Assets 2

WELCOME TO THE WONDERFUL WORLD OF PAM!

This is a project that allows users to import their PAM fluorometer data into the R programming language and calculate photosynthetic parameters as per Platt et al 1980 and Ralph et al

This code is brought to you by Rob Johnson, Simon Reeves, Shihong Lee, and Emma Flukes. We are PhD students at the University of Tasmania and we were fed up with the ridiculous amount of time it was taking to analyse PAM Rapid Light Curves using clunky and expensive stats software (copy... paste... copy... paste... SPSS... boooo!). So, we built the PAM Processor! using the free and open stats scripting language R and the web application tool Shiny.

At the moment this is release v1.0 of the PAM Processor! as of June 2015.

For Installation and running instructions please read the INSTALL.md document.

Feedback is appreciated:

Robert Johnson's homepage: http://www.robtheoceanographer.com

Email: robtheoceanographer@gmail.com

Install guide:

  • Download the latest release from github: https://github.com/RobTheOceanographer/pam_in_R/releases
  • The current PAM shiny app is in the "pam_app" folder.
  • Ensure that your R and RStudio install is up to date.
  • Install the following packages that the pam app depends on:
    install.packages("shiny") and install.packages("functional")

Running:

  • Start RStudio.
  • Load the shiny library: library(shiny)
  • Change the working directory to the folder you have the app stored in. e.g. setwd("~/PAM_in_R/") (N.B. this is the folder that contains the pam_app folder.)
  • Run the app using runApp("pam_app")