Plant Physiology and Ecology
Ecological Society of America's EcoPhys Section site
Look here for technician, graduate, post-doc, and faculty positions in ecophysiology. You can also find information here about the section, and resources related to doing research in the field. Promethius Wiki - Protocols in ecological and environmental plant physiology The name says it all. You can find protocols for measuring plant form and function, and environmental sensing. This is a great place to start if you are trying to nail down a new method or need the skeleton of a protocol for a class. Plants in Action An online plant biology textbook written by some of the best with a section devoted to physiological ecology. Environmental Biophysics This is the web compliment to the text An Introduction to Environmental Biophysics by Gaylon S. Campbell and John M. Norman. They have provided video lectures to accompany the book chapters. plantecophys R package This is an add on package for R by Remko Duursma that fits A-Ci curves. The link is for the PLoSONE paper describing the package, which is available on CRAN so can be installed using standard R syntax [i.e., install.packages("plantecophys")]. Fitting light response curves in R! This is a script I put together that provides a function for fitting photosynthetic light response curves to the standard non-rectangular hyperbola model. Drop in a dataframe of your curves and the names of important columns, and voila. LI-COR Bioscience's YouTube Channel Yes you will find lots of promotional materials here. But, you're also probably using their equipment and videos demonstrating how to do this or that might be useful. fitplc R package A new R package for fitting percent loss of conductivity curves and extracting relevant parameters. Link will take you to the paper in the Journal of Plant Hydraulics describing the package. The package itself is available via CRAN, so you can install it with install.packages("fitplc"). |
Data, visualization, #rstats, and the like.
USDA-NASS QuickStats R package
I haven't gotten the chance to try this out yet and don't want to lose it forever to the forgotten bowels of the internet. Created and maintained by Potterzot on his GitHub page the package offers communication with the QuickStats API from within R. R-graph catalog Exactly what it sounds like. Allows you to filter by the type(s) of figure you want to produce then provides examples with the necessary code to reproduce them (NB using ggplot2). The R graph gallery Same as above, by a different group. Lots of good stuff from bars to 3D to maps. Subtleties of color Are you using stock colors in your visualizations? Yes? Then read this. Another resource on colour, recommended by Hadley Wickham in his ggplot2 book. RStudio keyboard shortcuts I have Googled this too many times. Also worth remembering that a shortlist of the most useful shortcuts is available within RStudio with opt+shift+K (mac) or alt+shift+K (windows). Also, for my reference: opt+shift+R yields the per mille symbol (‰) on a mac. Reproducibility (not a link) This is a growing list, so no universal link. First Noam Ross has compiled a linkfest of reproducibility resources. Ben Bond-Lamberty recently shared slides to a workshop he gave on the topic. Another linkfest, focused on Git and GitHub and curated by Pakillo. Ecological Forecasting Mike Dietze has put together a great set of hands on activities to go along with his class and forthcoming book of the same name. You can download the whole GitHub repo and work through each chapter - as standalone Rmarkdown docs - at your leisure. Environmental computing from U of New South Wales A course-worth (and then some) of material to get anybody in the environmental sciences (broadly interpreted) started using R for data handling, analysis, and visualization. Stop using bar-charts! Just because you can make them easily in Excel (or SPSS, or SigmaPlot) doesn't mean you should. Read this paper to find out why you shouldn't hide your data behind a bar. Where food plants came from and where they've ended up This is an interactive set of graphics put together by folks at the International Center for Tropical Agriculture. To me this is the absolute pinnacle of data visualization and so I had to include it here. Keep clicking around on it and you will continue to find additional easter-eggs. |
Other miscellaneous items of interest
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