Merge branch 'development' for 0.8.4

Author: boutinb

Docs/development/jasp-building-guide.md

@@ -24,7 +24,7 @@ JASP depends on:
  - [boost](http://boost.org)
  - [libarchive](http://libarchive.org/)
  - [zlib](http://zlib.net/)
- 
+
 Links to specific versions for each platform are provided below.
 
 Windows
@@ -33,7 +33,7 @@ Windows
 Building JASP under windows is the most temperamental, and the versions listed here are known to work; slight variations on these numbers probably won't work.
 
  - [Qt 5.2.1 win64 GCC 4.8.2](https://static.jasp-stats.org/development/x64-Qt-5.2.1+QtCreator-3.0.1-(gcc-4.8.2-seh).7z)
- - [R 3.3.3 win64](https://static.jasp-stats.org/development/R3.3%20Win%20(2017-04-06).zip)
+ - [R 3.3.3 win64](https://static.jasp-stats.org/development/R3.3%20Win%20JASP%200.8.4.zip)
  - [boost 1.64.0](https://static.jasp-stats.org/development/boost_1_64_0.zip)
  - [boost 1.64.0 binaries, libarchive binaries](https://static.jasp-stats.org/development/Additional%20Binary%20Deps%20Win64%20for%20JASP%20(2017-06-06).zip)
 
@@ -56,17 +56,17 @@ The directory structure should be as follows:
 		- libarchive.dll.a
 		- libarchive.dll
 
- 
+
 Mac OS X
 --------
+To build JASP on mac you need to clone the JASP repository and download the following five packages:
 
- - [R 3.3.3](https://static.jasp-stats.org/development/R3.3%20OSX%20(2017-04-06).zip)
- - [boost 1.64.0](https://static.jasp-stats.org/development/boost_1_64_0.zip)
- - [boost 1.64.0 binaries, libarchive binaries](https://static.jasp-stats.org/development/Additional%20Binary%20Deps%20OSX%20for%20JASP%20(2017-06-06).zip)
-
-XCode: Qt on OS X relies on XCode to function, you can install this through the App Store. It's easiest if you install this, run it, accept the license agreement, and then close it down before installing Qt.
-
-Qt: building JASP on OS X is pretty robust, and most versions work. We currently use 5.4.0, but newer versions will probably work too. You can download it from [here](https://qt-project.org/downloads).
+ 0. Clone the JASP repository
+ 1. [XCode](https://developer.apple.com/xcode/) Easiest would be via the App Store.
+ 2. [Qt 5.4.0](https://download.qt.io/archive/qt/) Newer version not supported yet.
+ 3. [R 3.3.3](https://static.jasp-stats.org/development/R3.3%20OSX%20JASP%200.8.3.zip) This contains R and the packages
+ 4. [boost 1.64.0](https://static.jasp-stats.org/development/boost_1_64_0.zip)
+ 5. [boost 1.64.0 binaries, libarchive binaries](https://static.jasp-stats.org/development/Additional%20Binary%20Deps%20OSX%20for%20JASP%20(2017-06-06).zip)
 
 The directory structure should be as follows:
 
@@ -80,6 +80,17 @@ The directory structure should be as follows:
 		- libarchive.a
 		- libz.a
 
+ 0. **Clone** the JASP repository into a folder of your choice. Our default choice is *~/desktop/JASP/* and cloning results in the creating of *~/desktop/JASP/jasp-desktop*.
+ 1. **XCode**: Qt on OS X relies on XCode to function, you can install this through the App Store. It's easiest if you install this, run it, accept the license agreement, and then close it down before installing Qt.
+ 2. **Qt**: building JASP on OS X is pretty robust, but for the moment we're restricted to QT 5.4. We will upgrade to a newer version soon. **Note**: *For xcode 8 and above, to accept the license, Qt (v5.4) tries to find xcrun instead of xcodebuild, and the following has to be done,*
+- Open the file: *Qt_install_folder/5.4/clang_64/mkspecs/features/mac/default_pre.prf*
+- Replace the line *isEmpty($$list($$system("/usr/bin/xcrun -find xcrun 2>/dev/null")))* by  *isEmpty($$list($$system("/usr/bin/xcrun -find xcodebuild 2>/dev/null")))*
+ 3. **R 3.3.3**: Create the folder */Frameworks* in the directory of your choice in step 0. For our default choice this results in *~/desktop/JASP/Frameworks/* first and subsequently *~/desktop/JASP/Frameworks/R.frameworks*.
+ 4. **boost 1.64.0**: Unzip these files in the JASP folder. In our case, this results in *~/desktop/JASP/boost_1_64_0/*
+ 5. **boost 1.64.0 binaries, libarchive binaries**: We're almost there! Fire up QT and try to build JASP. QT will automatically create a */build-JASP-....* directory. In our case this leads to  *~/desktop/JASP/build-JASP-Desktop_Qt_5_5_1_clang_64bit-Debug*. QT will stop building JASP as it requires additional files. Thus, unzip the **boost 1.64.0 binaries, libarchive binaries** files and put them into the */build-JASP-....* directory that Qt created.
+ 6. Build JASP again from Qt. The first build might take a while, but after the first time it'll go very smoothly.
+
+
 Linux
 -----
 
@@ -110,13 +121,13 @@ Under Fedora, you need these packages:
  - qt5-qtwebkit-devel
  - boost-devel
  - libarchive-devel
- 
+
 And (under fedora only), in R (started as root so packages are installed systemwide), you need to install:
 
 ```
 install.packages(c("Rcpp","RInside"))
 ```
- 
+
 Finally, under Fedora only, you need to create a symlink so that R is found:
 
 ```
@@ -135,7 +146,7 @@ In order to run, you will need (Ubuntu and alike):
  - r-cran-logspline *
  - r-cran-hypergeo *
  - r-cran-rjson
- 
+
 Those marked with asterisks are available from Jonathon's PPA.
 
 ### Fedora
@@ -144,5 +155,3 @@ It works under Fedora, if you install these R packages manually in R:
 ```
 install.packages(c("BayesFactor","lme4","afex","car","effects","logspline","hypergeo","rjson"))
 ```
-
-

JASP-Common/analysis.cpp

@@ -28,9 +28,10 @@ using namespace boost::uuids;
 using namespace boost;
 using namespace std;
 
-Analysis::Analysis(int id, string name, Options *options, const Version &version, bool autorun, bool usedata)
+Analysis::Analysis(int id, string module, string name, Options *options, const Version &version, bool autorun, bool usedata)
 {
 	_id = id;
+	_module = module;
 	_name = name;
 	_options = options;
 	_autorun = autorun;
@@ -131,6 +132,7 @@ Json::Value Analysis::asJSON() const
 
 	analysisAsJson["id"] = _id;
 	analysisAsJson["name"] = _name;
+	analysisAsJson["module"] = _module;
 	analysisAsJson["progress"] = _progress;
 	analysisAsJson["version"] = _version.asString();
 	analysisAsJson["results"] = _results;
@@ -214,6 +216,11 @@ const string &Analysis::name() const
 	return _name;
 }
 
+const string &Analysis::module() const
+{
+	return _module;
+}
+
 int Analysis::id() const
 {
 	return _id;

JASP-Common/analysis.h

@@ -31,7 +31,7 @@ class Analysis
 
 	enum Status { Empty, Initing, Inited, InitedAndWaiting, Running, Complete, Aborting, Aborted, Error, SaveImg, Exception };
 
-	Analysis(int id, std::string name, Options *options, const Version &version, bool isAutorun = true, bool usedata = true);
+	Analysis(int id, std::string module, std::string name, Options *options, const Version &version, bool isAutorun = true, bool usedata = true);
 	virtual ~Analysis();
 
 	Options *options() const;
@@ -51,6 +51,7 @@ class Analysis
 	Json::Value asJSON() const;
 
 	const std::string &name() const;
+	const std::string &module() const;
 	int id() const;
 	bool isAutorun() const;
 	bool useData() const;
@@ -96,6 +97,7 @@ class Analysis
 private:
 
 	std::string _name;
+	std::string _module;
 	int _id;
 	bool _autorun;
 	bool _usedata;

JASP-Common/analysisloader.cpp

@@ -27,7 +27,7 @@
 using namespace std;
 using namespace boost;
 
-Analysis *AnalysisLoader::load(int id, string analysisName, const Version &version, Json::Value *data)
+Analysis *AnalysisLoader::load(int id, string moduleName, string analysisName, const Version &version, Json::Value *data)
 {
 	Options *options = new Options();
 
@@ -54,8 +54,8 @@ Analysis *AnalysisLoader::load(int id, string analysisName, const Version &versi
 
 		file.close();
 
-		return new Analysis(id, analysisName, options, version, autorun, usedata);
+		return new Analysis(id, moduleName, analysisName, options, version, autorun, usedata);
 	}
 
-	throw runtime_error("Could not access analysis definition.");
+	throw runtime_error(analysisName + " does not exist in your JASP version.");
 }

JASP-Common/analysisloader.h

@@ -25,7 +25,7 @@ class AnalysisLoader
 {
 public:
 
-	static Analysis *load(int id, std::string analysisName, const Version& version, Json::Value* data = NULL);
+	static Analysis *load(int id, std::string moduleName, std::string analysisName, const Version& version, Json::Value* data = NULL);
 
 };
 

JASP-Common/appinfo.cpp

@@ -17,7 +17,7 @@
 
 #include "appinfo.h"
 
-const Version AppInfo::version = Version(0, 8, 3, 256);
+const Version AppInfo::version = Version(0, 8, 4, 255);
 const std::string AppInfo::name = "JASP";
 const std::string AppInfo::builddate = __DATE__ " " __TIME__ " (Netherlands)" ;
 

JASP-Common/column.cpp

@@ -1187,9 +1187,12 @@ Column::Doubles::DoublesStruct()
 
 Column *Column::DoublesStruct::getParent() const
 {
-	// Apparently there was a good reason to get the parent in this weird way.
-	// If I try to add a private _parent (initialized with the column),
-	// the engine crashes when it tries to get the dataset in the shared memory...
+	// This code seems quite weird... but this is a technique to get the address of the parent object from
+	// a member. We could have used offsetof function though.
+	// We cannot give in the constructor of DoublesStruct or IntsStruct the pointer to the parent object (the column):
+	// we are here in the shared memory, this means this object cannot contain pointer pointing to the process space.
+	// Even if the Column object is also in the shared memory, it is mapped in the process space so that the Column pointer
+	// still points to the process space.
 	Column *column = (Column*) NULL;
 	char* intsAddress = (char*)&column->AsDoubles;
 	char* baseAddress = (char*)column;

JASP-Common/ipcchannel.cpp

@@ -31,7 +31,7 @@ IPCChannel::IPCChannel(std::string name, int channelNumber, bool isSlave)
 	_channelNumber = channelNumber;
 	_isSlave = isSlave;
 
-	_memory = new interprocess::managed_shared_memory(interprocess::open_or_create, name.c_str(), 4*1024*1024);
+	_memory = new interprocess::managed_shared_memory(interprocess::open_or_create, name.c_str(), 8*1024*1024);
 	tempFiles_addShmemFileName(name);
 
 	stringstream mutexInName;

JASP-Desktop/JASP-Desktop.pri

@@ -55,6 +55,7 @@ SOURCES += $$PWD/main.cpp \
         $$PWD/analysisforms/correlationpartialform.cpp \
         $$PWD/ribbons/ribbonwidget.cpp \
         $$PWD/ribbons/ribbonsem.cpp \
+        $$PWD/ribbons/ribbonnetworkanalysis.cpp \
         $$PWD/ribbons/ribbonanalysis.cpp \
         $$PWD/ribbons/ribbonhome.cpp \
         $$PWD/widgets/boundtextedit.cpp \
@@ -181,6 +182,7 @@ SOURCES += $$PWD/main.cpp \
         $$PWD/analysisforms/SummaryStatistics/summarystatsbinomialtestbayesianform.cpp \
         $$PWD/analysisforms/SummaryStatistics/summarystatsregressionlinearbayesianform.cpp \
         $$PWD/analysisforms/SummaryStatistics/summarystatscorrelationbayesianpairsform.cpp \
+        $$PWD/analysisforms/Network/networkanalysisform.cpp \
         $$PWD/analysisforms/R11tLearn/r11tlearnform.cpp \
 		$$PWD/simplecrypt.cpp \
 		$$PWD/importers/convertedstringcontainer.cpp \
@@ -190,7 +192,10 @@ SOURCES += $$PWD/main.cpp \
 		$$PWD/importers/csvimportcolumn.cpp \
 		$$PWD/preferencesdialog.cpp \
     $$PWD/analysisforms/regressionlogisticform.cpp \
-    $$PWD/analysisforms/multinomialtestform.cpp
+    $$PWD/analysisforms/multinomialtestform.cpp \
+    $$PWD/ribbons/ribbonmeta_analysis.cpp \
+    $$PWD/analysisforms/classicalmetaanalysisform.cpp \
+    $$PWD/module.cpp
 
 HEADERS  += \
         $$PWD/aboutdialog.h \
@@ -250,6 +255,7 @@ HEADERS  += \
         $$PWD/analysisforms/correlationpartialform.h \
         $$PWD/ribbons/ribbonwidget.h \
         $$PWD/ribbons/ribbonsem.h \
+        $$PWD/ribbons/ribbonnetworkanalysis.h \
         $$PWD/ribbons/ribbonanalysis.h \
         $$PWD/ribbons/ribbonhome.h \
         $$PWD/widgets/boundtextedit.h \
@@ -375,6 +381,7 @@ HEADERS  += \
         $$PWD/analysisforms/SummaryStatistics/summarystatsregressionlinearbayesianform.h \
         $$PWD/analysisforms/SummaryStatistics/summarystatscorrelationbayesianpairsform.h \
         $$PWD/analysisforms/R11tLearn/r11tlearnform.h \
+        $$PWD/analysisforms/Network/networkanalysisform.h \
 		$$PWD/simplecrypt.h \
 		$$PWD/simplecryptkey.h \
 		$$PWD/importers/convertedstringcontainer.h \
@@ -395,7 +402,10 @@ HEADERS  += \
 		$$PWD/importers/ods/odsxmlhandler.h \
 		$$PWD/importers/ods/odsxmlmanifesthandler.h \
     $$PWD/analysisforms/regressionlogisticform.h \
-    $$PWD/analysisforms/multinomialtestform.h
+    $$PWD/analysisforms/multinomialtestform.h \
+    $$PWD/ribbons/ribbonmeta_analysis.h \
+    $$PWD/analysisforms/classicalmetaanalysisform.h \
+    $$PWD/module.h
 
 FORMS += \
         $$PWD/analysisforms/anovabayesianform.ui \
@@ -422,6 +432,7 @@ FORMS += \
         $$PWD/ribbons/ribbonhome.ui \
         $$PWD/ribbons/ribbonsem.ui \
         $$PWD/ribbons/ribbonanalysis.ui \
+        $$PWD/ribbons/ribbonnetworkanalysis.ui \
         $$PWD/analysisforms/ttestbayesianindependentsamplesform.ui \
         $$PWD/analysisforms/ttestbayesianpairedsamplesform.ui \
         $$PWD/analysisforms/ancovabayesianform.ui \
@@ -438,6 +449,7 @@ FORMS += \
         $$PWD/analysisforms/binomialtestbayesianform.ui \
         $$PWD/analysisforms/bffromtform.ui \
         $$PWD/ribbons/ribbonsummarystatistics.ui \
+        $$PWD/ribbons/ribbonmeta_analysis.ui \
         $$PWD/variableswidget.ui \
         $$PWD/backstage/authwidget.ui\
         $$PWD/aboutdialog.ui \
@@ -454,8 +466,10 @@ FORMS += \
         $$PWD/analysisforms/SummaryStatistics/summarystatsregressionlinearbayesianform.ui \
         $$PWD/analysisforms/SummaryStatistics/summarystatscorrelationbayesianpairsform.ui \
         $$PWD/analysisforms/R11tLearn/r11tlearnform.ui \
+	$$PWD/analysisforms/Network/networkanalysisform.ui \
     $$PWD/analysisforms/regressionlogisticform.ui \
-    $$PWD/analysisforms/multinomialtestform.ui
+    $$PWD/analysisforms/multinomialtestform.ui \
+    $$PWD/analysisforms/classicalmetaanalysisform.ui
 
 RESOURCES += \
         $$PWD/backstage/backstage.qrc \

JASP-Desktop/analyses.cpp

@@ -44,17 +44,17 @@ Analyses::Analyses()
 	//timer->start();
 }
 
-Analysis *Analyses::create(const QString &name)
+Analysis *Analyses::create(const QString &module, const QString &name)
 {
-	return create(name, _nextId++, AppInfo::version, NULL, Analysis::Empty);
+	return create(module, name, _nextId++, AppInfo::version, NULL, Analysis::Empty);
 }
 
-Analysis *Analyses::create(const QString &name, int id, const Version &version, Json::Value *options, Analysis::Status status)
+Analysis *Analyses::create(const QString &module, const QString &name, int id, const Version &version, Json::Value *options, Analysis::Status status)
 {
 	if (id >= _nextId)
 		_nextId = id + 1;
 
-	Analysis *analysis = AnalysisLoader::load(id, name.toStdString(), version, options);
+	Analysis *analysis = AnalysisLoader::load(id, module.toStdString(), name.toStdString(), version, options);
 	analysis->setStatus(status);
 
 //	if (options == NULL)