gMCP GITHUB README
For a full list and description of features, please see the Wiki.
The development version of this package can be directly installed with the R package devtools from Hadley Wickham et al. using:
install.packages("devtools")
library(devtools)
install_github("kornl/gMCP", subdir="pkg/gMCP", dependencies = TRUE, build_vignettes = TRUE)
(If some LaTeX packages are missing, consider build_vignettes = FALSE
or install them.)
But note that the gMCP jar file is only rarely updated and it may be appropriate to build it yourself from the Java source code.
Otherwise just use the current version from CRAN.
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Releases
v0.89  Aug 10, 2015

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 onesided 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 pvalues 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 pvalues 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) mixup 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()
v0.88  Oct 3, 2014
 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 preR3 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 "simpleparametric". 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 "simpleparametric" 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 EventDispatchThread 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.
v0.87  Aug 26, 2014
 Compatible to CommonJavaJars 1.05.
 Fixed CRAN warnings.
 Moved Java source to /java as requested by CRAN.
 Dropped Deducer integration for now.
v0.86  Feb 18, 2014
 Improved memory settings. Especially in R 2.15.1 and 2.15.2 on 32bit 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: https://github.com/klutometis/roxygen/pull/112 and A. Alfons's pull request: https://github.com/klutometis/roxygen/pull/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()
v0.85  Jul 18, 2013
 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.