v0.8-16

• Corrected some confidence interval calculations. Thanks to Liane Kluge for spotting!
• Dropped Java 5 and 6 compatibility
• No online version check anymore - gMCP is pretty stable now
• Removed Deducer from suggest list
• Corrected links (https and doi were appropriate)
• Using inherit function instead of class comparisons
• Updated homepage from r-forge to gitlab
• Using bibentry instead of citEntry for citation
• Removed old-style PersonList syntax from CITATION file

57 files changed, 423 insertions(+), 371 deletions(-)

v0.8-9

• New function gMCP.extended, which mostly does the same as the old
  gMCP function, but separates more clearly between weighting scheme
  and the subsequent closed testing procedure (with possible shortcuts).
  See ?gMCP.extended for the documentation of this new function.

• gMCP.extended can take any weighted test function as argument.
  The trimmed one-sided Simes test for two hypotheses and the weighted
  Simes test for specified subsets (and Bonferroni otherwise) are two
  new weighted test functions provided by this package.
  See ?bonferroni.trimmed.simes.test and ?simes.on.subsets.test for details.

• When a graph is saved, the user now can decide whether p-values and
  chosen test (including possible correlation matrix) should also be
  saved as attributes attached to the graph. If such a graph is loaded
  the user can choose whether he wants to restore p-values and/or test
  information.

• Saving a graph as PNG image file opens a dialog with the following
  options and a live preview: Color, transparent background, drawing
  of hypotheses names and weights, drawing of edge weights and node
  radius.

• Node size can be changed (e.g. for longer hypotheses names).

• Fixed some help documents not showing up as expected.

• Added new help buttons in the GUI which directly open the relevant
  sections of the user manual.

• Better layout for result window when large graphs or Simes test
  is used.

• Function calcPower now also takes graphMCP objects.

• Improved Edges

• Fixed call of corMatWizard if only a matrix is given without names
  and dimensions.

• Fixed confusing (but mostly not relevant) mix-up between NA and NaN
  during R/Java conversions.

• Better handling of invalid LaTeX terms.

• graph2latex gains argument 'fig.caption.short' for an optional short
  version of fig.caption for the list of figures.

• Fixed logging errors/warnings when two different users used the gMCP
  GUI on the same system.

• Improved dialog in case of errors.

• Warning if R was compiled without shared library support and the
  graphical user interface will not be available due to missing JRI.

• Lots of small interface improvements and documentation additions.

• Extended RUnit tests

  144 files changed, 10027 insertions(+), 1106 deletions(-)

v0.8-8

• API FUNCTION PARAMETER CHANGE: The argument 'exhaust' in the functions
  'generateBounds', 'generatePvals' and 'generateTest' was renamed to
  'upscale' to reduce misinterpretation.
• Since CRAN currently will build binaries only for 3.0 and 3.1, we drop support
  for R < 3.0.0 in the official releases to make our lives easier. Nevertheless
  there is a branch pre-R3 on github for those interested (or simply contact us
  if you are using an older version of R).
• Up to now the parameter 'test' of function gMCP could be one of the following:
  "Bonferroni", "Simes", "Bretz2011" or "simple-parametric".
  We now introduced a new parameter 'upscale' (default FALSE) and restricted 'test' to:
  "Bonferroni", "Simes" and "parametric",
  where the old "Bretz2011" corresponds to 'test="parametric", upscale=TRUE' and
  the old "simple-parametric" to 'test="parametric", upscale=FALSE'.
  For compatibility the old function calls actually still work, but are discouraged.
• The parameters 'cr' and 'sigma' in function 'calcPower' were renamed into 'corr.test'
  and 'corr.sim' respectively to further clarify that both are correlation matrices,
  the first used for the test (this matrix may contain NAs if the full correlation is
  not known for the test) and the second one for the simulation (which can not contain
  NAs and may also differ from the first one if power under misspecification is
  investigated).
  For compatibility the old function calls actually still work, but are discouraged.
• Fixed: The (experimental) power calculations were off for graphs where not all
  subgraphs created by rejections have the full alpha level.
  Thanks to Yevgen Tymofyeyev for spotting this!
• The function graph2latex got a new parameter 'showAlpha'. Now per default the graph
  weights are shown and not the local alpha levels in the nodes. The old output
  can be reproduced by setting 'showAlpha' to TRUE.
• Fixed: Graph image exports were not possible due to some recently introduced bug.
• Fixed: Some matrices were completely grayed out although only the diagonal
  was not editable.
• Random seed is shown for results from methods which use random numbers and can
  be set via options.
• Support for entangled graphs is no longer highly experimental,
  but enabled as default.
• Support for parametric tests for entangled graphs, i.e. 'generatePvals'
  and 'generateWeights' accept entangled graphs now.
• For entangled graphs there is now more than one tab showing the graph:
  The first tab still shows the combined graphs and then a separate tab
  for each graph follows.
• Settings for power calculations are saved temporarily or between sessions.
• The (disabled) menu entry for PDF reports was replaced by functionality
  for Office Open XML (MS Word docx) support. Package xlsxjars is therefore
  now a dependency (IMPORTS), since it already provides the necessary
  Apache POI jar files.
• Settings in the dialogs for power analysis and sample size calculations
  are remembered and can be saved and loaded as XML files.
• Improved Graph Analysis checks whether weights sum up to 1 for all subgraphs.
• In case of unexpected errors on Java's Event-Dispatch-Thread no error dialog
  was shown if Java >=7 was used. This is now fixed. Also error handling
  is now more robust.
• Edges are highlighted if transition matrix cells are edited.
• New example graph from Wang, B. and Ting, N. (2014): "An Application of Graphical
  Approach to Construct Multiple Testing Procedures in a Hypothetical Phase III Design."
  Frontiers in public health, 1 (75).
• Fixed: In some cases the description of the graph objects was not loaded.
• Fixed: A backslash '' in the graph description could crash the GUI including R.
• Better handling of unintentionally entered NaN or infinity values.

v0.8-7

• Compatible to CommonJavaJars 1.0-5.
• Fixed CRAN warnings.
• Moved Java source to /java as requested by CRAN.
• Dropped Deducer integration for now.

v0.8-6

• Improved memory settings. Especially in R 2.15.1 and 2.15.2 on 32-bit systems
  errors like the following could occur when the GUI was used:
  java.lang.OutOfMemoryError: unable to create new native thread
• Fixed: When the value of the alpha field was not a valid number in the GUI,
  an infite loop of warning dialogs popped up.
• Fixed: Loading old graph objects from version 0.6.x, i.e. from before August 2011,
  without package 'graph' asks to install this package. If this is refused or
  the installation failed, bad things happened like a complete crash of the current
  R session.
• Function 'graph2latex' gains an argument 'scaleText'. If TRUE (default)
  a scalebox is used in LaTeX instead of the optional parameter 'scale'
  from the tikzpicture environment.
• Improved documentation. Some Rd files are built by a patched version of
  roxygen2 that escapes "" in arguments and understands "returnItem":
  install_github("roxygen2", username="kornl")
  (This version includes especially Yihui's pull request:
  r-lib/roxygen2#112
  and A. Alfons's pull request:
  r-lib/roxygen2#30 )
• Using RCallServicesREngineWrapper to eval each expression in the environment
  gMCP:::gMCPenv instead of the global environment.
• Some errors were catched in Java or R, but still showed up in the console.
  We now use 'try(..., silent=TRUE)' in these cases.
• Adjacency Matrix is renamed to Transition Matrix (since some people
  use the word Adjacency Matrix for the binary matrix).
• We always use correlation matrices instead of covariance matrices in the GUI.

139 files changed, 5526 insertions(+), 3428 deletions(-)

v0.8-5

• Removed dangerous parameter seed from function rqmvnorm and calcPower.
• POSIX conforming Makefile fixes problems under Solaris.
• Fix for problems with knitr 1.3.
• Fixed: The rarly used offset parameter did not work well with the new edges consisting of arcs in TikZ.

v0.8-4

• R's base function chol for the Choleski Decomposition now defaults to LAPACK
  resulting in meaningless results for not non-negative definite matrices (without
  any numerical tolerance!). Therefore power calculations for only semi-positive
  definite correlation matrices could have been off under R 3.0 in previous versions.
  We switched to the singular value decomposition.
• Fixed: List of user defined power functions doesn't need to have names.
• Further work on the experimental entangled graphs feature.
• Since the vignettes were moved from gMCP/inst/doc to gMCP/vignettes
  most likely they will only be build with R >= 2.14.0.
• Moved MASS, PolynomF, multcomp, lattice, mvtnorm, Matrix, CommonJavaJars and methods
  from DEPENDS to IMPORTS. Therefore loading gMCP will no longer add these packages to
  the search path and if for example you want to use contrMat you have to load/attach the
  package yourself.

v0.8-1

• An rJava update to 0.9-4 removed necessary files for gMCP 0.8-0.
  This is now fixed and CommonJavaJars (>= 1.0.3) are required.

• Since package highlight is now orphaned we instead use knitr.

• Fix for loading the namespace when just the base namespace is loaded.

  28 files changed, 177 insertions(+), 197 deletions(-)

v0.8-0

• Fixed: If edges or nodes were changed with a double click,
  after that an error dialog was shown although nothing was wrong.

• Fixed: You could not change the type of parametric test in the options.

• You can select more than one node or edge and move them around.

• New class for entangled graphs (graphs with memory, i.e. linear convex
  combinations of graphs with the same nodes).

• Better error messages when input doesn't meet demands.

• Improved: Power simulations for singular correlation matrices.

• Entangled graphs (graphs with memory, i.e. linear convex combinations of graphs
  with the same nodes) as experimental feature (has to be activated in the options).

• Two entangled example graphs (Entangled1Maurer2012, Entangled2Maurer2012)
  from Maurer et al.

• New example graph from Ferber et al. 2011.

• Tooltips in options dialog.

• Improved power dialog.

  86 files changed, 3005 insertions(+), 1600 deletions(-)

v0.7-9

• calcPower gained a parameter "cr" for specifying
  a correlation for parametric power simulations.

• Added option to allow non-alpha-exhaustive parametric tests.

• Improved dialog in GUI for power simulations,
  including multiple settings for power analysis.

• Improved font size adjustment for edge labels.

• Show syntax error instead of infinite loop if an unparseable edge weight is entered.

  33 files changed, 720 insertions(+), 190 deletions(-)