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Unconstrained ordinations in JUICE+R

ordijuice:install

How to install:

Are you new to JUICE and R?

  1. Download and install the latest version of the JUICE program. To learn more about JUICE, visit JUICE website.
    1. If you install JUICE for the first time, you need to manually update the program to the latest version (after installation, start JUICE, and in the menu go to Help > Quick JUICE Update, and follow the automatic update procedure).
    2. There have been changes in the way how does JUICE links to R. Tn the 7.0 version of JUICE, the data were exported to R using the same folder at which Rgui.exe is located (in Program Files folder), while in 7.1 version of JUICE, there is a dedicated folder for this purpose in c:/users/your_username/JUICE, where “your_username” is your home folder.
  2. Download and install R-project. Note: the function is optimized for R version 3.6.1, and does not work in the R 4.0.0 or higher. To learn more about R, visit R-project website.
  3. Import and open your data in JUICE (if you don't have any, download training data and import them into JUICE).
  4. in JUICE go to Analysis > Ordinations > R-PROJECT > DCA analysis and
    1. click on folder Script update,
    2. click on Associate R-project with JUICE and set up the path to Rgui.exe file (located usually in C:/Program Files (x86)/R/R-x.xx.xx/bin/Rgui.exe or C:/Program Files/R/R-x.xx.xx/bin/Rgui.exe, where x.xx.xx is the version number of R you are using). Note that you need to associate it with Rgui.exe file, not R.exe file!
    3. click on Update ORDIJUICE script to install necessary R packages (your computer needs to be connected to the Internet). Your screen will indicate that the library is being updated.
    4. If all setting is done correctly, when you open again the ordination wizard and run the ordination, you should see the progress bar announcing the installation of several R libraries. There are several packages to be installed at first (> 70), so please, be patient.
    5. After installing all packages, you should get functional JUICE-R ordination. If, in future, you associate JUICE with a new R-program version, you need to repeat the procedure above.

Are you already working with JUICE and R?

  1. Update JUICE to version >= 7.0.25 (from Help JUICE menu or installing the new JUICE from website).
  2. Install the latest R-program version.
  3. In JUICE go to Analysis > Ordinations > R-PROJECT > DCA analysis and click on Associate R-project with JUICE and set up the path to Rgui.exe file (located usually in C:/Program Files (x86)/R/R-2.11.0/bin/Rgui.exe or C:/Program Files/R/R-x.xx.xx/bin/Rgui.exe). Note that you need to associate it with Rgui.exe file, not R.exe file!
  4. Make sure you have updated all required R packages (in JUICE, go to Analysis > Ordinations > R-PROJECT > DCA analysis > Script update and click on Installation of R libraries button. Your computer needs to be connected to the internet!)
ordijuice/install.txt · Last modified: 2020/07/23 13:11 by david