IsoplotRgui

Graphical User Interface to the IsoplotR R package for radiometric geochronology.

Offline installation and use

1. You must have R installed on your system (see http://r-project.org) as well as the devtools and shiny packages. These can be installed by typing the following code at the R command line prompt:

install.packages('devtools')
install.packages('shiny')

2. The latest version of IsoplotR and IsoplotRgui can both be installed from GitHub with the following commands:

library(devtools)
install_github('pvermees/IsoplotR')
install_github('pvermees/IsoplotRgui')

Please note that the latest stable version of IsoplotR is also available from CRAN at https://cran.r-project.org/package=IsoplotR

3. Once all these above packages have been installed, you can run the browser-based graphical user interface by typing:

library(IsoplotRgui)
IsoplotR()

at the command prompt. Alternatively, the program can also be accessed online via the IsoplotR website at http://isoplotr.london-geochron.com, or from your own server as discussed in the next section.

Setting up your own online mirror

The following instructions assume that you have access to a Linux server with git and nginx installed on it.

1. Install R and shiny-server using the instructions provided at https://www.rstudio.com/products/shiny/download-server

2. Save the following code in a file called /srv/shiny-server/IsoplotR.sh:

# i. update IsoplotR from GitHub:
sudo su - -c "R -e \"devtools::install_github('pvermees/IsoplotR',force=TRUE)\""

# ii. clone IsoplotRgui from GitHub to /tmp:
cd /tmp
git clone https://github.com/pvermees/IsoplotRgui

# iii. copy the app to the shiny-server directory:
cd IsoplotRgui/inst/shiny-examples/myapp
sudo cp -R www /srv/shiny-server/IsoplotR
sudo cp -R server.R /srv/shiny-server/IsoplotR

# iv. clean up and restart shiny-server
sudo rm -rf /tmp/IsoplotRgui
sudo systemctl restart shiny-server

3. Run the IsoplotR.sh script by entering the following code at the command prompt:

cd /srv/shiny-server
mkdir IsoplotR
chmod 755 IsoplotR.sh
./IsoplotR.sh

IsoplotR should now be available at http://localhost:3838/IsoplotR. You will need to set up port forwarding to release it over the Internet.

4. To ensure that IsoplotR is up-to-date, it is a good idea to set up auto-updating. One way to do this is with crontab. First enter crontab -e at the command prompt and then enter:

# Minute    Hour   Day of Month    Month            Day of Week           Command
# (0-59)   (0-23)    (1-31)    (1-12 or Jan-Dec) (0-6 or Sun-Sat)
    0        0         *             *                  0        /srv/shiny-server/IsoplotR.sh

which will automatically synchronise IsoplotR and IsoplotRgui with GitHub on every Sunday.

Further information

See http://isoplotr.london-geochron.com

Author

Pieter Vermeesch

License

This project is licensed under the GPL-3 License