Difference between revisions of "Option dialog"

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To open the [[option dialog|options dialog]], choose '''file''' and '''options...''' in the menu.
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[[File:open_options_dialogue.jpg|600px]]
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The dialog reveals several tabs discussed below.
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== general ==
 
== general ==
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[[File:options_dialogue_general.jpg]]
  
 
* enable anti-aliasing: specifies whether anti-aliasing shall be used (recommended)
 
* enable anti-aliasing: specifies whether anti-aliasing shall be used (recommended)
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== R - connection ==
 
== R - connection ==
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To connect with R you have to tell visone where your R is installed. You do this on tab '''R-connection'' in the [[option dialog|options dialog]]
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'''Important note: Due to recent changes in R and/or Rserve the connection will not be usable with the current R versions (> 2.13). This problem is limited to Windows and Macintosh. So please ensure that your R version is not later than 2.13.'''
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To get the latest R version that works with Rserve, follow the download links on http://www.r-project.org/ for your operating system (e.g. Windows or MacOS) and choose "Previous Versions" at the download site (2.13.2 is what you want).
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[[File:options_dialogue_Rconnection.jpg]]
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If you are working on a '''Windows''' system:
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* check box "use Rserve" and paste the path to file "Rserve.exe" (normally <code>C:\Program Files\R\R-2.13.1\bin\i386</code>, [[Installation_(tutorial)#Rserve_installation|see]]) in "path to R/Rserve dir"
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* paste the path where your libraries are installed or should be installed (normally <code>C:\Users\'yourName'\Documents\Rnwin-library\2.13\Rserve</code>) in "library path"
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If you are working on a '''Linux''' or '''MacOS''', try not to touch anything.
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If this does not work for you, configure the following options:
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* "use R in system path" - use this option if you have a regular R installation on a Linux or MacOS and the binary is in the path
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* "path to R/Rserve dir" - if the first option does not work for you (or you want to start a specific R installation) give the path to the executable here (the directory where the executable "R" (all other) file is located)
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===installation===
 
===installation===
 
We assume that you have an [http://www.r-project.org R] installation running (install the latest version fitting to your system from the link).
 
We assume that you have an [http://www.r-project.org R] installation running (install the latest version fitting to your system from the link).
 
For a connection between visone and R we additionally need the RServe packages.
 
For a connection between visone and R we additionally need the RServe packages.
 
You can install this package directly from R:
 
You can install this package directly from R:
* start an R console (the R GUI under windows, or type "R" on a terminal in Linux/MacOS)
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* start an R console (the R GUI under Windows or MacOS, or execute the command "R" in a terminal in Linux/MacOS)
* in the R console run the command: <code>install.packages("Rserve", dependencies=T)</code>
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* in the R console run the command:  
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    install.packages("Rserve", dependencies=T)
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    install.packages("xtable", dependencies=T)
 
* make sure the installation completed successfully
 
* make sure the installation completed successfully
 
* you can close R (i.e. by running the command <code>q()</code>, no need to save anything)
 
* you can close R (i.e. by running the command <code>q()</code>, no need to save anything)
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On '''Windows''', it is mostly necessary to copy file ''Rserve.exe'' from library folder ''Rserve'' to the folder that contains file ''R.dll''. If you were using the standard settings during your R installation, you should find file ''Rserve.exe'' in
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<code>C:\Users\'yourName'\Documents\Rnwin-library\2.13\Rserve</code>
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and file ''R.dll'' in
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<code>C:\Program Files\R\R-2.13.1\bin\i386</code>
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Now, your R should be ready for visone.
 
Now, your R should be ready for visone.
===basic connection properties===
 
Here you tell visone where your R installation resides.
 
On some systems this is not problematic, sometimes you have to give the exact place where R is installed.
 
If you try this on a Linux or MacOS, try not to touch anything.
 
If this does not work for you, configure the following options:
 
  
* "use R in system path" - use this option if you have a regular R installation on a Linux or MacOS and the binary is in the path
 
* "path to R/Rserve dir" - if the first option does not work for you (or you want to start a specific R installation) give the path to the executable here (the directory where the executable "RServe.exe" (Windows) or "R" (all other) file is located)
 
* "use Rserve" - if you are on a windows system, R needs to be started using a specific command, in this case check this box and give the path to the "Rserve.exe" to the option above
 
Sometimes it is necessary to copy the file "Rserve.exe" from the library section (i.e. <code>C:\Users\Peter\Documents\R</code>) to the bin section (i.e. <code>C:\Program Files\R\R-11.1\bin</code>) of your R installation.
 
 
===library configuration===
 
===library configuration===
 
In some cases R has a problem to find its libraries when started from visone. If you experience problems with library installation, i.e. visone connects, but cannot install
 
In some cases R has a problem to find its libraries when started from visone. If you experience problems with library installation, i.e. visone connects, but cannot install
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This is also an option to have a unique place where all the visone installed R libraries will reside.
 
This is also an option to have a unique place where all the visone installed R libraries will reside.
 
The option is  
 
The option is  
* "library path" - paste the path were your libraries are installed or should be installed. Use "NULL" for default (system) path.
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* "library path" - paste the path where your libraries are installed or should be installed. Use "NULL" for default (system) path.
  
 
If you change the library path from its default value, remind to use this location when [[R_console_tab#console|installing or loading]] your own libraries.
 
If you change the library path from its default value, remind to use this location when [[R_console_tab#console|installing or loading]] your own libraries.
  
===start your own R===
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===start your own R (needed on MacOS)===
 
If you're planning to start R on a remote machine or the other options do not work for you, you can run your own instance of R and have visone connect to it:
 
If you're planning to start R on a remote machine or the other options do not work for you, you can run your own instance of R and have visone connect to it:
 
* "dont't start R, but use"  - check this if you would like visone to use an R instance started by you
 
* "dont't start R, but use"  - check this if you would like visone to use an R instance started by you
* "server or ip" - give the name of the server or its ip adress
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* "server or ip" - give the name of the server or its ip adress (no need to change anything here)
* "port" - the port visone should connect to
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* "port" - the port visone should connect to (no need to change anything here)
In case you have trouble connecting, you can always start your own R-session.
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In case you have trouble connecting, you can always start your own R-session.
To do this, start the usual R console, make sure your completed the [RServe_Installation RServe-Installation] and run:
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On MacOS this is currently the only way to establish the connection: check the "dont't start R, but use" option in the dialog and start your own R-session before connecting to it in visone.
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To do this, start the usual R console, make sure you completed the RServe installation and run:
  
 
   library(Rserve)
 
   library(Rserve)
   Rserve()
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   Rserve(args="--vanilla")
  
  
 
Learn more about R - especially RSiena and some more on the connection options in a
 
Learn more about R - especially RSiena and some more on the connection options in a
 
[http://visone.info/lib/exe/fetch.php?media=docs:visonesiena_man.pdf short guide on how to use Rsiena from within visone].
 
[http://visone.info/lib/exe/fetch.php?media=docs:visonesiena_man.pdf short guide on how to use Rsiena from within visone].

Latest revision as of 15:24, 19 July 2012

To open the options dialog, choose file and options... in the menu.

Open options dialogue.jpg

The dialog reveals several tabs discussed below.

general

Options dialogue general.jpg

  • enable anti-aliasing: specifies whether anti-aliasing shall be used (recommended)
  • paint nodes above links: specifies whether nodes shall be painted above links (recommended)
  • multi-link distance: specifies the distance between multi-links
  • decimal places for numbers: specifies how many decimal places to display


background

Background settings apply to all opened visone tabs.

  • background color: sets the background color
  • line color: sets the color of contour lines and their labels
  • show scale values: specifies whether contour line labels shall be displayed

As an example, contour lines are used in a centrality layout.


R - connection

To connect with R you have to tell visone where your R is installed. You do this on tab 'R-connection in the options dialog

Important note: Due to recent changes in R and/or Rserve the connection will not be usable with the current R versions (> 2.13). This problem is limited to Windows and Macintosh. So please ensure that your R version is not later than 2.13. To get the latest R version that works with Rserve, follow the download links on http://www.r-project.org/ for your operating system (e.g. Windows or MacOS) and choose "Previous Versions" at the download site (2.13.2 is what you want).


Options dialogue Rconnection.jpg

If you are working on a Windows system:

  • check box "use Rserve" and paste the path to file "Rserve.exe" (normally C:\Program Files\R\R-2.13.1\bin\i386, see) in "path to R/Rserve dir"
  • paste the path where your libraries are installed or should be installed (normally C:\Users\'yourName'\Documents\Rnwin-library\2.13\Rserve) in "library path"

If you are working on a Linux or MacOS, try not to touch anything. If this does not work for you, configure the following options:

  • "use R in system path" - use this option if you have a regular R installation on a Linux or MacOS and the binary is in the path
  • "path to R/Rserve dir" - if the first option does not work for you (or you want to start a specific R installation) give the path to the executable here (the directory where the executable "R" (all other) file is located)


installation

We assume that you have an R installation running (install the latest version fitting to your system from the link). For a connection between visone and R we additionally need the RServe packages. You can install this package directly from R:

  • start an R console (the R GUI under Windows or MacOS, or execute the command "R" in a terminal in Linux/MacOS)
  • in the R console run the command:
   install.packages("Rserve", dependencies=T)
   install.packages("xtable", dependencies=T)
  • make sure the installation completed successfully
  • you can close R (i.e. by running the command q(), no need to save anything)

On Windows, it is mostly necessary to copy file Rserve.exe from library folder Rserve to the folder that contains file R.dll. If you were using the standard settings during your R installation, you should find file Rserve.exe in

C:\Users\'yourName'\Documents\Rnwin-library\2.13\Rserve

and file R.dll in

C:\Program Files\R\R-2.13.1\bin\i386

Now, your R should be ready for visone.

library configuration

In some cases R has a problem to find its libraries when started from visone. If you experience problems with library installation, i.e. visone connects, but cannot install libraries or send graphs to R, you can configure the location of your libraries here. This is also an option to have a unique place where all the visone installed R libraries will reside. The option is

  • "library path" - paste the path where your libraries are installed or should be installed. Use "NULL" for default (system) path.

If you change the library path from its default value, remind to use this location when installing or loading your own libraries.

start your own R (needed on MacOS)

If you're planning to start R on a remote machine or the other options do not work for you, you can run your own instance of R and have visone connect to it:

  • "dont't start R, but use" - check this if you would like visone to use an R instance started by you
  • "server or ip" - give the name of the server or its ip adress (no need to change anything here)
  • "port" - the port visone should connect to (no need to change anything here)

In case you have trouble connecting, you can always start your own R-session. On MacOS this is currently the only way to establish the connection: check the "dont't start R, but use" option in the dialog and start your own R-session before connecting to it in visone. To do this, start the usual R console, make sure you completed the RServe installation and run:

 library(Rserve)
 Rserve(args="--vanilla")


Learn more about R - especially RSiena and some more on the connection options in a short guide on how to use Rsiena from within visone.