v0.7-1

• The GUI will (optionally) look for a newer version of
  gMCP on CRAN.

• Simes test is available.

• New function "subGraph" for the creation of subgraphs.

• User defined power functions.

  52 files changed, 551 insertions(+), 266 deletions(-)

v0.7-0

• 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(-)

v0.6-6

• 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(-)

v0.6-5

• 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(-)

v0.6-4

• 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(-)

v0.6-3

• 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(-)

v0.6-2

• 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(-)

v0.6-1

• 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(-)

v0.6-0

• 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(-)

v0.5-0

• 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(-)