UCSB workshop – programming for ecologists

A two day work session at UCSB was extremely informative covering a wide range of topics for programming and ecology. The course was divided into four components: bash-cmd, intro to R-studio, Github, and data manipulation in R-studio. I especially liked how the course took a more abstract approach without going through statistics. Rather it was focused on data manipulation for the day to day ecologist. One of the more unexpected things I learned from the process was R-markdown and developing websites using it with Github. All of these tools can significantly help with collaboration. Although most of what I had been doing in R is not wrong, it may be difficult for a collaborator to pick up my code and start using it. I think this course really helps me bridge that gap and it is something I am going to push forward on. Gone are the days of sharing Word Documents with 6 versions of the same figure.

All the course materials are found on the website here! I would recommend anyone even slightly interested in the above topics to go through it. Below are some highlighted parts that I believe deserve a little extra attention.

Bash shell

One thing that was lightly talked about within the short 3 hour time frame we had, is the power of Bash Shell.  Bash Shell (cmd) is Neo from the matrix. All the rules are off and boundaries are endless. It has happened to me before on simple tasks that files or hard drives will be written off as corrupt, yet all the files are still there. Bash Shell has allowed me to see what my OS restricts. This unrestricted access and combination for programming can allow tasks to be committed that otherwise are not possible in real-time or at all. To bring in another movie reference, “with great power comes great responsibility”. Despite the overwhelming power of Bash Shell, it is easy to do things wrong… very wrong. It that way it may be intimidated to users because there is no undo or recycling bin. Still, a very powerful tool for the ecologist who wants to do something on their computer, but can’t.


Base vs Dplyr

Why is Dplyr better than Base? I haven’t quite found out if Dplyr better, but I have noticed that it is easier to understand when sharing with collaborators. Nesting functions within funtions may make sense to you, but to others it can look like a disaster. Will I switch over to dplyr? Maybe. It does mean learning a bunch more commands and most are the same character length as base. However, collaboration is everything and seeing subset(subset(subset… may scare a few people off.

R Markdown

Such an unexpected surprised! I really like Rmarkdown and how easy it is to generate a quality website with little code. The best part is that it still has easy functionality to link to CSS or HTML files. Nothing is perfect, and it unfortunately means learning another series of commands and codes for something that already exist. However, it does tie in better with R scripting. This allows for the development of half-websites, half-experiment results that can be used as a blog post, shared with others, etc. The course taught us a lot about it and I’m already forgetting much of what I heard, but I will begin to incorporate as much as I can.


Plant field season 2016

As the plant field season comes to a close, the lizard field season kicks off. Here are some picture highlights.

Phacelia tanacetifolia glistening in the sun at Carrizo plain – cred to ARL

Eschscholzia californica in Cuyama Valley

Eschscholzia californica in Cuyama Valley

Rocking my favourite phytometer species: Salvia columbariae

Rocking my favourite phytometer species: Salvia columbariae


Herbivory? Check


The hemi-parasitic Castilleja exserta, surrounded by Lasthenia


#YorkU summer research practicum positions available!

Our lab is looking for two York University undergraduate students to partake in research practicum positions focused in plant ecology research. Students will be working closely with graduate students on on-going research projects related to desert plant ecology research.

Position title: Research practicum (BIOL1603; BIOL2603; BIOL3603; BIOL4603)

Duties: Process plant biomass samples, process soil cores, review animal camera trap photos, greenhouse/growth chamber germination experiments

Location: York Univeristy, Keele Campus

Hours per week: 8-10 hours

Duration: June 2016 – August 2016, with potential to extend into Fall 2017

Qualifications: eager to learn, enthusiastic, detail-oriented, dedicated. No prior experience is required, all training will be provided. Upon accepting the position, students must complete WHMIS training providing at York University.

Preferred Education level: Completion of second year undergraduate studies

Preferred Major: Biology, Ecology, Environmental Science

To apply: Interested applicants should contact Amanda Liczner via email (aliczner AT yorku. ca). Please include “summer research practicum application” in the subject heading and include your unofficial transcript (screenshots are acceptable).

Please apply before April 30, 2016


Panoche Hills California #flowering: #fieldwork updates

Although this season has been wetter than last year, it is not quite the big El Nino event that was expected. Nonetheless there has been something of a superbloom for the Panoche Hills which is typically dominated by invasive Mediterranean annual grasses.

This year, this bloom was especially apparent along the access road with Monolopia, Phacelia and Amsinckia dominating with a few lupines

monolopia flowers shrub facilitation ephedra facilitating flowers lupines

We have had a great deal of success with our experimental plots up at the plateau area too!

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There are tons of flowers it the valleys and slopes within the hills too

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Although things are starting to seed and brown up here, there are still some remnants of flowers on north facing slopes


unlike the very green hills we observed earlier in the year




Loggers, micro-environments and ecology: an ESA 2016 Workshop

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We would like to advertise our ESA workshop: How to Set Up Automated Sensors Arrays for Measuring Micro-Environmental Characteristics and Synthesize to Larger Scales

Abstract: Tracking the consequences of environmental change requires information on both the physical and biological characteristics of ecological systems. Large-scale environmental data are now widely available from many data repositories. However, these data sets often need to be down-scaled in order to be paired with local ecological measurements. Hence, micro-environmental sensors are sometimes useful to integrate scales of ecological information relevant to global change. In this workshop, we will demonstrate the use of all major affordable types of micro-environmental sensors available to collect fine-scale environmental data. Using the R environment, we will also provide the means to analyze these data and also to integrate this information with ecological data and macro-environmental data streams. The overall purpose of this workshop is to provide attendees with hands on experience on the use of automated sensors of micro-environmental variables, their appropriate deployment in the field in relation to ecological questions, and an introduction to the integration of micro-scale data to larger environmental datasets. This workshop will also serve to launch MicroNet. This is an open-source, collaborative network of micro-environmental sensors deployed globally.


And this is the link to the ESA Programme: https://eco.confex.com/eco/2016/webprogram/Session11870.html


The workshop will take place on Monday August 12 at room 304 of the Fort Lauderdale Convention Center, between 11:30am and 1:15 pm.


We hope to see you there!


San Joaquin Desert #phenology update

An excellent post from near (and at one) of the sites within the San Joaquin Desert gradient that Alex and others study was written by the director of the Tejon Ranch. The Cuyama Valley where I have been leading some field research on the capacity for foundation plant species to buffer global change is about in the middle of the extended gradient we work on from Panoche Hills Ecological Reserve to the Mojave.

The phenology was incredibly variable from site to site within the Cuyama Valley. We did not pick up an elevation or aspect signal to explain the variation from emergent and established plants to individuals nearing senescence. Apparently, prolonged drought and very sporadic rains even for desert ecosystems have introduced considerable micro-environmental variation.

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Whilst in other spots, within just a few miles, same species, similar micro-environmental strata, we had these glorious showings!

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Over at Carrizo National Monument, there were similar sets of patterns from full flower to early senescence.


The shifted phenology of California deserts 2016 – utter madness

Hitting the field again tomorrow. Likely at least two weeks early from ‘regular’ desert seasons. A bit of rain and high temperatures has apparently lead to massive ‘all-chips-in’ for the native annuals that have been holding on for 5+ years of drought.

The very likely consequence is a mismatch with the pollinators within the region that are NOT up and busy yet.

Leap year indeed.


Photos by Brent Johnson on Feb 27th, 2016.