguments: approxEps=TRUE, eps=10^(-4)
  
- 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".
  
 40 files changed, 599 insertions(+), 339 deletions(-)


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.
