R Shiny - Getting your data/analysis onto the web with Shiny apps.

A few years ago a I worked in a lab that was spending a lot of money using commercial statistical software to analyse Phytoplankton physiological data collected with a PAM and a group of PhD students, including me, decided that we could do the same analysis using the free and open statistical programming language R. We produced a set of functions to do all of the analysis needed by the team but after a while we realised that people were not using them as they weren't comfortable with the command line or with R. Therefore we set about building a simple Graphical User Interface designed specifically to use our R analysis tools using a Shiny app. Here are a few notes on how to get started in Shiny and a link to the PAM Light Curve analyser we built.

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eReefs Satellite Data Workshop - Townsville

Today I'm teaching at the first Bureau of Meteorology eReefs satellite data training workshop in Townsville, QLD. I've spent the last week or so preparing and putting together a sensible series of short lessons and I thought i'd share some of my thoughts on the prep.

Townsville Reef HQ
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Migrating to GitHub and Jekyll

I used to host this site on Weebly as it's pretty much set and forget website hosting, but since i've been using git and markdown more and more in my daily work I've decided to move to GitHub and Jekyll.

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How to calibrate a Turner Fluorometer for phytoplankton Chlorophyll a

Chlorophyll a (chl) measurements are a useful estimate of algal biomass and have been used extensively for decades. Turner designs (http://www.turnerdesigns.com/ fluorometers are used extensively to quantify chl as they are fast, reliable, and relatively cheap. Nevertheless, errors can be introduced if the fluorometer isn't calibrated with a commercially available chlorophyll a standard (e.g. crystallised Chlorophyll a from Anacystis nidulans algae from Sigma Chemical Company) regularly. The procedure described here is appropriate for algal chl in the marine environment. Scientists who employ this or other methods to measure pigments should make themselves aware of the issues that surround fluorescence based techniques and make appropriate decisions about the use of this technology for their application based on the scientific requirements and constraints of their individual programs.

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