Git is a type of version control software that allows tracking to occur within within and among documents of a given project. If this sounds vague, it may be easier to think of Word's 'track-changes' setting. Track changes allows Word users to make comments, edits, etc. that are recorded and highlighted in the word program. Git provides a similar function, but for individual documents and specific files. So, instead of having several versions of a manuscript each with a co-author's initials at the end of the document, Git sort of does this automatically by tacking anyone who is working from the same file. Now, maybe this isn't an issue if you don't create may versions of a document or are content with the 'initial system', but for anyone writing and revising things on a regular basis - like an R script - Git is likely to be very useful. This is especially true for anyone working on group projects, which is increasingly the case in science (there is a general trend for more authors per manuscript through time).
Git also makes sense from an ethical perspective particularly for scientist. Git repositories, like Github, are ideal centralized locations to store code, which allow others to vet, learn, or contribute to existing code.
Of course, this is my naive perception of if git so far and other's have spent a lot more time developing introductions to git and Github.(It's also worth mentioning that Github is one of several cloud Git repositories), Anyways, I figured I'd include some resources for learning about how to use Git, Github, and their integration with RStudio below for myself and others that may be interested.
A good video tutorial of how to use terminal to upload and download items from a Github repository directly to your computer:
Two websites with similar information about using Git Github and Rstudio (I honestly found the video about more effective):
For uploading large files to Github:
Last Friday I successfully defended my dissertation research! Below is the poster that I used to advertise my talk around campus. The talk itself went well, but was a surprisingly emotional experience - the combination of nerves and fatigue, plus having some of the most important people in my life (family, friends, & colleagues) there to support me had me tearing up at the beginning and end of the talk! Thanks to everyone who's helped me to get this far!
I'm very happy and honored to have been selected for the Garden Club of America's (GCA) award in Tropical Botany. I look forward to putting my award to good use this summer working with high school interns in Fairchild Tropical Botanic Garden's (FTBG) Fairchild Challenge. This summer, interns and I will use FTBG's extensive collections of tropical plants to understand which kinds of species are most susceptible to thermal damage as a result of climate change.
I'm also happy to say that Nichole Tiernan, friend, other PhD student from my FIU cohort, and FTBG Fellow, has also received this award. Nichole studies the phylogeny and systematics of the genus Plumeria. See FTBG's blog post to read more about Nichole's work.
I encourage other botanists and graduate students whose interests extend beyond plants to apply to GCA awards in upcoming months. The GCA has several types of grants not limited to botany and several appear to target master's students. Check out the GCA and its scholarships here: www.gcamerica.org/
(Above is an image assembled in the Inkscape and GIMP programs -- it shows the silhouette of an unidentified Piper sp. from Peru superimposed with a map generated in R. Below are some thoughts that Ken and I had on a 2016 Nature Plants paper entitled, "Global plant traits estimates biased due to plasticity in the shade," by Keenan and Niinemets.)
Much of the variance observed in the functional niche-space of plants can be explained by light. Despite the long-established and well-studied roles of light in plant ecology, Keenan and Niinemets1 highlight potential biases in studies of the global spectrum of leaf form and function that may arise through neglect of standardized light measurements. To correct for these biases, the authors advocate several important modifications in the procedures for sampling and reporting leaf functional data. Below, we expand upon some of these recommendations and highlight other sources of error in estimates of the leaf economics spectrum.
We agree with Keenan and Niinemets (1) that studies investigating functional plant ecology should report some level of light exposure associated with trait data. While photon-flux density or canopy density estimates (e.g., from hemispherical photography) is ideal, these measurements may be prohibitive at times due to cost and/or feasibility (e.g. it can be extremely difficult to take measurements over mature canopy trees). However, crown illumination indices (CIIs) require no special equipment and are reasonably correlated with estimates of light exposure derived from hemispherical photography (2). Future meta-analyses amalgamating CII and trait data would inevitably suffer from inter-observer error, and additional error would be introduced through different methods of CII estimation (namely the number illumination categories). Therefore, we propose that ecologists use the 7 categorical light classes used by Clark and Clark (4) as the standard for quantifying light exposure when more sophisticated quantifications are unavailable.
Standard protocol for measurements of leaf traits generally calls for sampling of fully sun-exposed leaves. Sampling sun leaves from tall canopies can be difficult and the failure to properly sample fully-exposed canopy leaves has potentially introduced considerable error in estimates of leaf form and function, particularly for tropical forests (1). Canopy sampling techniques have traditionally relied on shotguns, which often require hard-to-obtain ammunition and permits. Until terrestrial laser technology and radiative transfer modeling become more accessible, some sampling constraints may be removed through the use of low-tech methods. Although infrequently reported in the literature, slingshots are commonly used in arboriculture for canopy-ascension and provide a less-invasive and more precise method for sampling canopies compared to shotguns. More specifically, slingshots can be used to position weighted lines over small branches with fully sun-exposed leaves, which can then be harvested with the aid of serrated wires or modified chainsaw chains. Since slingshots can reliably reach heights up to approximately 50m, they are suitable for sampling all but the very tallest forest canopies.
Standard sampling protocol also calls for recently matured leaves. As leaves age, they can undergo marked changes in traits such as leaf mass area and photosynthetic rate (5). It is also common for old leaves to develop epiphylls, which influence host leaf physiology through light preemption (6) and nutrient leaching (7). However, without previous information regarding phenology, determining which leaves are newly matured is inherently subjective. Assuming that studies have accurately sampled leaves with the same relative development, measurements of leaf traits are still likely to misrepresent the majority of leaves in a given canopy because newly matured leaves may be proportionally rare compared to all leaves in the canopy.
When scaled up from individuals, unrepresentative measurements in leaf traits due to shading and age may result in gross stoichiometric miscalculations at the global level. For now, the implications of Keenan and Niinemets’ findings suggest that studies based on the reported global spectrum of leaf form and function may require some re-evaluation. We propose that increased use of CIIs, improved sampling techniques, and more detailed study of the within-canopy and age-related trait variation are effective ways to correct the observed bias in the leaf economics spectrum.
1.Keenan, T. F. & Niinemets, Ü. Nat. Plants 16201, 1020–1029 (2016).
2.Keeling, H. C. & Phillips, O. L.. For. Ecol. Manage. 242, 431–437 (2007).
3.Jennings, S. B., Brown, N. D. & Sheil, D. Forestry 72, 59–73 (1999).
4.Clark, D. A. & Clark, D. B. Ecol. Monogr. 62, 315–344 (1992).
5.Kitajima, K., Mulkey, S. S. Am. J. Bot. 89, 1925–1932 (2002).
6.Anthony, P. A., Holtum, J. A. M. & Jackes, B. R. Funct. Ecol. 16, 808–816 (2002).
7.Wanek, W. & Pörtl, K. New Phytol. 166, 577–588 (2005).
I am proud to announce that I was recently appointed secretary for the Alliance for a Sustainable Amazon (ASA). ASA is a US-based 501(c)3 non-profit organization started by Dr. Geoff Gallice and Johana Reyes Quinteros as way to promote sustainable agriculture in the Amazon Basin. ASA is based out of Puerto Maldonado, Peru - a region that is experiencing rapid agricultural and urban expansion following the construction of the Interoceanic Highway that links the Atlantic and Pacific coasts of Brazil and Peru, respectively. Although the Interoceanic Highway is an important stimulus for economic growth, it has also facilitated the expansion of illegal activities such as gold mining and logging. The scars left from mining and logging are so great that they are visible from space.
As Amazonian countries vie for positions in the global economy, ASA's mission is to promote the sustainable use of natural resources and the conservation of biodiversity for the benefit of all who live in and depend upon the Amazon rainforest. ASA offers several ways that you can help conserve the Amazon including research, internships, and field courses.
Visit ASA's website to learn more!
Yale Climate Connections recently covered our Thermal Trouble in the Tropics article published in Science (http://science.sciencemag.org/content/351/6280/1392). I was quite nervous during the interview - I think I need brush up on my non-existent interview skills. Here's the link to Yale Climate Connection's website:
I got some practice climbing a Chrysophyllum cainito at Fairchild Tropical Botanic Garden this morning. On my descent from the canopy I made a small re-route and almost stepped in some poo! I suspect a raccoon is the culprit. As you can see in the picture, there is some scat carefully placed in this tree hole ~ 20m above the ground. I say carefully because, from the looks of the hole and its many old seeds, I bet this is a favorite latrine-site for some mischievous dumpster panda. Below, Jess and Rachel enthusiastically react to my discovery.
I'm happy to report that I've just received the O.K. from La Selva Biological Station in Costa Rica to perform research there this summer! I'm very excited to get back into the field and back to Costa Rica - I feel especially lucky to spend time at La Selva because of all its tropical ecological history. Anyway, now for the securing permits...