Category Archives: R

Install Useful Eclipse Plugins in Bio7 for R, Data Science and Programming

20.10.2017

Beside a massive of amount of R packages and ImageJ plugins Bio7 can be extended with Eclipse plugins useful for data science and programming.

Some of them could also be very useful for R related developments (e.g., to develop R packages or distribute Shiny apps).

Installation of Eclipse Plugins

One  way to install Eclipse plugins is by using the Update Manager in the help menu (Help->Install New Software).

Thus the first step to install a plugin is to open the Update Manager and selecting the category “Eclipse Repository – http://download.eclipse.org/releases/neon” (see screenshot below!)

Another handy way of searching and installing Eclipse plugins is by using the Marketplace Client plugin which must be installed firstly with the Update Manager.

Search for the Marketplace Client (e.g., “marketplace”) plugin to filter, select and install the Marketplace Client.

The following plugins can be installed using either the Marketplace Client or the Update Manager.

Database Remote Files and Shells

EGit

https://marketplace.eclipse.org/content/egit-git-team-provider
The powerful Eclipse Git plugin to connect Bio7 with Git repositories.

TM-Terminal

http://marketplace.eclipse.org/content/tcf-terminals
A true native terminal with SSH,Telnet and Serial line support. Bio7 comes already with a pseudo-terminal but lacks the support of a pty connection and ANSI escape sequences (but can be controlled from a Bio7 API interface). The terminal can also be installed with the Update-manager searching for “tm” (see screenshot below).

Remote System Explorer

https://marketplace.eclipse.org/content/remote-system-explorer-ssh-telnet-ftp-and-dstore-protocols
A plugin to connect Bio7 with SSH, Telnet, FTP and DStore protocols.This plugin work very well with a remote connection and makes it easy to transfer data from a local workspace to a remote server. Remote files can be opened, edited and stored with the available Bio7 editors (e.g., a *.html file with the JavaFX editor – see screenshot below).
Apropos, please use an OpenSSH key for, e.g. a SFTPconnection!). It works great together with the TM-Terminal plugin.

DBWeaver

https://marketplace.eclipse.org/content/dbeaver
“DBeaver is free universal SQL client/database tool for developers and database administrators. It can work with any database server which has JDBC driver.” (source: website DBWeaver)
DBWeaver is a great database tool and plugin for Eclipse and can also be installed into Bio7 to control and edit R database connections.

Scripting Editors with Bio7 interpret support

The following three editors can be used within the current Bio7 process to execute scripts using the Bio7 interface. It is important however to create a language project first to profit from the advanced editor features.

Bio7 will recognize the opened editor type and interpret the current opened script with the embedded script interpreter of Bio7 when using the dedicated toolbar action.

Please use the context menu action “Open with” to open the scripts with the installed editors instead of the default Bio7 editors (Groovy, Jython/Python editors are available by default in Bio7).

Here a video installing and using the JavaScript editor as an general example.

JSDT

https://eclipse.org/webtools/jsdt/
JavaScript editor and development tools. Install with the Update-manager (search for JavaScript – see video above).

PyDev Editor

https://marketplace.eclipse.org/content/pydev-python-ide-eclipse
A very powerful Python editor which can be used to execute Bio7 Jython and Python scripts instead of the Bio7 default editor.
In addition Bio7 can use the PyDev editor to execute scripts running on the Bio7 Java classpath. If you open Jython/Python scripts with the PyDev editor the default Bio7 action will be visible to execute the scripts on the Bio7 classpath.

Groovy Editor

https://github.com/groovy/groovy-eclipse/wiki
(Add site: http://dist.springsource.org/snapshot/GRECLIPSE/e4.7/ to the Update Manager)
A more powerful Groovy editor. Can also be used with the Bio7 classpath if scripts are opened with this editor instead.

General programming editors and extensions

Eclipse CDT

https://marketplace.eclipse.org/content/eclipse-cdt-cc-development-tooling
Powerful C/C++ editor and development tooling.

Arduino C++ IDE:

https://marketplace.eclipse.org/content/arduino-c-ide
A great Arduino extension of the C++ editor of Eclipse. See this video for an introduction. Bio7 embedds some Java libs to communicate with an Arduino (see Bio7 examples).

Photran (comes with PTP)

https://eclipse.org/ptp/
http://www.eclipse.org/photran/
An Integrated Development Environment and Refactoring Tool for Fortran

Julia Editor

https://github.com/JuliaComputing/JuliaDT
A Julia editor in an early stage. But very promising.

Bash Editor

https://marketplace.eclipse.org/content/bash-editor
A bash editor for bash scripts. Perfect for the use with the above linked TM-Terminal and Remote Systems Explorer.

Jeeeyul’s Eclipse Themes

https://marketplace.eclipse.org/content/jeeeyuls-eclipse-themes
To install more themes into Bio7.

pde-tools

https://github.com/jeeeyul/pde-tools#crazy-outline
A plugin which adds clipboard history support and a crazy outline view.

WindowBuilder

https://marketplace.eclipse.org/content/windowbuilder
A very powerful builder for Graphical User Interfaces for SWT, etc.
In Bio7 a wizard is available to create a template for the builder (File->New->Bio7 Java Projects->Bio7 Java Project (WindowBuilder template)).
You can then open this template with the WindowBuilder to create interfaces (e.g., to create R interfaces using the new Bio7 R API). The created interface can be compiled dynamically with Bio7 (compiling the main class) and executed instantly in the current Bio7 process (see screenshot below)

More plugins can be found with the Eclipse Marketplace Client. It depends however how useful the plugins are in the context of Bio7.

 

 

 

Bio7 2.6 for MacOSX Released

19.10.2017

I released a new version of Bio7 for MacOSX.

(Screenshots: Bio7 with Dark theme enabled. Scrollbars are set to “When scrolling” in the preferences.)

For an overview of the new features please consult the release notes of Windows and Linux here:

Installation:

Download and extract the installation file from http://bio7.org.

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition For MacOSX you have to install R and Rserve.

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default MacOSX R library install location has writing permissions! – normally you don’t have to worry about this on MacOSX!).

The special version of Rserve can also be downloaded here:
https://bitbucket.org/maustenfeld/bio7-new/downloads

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

> install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the main menu “Scripts” action:

Scripts->R-Scripts->InstallDefaultRPackages

Bio7 Documentation and Examples

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.

The latest Bio7 examples can be downloaded (download and import as *.zip) from Github here!

 

Bio7 2.6 for Windows and Linux Released

17.10.2017

A new version of Bio7 for Windows and Linux is available. The MacOSX version will be released soon, too.

The application Bio7 is an integrated development environment for ecological modelling, scientific image analysis and statistical analysis. Beside many different tools it contains a complete Graphical User Interface for R.

The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

For  a short overview see this older video.

New Features:

General

  • Improved the dark theme for Bio7 2.6 (see Windows and Linux screenshot below)
  • Improved the default Bio7 theme (see Linux screenshot below)

  • Improved the theming of some Bio7 views (e.g., tables, text editors)
  • Added a new shortcut for Windows and Linux to show or hide the Bio7 main menus  – CTRL(CMD)+2, CTRL(CMD)+3). By default the application frame, toolbar and the status bar can be hidden, too. (see screenshot below with hidden window and menu – set the key shortcuts in the preferences!)
  • Bio7 2.6 is based on Eclipse 4.7.1a
  • Added the ‘Project Explorer’ view to many perspectives and deleted the ‘Navigator’ view in some of the perspectives (the ‘Project Explorer’ view displays errors and warnings and supports pasting of clipboard Java code, etc.)
  • Added a break and interrupt action for the windows shell to end ,e.g., a ssh connection (CTRL+BREAK) or interrupt an ongoing shell process (CTRL+C)
  • Added an API to send commands to the Windows/Linux/MacOSX shell
  • Added SSH for Windows
  • Added the embedded SSH application path to the shell
  • Added a new ‘ImageJ Edit’ perspective to execute ImageJ scripts, macros side by side with the ImageJ-Canvas (see ImageJ section below)
  • Added a easy to use R API for Java/BeanShell/Jython/Groovy/JavaScript to execute R commands or scripts in an extra job (thread)
  • Improved several import/export scripts (now with Groovy) with the new Bio7 R API.
  • Improved the Linux shell (added the default xterm path)
  • The R package install script now works with a native R shell connection.
  • Shiny applications can now be tested from all folders (not only project folder – e.g.; from Git folders)

R Editor

  • Added an action to surround selected code with a “try and catch” skeleton
  • Added an Project view/Navigator view popup action to start a shiny app in a arbitrary folder
  • Added an action to open and insert a hex color in the editor
  • Added a hoover dialog to display and replace selected hex and R colors (see screenshot below)

  • Added an action in the hoover dialog to select hex colors
  • Added an action in the hoover dialog to select default R colors by name (see screenshot below)

  • Added a new database view to the R perspectives to store or apply database profiles and connections

  • Added SSH support for the database view (also for Windows!). Bio7 comes bundled with the latest SSH version of Windows

  • Improved the code completion of the R-Shell
  • Improved the default R package install script for Bio7
  • Restructured the R editor context menu

ImageJ

  • Added a full featured ImageJ macro editor with the following features:
    • Dynamic error detection (grammar derived from the ECMA grammar by Bart Kiers)
    • Toolbar action to execute ImageJ macros
    • Syntax highlightening
    • Editor debugging support (reusing and implementing interfaces and methods from – same keyboard shortcuts)
    • Code completion (with browser help)
    • Code templates (add you own templates)
    • Info popups (text hoover)
    • Outline view (var variables, variables, methods and macros)
    • Automatic closing of braces, parentheses and strings
    • Automatic indention of functions,loops, etc.
    • Code folding
    • Code formatting (based on the Eclipse-javascript-formatter by Sebastian Moran)
    • Resize fonts functions (with Ctrl++ or CMD++, CTRL+- or CMD +-)
    • Font preferences
    • Mark occurences (scope independant)
    • A copy function for the ImageJ forum

  • The ImageJ view menu is now right aligned and foldable to the left
  • Updated ImageJ to version 1.51r
  • Several bugfixes for the ImageJ compatibility

Download and Installation:

Windows:

Just download the *.zip distribution file from http://bio7.org and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.

Linux:

Download and extract the installation file from http://bio7.org.

For Linux you have to install R and Rserve.

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!).

The special version of Rserve can also be downloaded here:

https://bitbucket.org/maustenfeld/bio7-new/downloads

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the main menu “Scripts” action:

Scripts->R-Scripts->InstallDefaultRPackages

Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.

 

 

Bio7 2.5 for MacOSX Released

11.04.2017

A new release of Bio7  for MaxOSX (64-bit) is available.
This release comes with a plethora of new functions for MacOSX and R.


(Screenshot with Bio7 Dark theme enabled and custom font colors of the R editor)

Bio7 2.5 Release Notes

Installation:

Download and extract the installation file from http://bio7.org.

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! Please see this post for a solution (Go to System Preferences>Security & Privacy>General, set ‘Allow Apps etc’ to ‘Anywhere’. Change it back after you download and executed this app.).

In addition For MacOSX you have to install R and Rserve.

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default MacOSX R library install location has writing permissions! – normally you don’t have to worry about this on MacOSX!).

The special version of Rserve can also be downloaded here:
https://bitbucket.org/maustenfeld/bio7-new/downloads

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

The latest Bio7 examples can be downloaded (download and import as *.zip) from Github here!

For more information about the installation and adding  LaTeX, Knitr and rmarkdown support please consult the Bio7 User Guide.

Bio7 2.5 for Windows and Linux Released

07.04.2017

A new release of Bio7 is available for Windows (64-bit) and Linux (64-bit).
The MacOSX version will be released soon, too. This release comes with a plethora of new functions for R.

General

  • Bio7 is now based on Eclipse 4.6.3
  • Redesigned all Bio7 icons and created new icons, too
  • Nearly all icons are now available for high dpi displays
  • Added a dark Theme for Bio7

  • Added the default Eclipse theme as optional to Bio7
  • Added a new action for Linux and MacOSX to download and install Rserve (see Video in R section)
  • Added JavaScript editor support (default opened in text editor but if Eclipse JavaScript editor installed it can be opened and executed in the advanced editor)
  • Added a new action for the execution of JavaScript (and ImageJ macro)
  • JavaScript can be executed in the current opened browser if enabled in the preferences
  • Added JavaScript support to the console

  • Custom views are now entitled with the id of the view
  • Added a new „Document“ perspective for LaTeX, Sweave, knitr and rmarkdown documents
  • Added a new PDF viewer in the JavaFX browser to display PDF’s from LaTeX, knitr, rmarkdown and R plots („Display“)

  • Added options and actions to fullscreen a PDF on different monitors (press the key ‘t’ and the PDF will be centered and the toolbar will be removed)
  • Added several PDF options (scroll to selected page, etc.)
  • Added a new JavaFX browser for *.html and *.pdf files based on PDF.js
  • PDF files can be opened within the Navigator view with a double-click of the mouse device (also popular image types with ImageJ).
  • Added drag and drop support for the browser for *.html and *.pdf files
  • All editor fonts can now be scaled with the key combination ‘Ctlr +’
  • Added new global preferences for the editor fonts
  • Added preferences links for an improved navigation
  • Updated the default scientific Java libraries
  • Implemented a reload of the JavaFX Browser to avoid a cached display
  • Improved the resizing of the Quadgrid (Hexgrid) view
  • Added a new preference to disable the scrollbars of the Quadgrid (Hexgrid) view

R

  • Updated R to 3.3.3 on Windows
  • Added an action to download and install ‘Rserve cooperative mode’  for Linux and MacOSX
  • Improved the speed of the „Load packages“ dialog
  • Improved the speed of the „Install packages“ dialog.
  • Improved the speed of the refresh action in the R-Shell view
  • Added browser preferences to select the browser and the display
  • Added a new toolbar action for Sweave
  • Added an extra view for plots
  • Added the package install dialog as an view
  • Added an option to open a HTML package info for a selected package in the package install view (see video below).

  • Added a preference for a custom Rserve client connection port if you start the Rserve server with a different port
  • Added code completion in the R-Shell view for s3 and s4 methods (see video below)

  • Added an option to automatically open code completion when typing in the R-Shell
  • R-Shell R help now recognizes the selected browser
  • Added several actions to create, built, and test R packages to the context menu of the Navigator view (using the ‘devtools’ package)
  • Added a Shiny test action in the context menu of the Navigator view which opens a browser with the running shiny application (select a project folder with the server and ui files – to stop the server use the interrupt action in the R-Shell console or press ‘Strg c’ in the Console).
  • Improved the transfer of variables and sheet names from the Table view and LibreOffice
  • Improved the display of the R preferences (opening the default preferences structure)

R editor

  • Improved the code completion in general
  • Code completion dialogs are now synchronized with the other dialogs
  • Added code completion for
    • S3 objects (after $)
    • S4 object slots (after @)
    • the library function (library())
    • the data function (data())
  • Added new individual images to the code completion
  • Improved the close parentheses functions
  • Improved the visual appearence of the hoover dialog
  • Corrected the code completion images to match the Outline view images
  • Improved the display of markers
  • Added a popup display for the ‚str‘ function when hoovering over a workspace variable
  • Fonts can now be scaled with the key shortcuts ‘Strg +’
  • Added automatic indention after parentheses (loops, function, etc.)
  • Added preferences for the formatR package
  • Added an formatR action to format editor selections only
  • Added a refactor rename method for a selected scope
  • Added roxygen code completion in comments

  • Added an action to create roxygen templates from selected function, S3, S4, Reference and R6 classes (see video below)

  • In the popup menu added several actions of the devtools package to create, test and install R packages (select a project or regular folder)
  • Added plot preferences to open plot images individually and an option to execute an ImageJ macro after plot creation (e.g. to scale a plot after creation, etc.)
  • Added an ‘Open File’ and ‘Save File’ dialog to create file templates with selected files in the R editor and the R-Shell view (see video)
  • Added a new shortcut to create an assign operator (‘ALT   _’)
  • Added a new shortcut to create a pipe operator (‘CTRL SHIFT M’)
  • Added simple editor templates for S3, S4, Reference and R6 classes
  • Improved the preferences navigation
  • Reorganized some preferences
  • Updated the parser to ANTLR 4.6

R Markdown

  • Improved the R markdown editor
  • Header and R chunks are now displayed in the Outline view
  • Added spell checking to the rmarkdown editor

  • Compiled documents are now displayed in a special custom view of Bio7 if enabled (by default enabled)
  • Added font and color preferences to the editor
  • Added new browser preferences (use of JavaFX webkit browser or system browser) and additional preferences for the control of the output
  • Added preferences to compile the document automatically after a specific time intervall (adjustable in the preferences – see video below)

  • Added code templates for popular markdown commands
  • Added an option to open word documents embedded in a custom view with Word (Windows only)

  • Added a key shortcut for the action to compile markdown documents

LaTeX

  • Improved the compile actions in the Bio7 toolbar (new icon) and removed the popup actions in the Navigator view
  • Added a key shortcut for the compilation
  • By default Latex documents are opened in the new PDF viewer (custom view)
  • Added new Bio7 LaTeX preferences to compile documents easily (without the need to create a LaTeX project with Texclipse)
  • Added new preferences to optional use XeLaTex and cleanup auxiliary files in the project folder
  • Added an option to compile BibTeX along with the *.tex file (several compilation iterations are performed)

ImageJ

  • Updated ImageJ to version1.51m
  • Improved the ImageJ menus to display all ImageJ menus correctly and nested (with key shortcuts and seperators)
  • ImageJ plugins now extend the respective SWT menu analogue to the ImageJ AWT menu.
  • Plugins, scripts and macros are now displayed in their defined menus or submenus.
  • Some popular image types can now be opened (double-click) directly from a Navigator folder (registered as a fake editor type)
  • Added two preferences to define the install location of plugins and macros (e.g external locations for teams).
  • Plugins now contribute to all ImageJ menus (SWT) like it is known from ImageJ
  • Dramatically improved the compatibility for ImageJ plugins (partially AWT)
  • Added a menu option to open images in a nested JavaFX panel (fullscreen on different monitors possible)
  • Addded JavaScript support for ImageJ (default editor is the text editor but a advanced Eclipse JavaScript editor can easily be installed)
  • Added a ImageJ macro wizard action to create ImageJ macros
  • Added an JavaScript wizard action to create a JavaScript file
  • JavaScript and ImageJ macros can now be executed with a toolbar (JavaScript) action.

WorldWind

  • Updated WorldWind to version 2.1
  • Made improvements for the dark theme

Installation:

Windows:

Just download the *.zip distribution file from http://bio7.org and unzip it in your preferred location. Bio7 comes bundled with the latest Java Runtime Environment, R and Rserve distribution and works out of the box.

Linux:

Download and extract the installation file from http://bio7.org.

For Linux you have to install R and Rserve.

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!).

The special version of Rserve can also be downloaded here:
https://bitbucket.org/maustenfeld/bio7-new/downloads

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

For more information please consult the Bio7 User Guide.