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Setting up GitHub at UTS
Asked my system admins to install GitHub on my university computer. However I couldn't get it to download any of my existing projects.Â
Changing the "default storage directory" from the default to my user folder fixed it. You can find this setting under Tools -> Options.
Previously the path was some folder inside the application data folder. Now it is:
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How to batch rename .dat to .csv (under Unix)
adapted from http://lab.artlung.com/unix-batch-file-rename/
# change .dat files to .csv for file in *.dat ; do mv $file `echo $file | sed 's/\(.*\.\)dat/\1csv/'` ; done
How to get ProjectTemplate to load your logger data into R automatically.
ProjectTemplate is an R package which helps lay out your R scripts and data in a standardised and well conceived folder structure. The idea is that what each script is for (ie pre-processing, analysis, plotting) will be more obvious both to any colleagues you might like to share your work with, and also more obvious to your future self when you need to revisit the analysis in the future. It seems like a brilliant idea, implemented by experts, and introduced to me by Richard (Xuanlong Ma).
Over the weekend I had a go at putting in some data files from my Queensland field sites. The idea behind ProjectTemplate is that your data files and R libraries are automatically loaded when you load a project's directory, according to the template configuration files which you are free to edit. So first things first, I had to figure out what I need to do to the raw .dat files produced by our Campbell Science loggers so they can be loaded by ProjectTemplate. Our lab usually seems to download .dat files with "Long Headers (TOA5)". In short, to use these you need to: 1. Rename the files to .csv. According to the Campbell Science manual they already are CSV files (and it is unclear to me why they don't have this extension already - if you know of the reason, please let me know). 2. Delete the extra header rows, so that there is only the single row of column names above your data. If you do this, ProjectTemplate will automatically load these files if they're placed in the pre-defined /data/ subfolder.
'Point dendrometers' manufactured by Roman Zweifel in Switzerland. They arrived just last week, and you can see Roman included one that was already assembled. These guys are fixed onto the side of trees to capture growth rates. As the tree grows, the growing trunk will slightly push on the probe. This push is converted into a voltage, which is recorded, so we can monitor how the trunk expands over time.
Studies using these before also record slight shrinkage and swelling of the trunk each 24 hours, as trees use up stored water during the day and replenish at night.Â
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Today I was bench-testing my new down hole pressure logger. Its called the LevelTROLL500, which I think is a funny name. By In-Situ Inc.
I decided to add blue food dye, to help me keep track of the changes in water level in this bucket, as I add water.
When I eventually hang this down a bore in the field, it will allow me to track changes int he groundwater level at a very high resolution. I might even be able to see the groundwater level fall slightly during the day, as the trees suck up water.
L: Eucalyptus fastigata, Southern Highlands, NSW
R: Acacia aneura, Ti Tree, NT
My second log from Queensland arrived today
I've been finishing off my work-day in the lab, making components for sap-flow sensors. I've the goal of making 50 sensors, by which time I should have learnt to make sensors of a decent quality. In these photos you can see the first step, cutting down medical needles to 1cm probe-tips.