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ESA 2016 – my highlights

Functional traits

I have known for a while that functional traits are at the core of ecology. Unfortunately, for most of my experiments I focus solely on biomass and abundance. However, at ESA this year I noticed many researchers who measured community abundance and used a secondary database such as TRY for extracting functional traits per plots. This is a great re-purposing of already collected data to be reused to answer different questions. I am definitely going to consider analyzing data sets I currently have the species composition for to answer questions about functional diversity rather than typical species richness.

functional traits

Statistics

There was a considerable amount of NMDS usage this year, furthering that ecological analyses are becoming more complicated and requiring ordinations. Although ecologists may love NMDS, there is a preference in the statistical world to avoid it. I won’t get into the pros and cons here, but I believe ordinations such as PCoA, CA and RDA can accomplish the same as NMDS with less limitations. I will need to explore this further but I found this document a good starting point. Permuted ANOVAs were also another particularly popular statistical test and one I need to find a good R package for.

Another great talk from the conference discussed the advantages of the Negative Binomial distributions particularly for species abundance distributions. The talk discussed the tendency to fit discrete count data into log-normal distributions or Poisson. Often these distributions do not fit the data, while negative binomial does. The author A. Rominger promised me that he would be publishing an article detailing this commonality later in the year. I will hold him to that! In the mean time, here is an R package that he developed for species abundance distributions and the negative binomial distribution called pika.negative binomial distribution

Species distribution modeling

I had the opportunity to sit in on a talk by C. Merow that discussed used “expert maps” to further refined predictions of species distributions. It was a great talk and introduced a new concept to refine species predictions. Using the Map of Life (MOL), ecologists create species boundary maps that are would go into an SDM. The maps are compatible with MaxEnt and were shown to be effective at better predicting species occurrence. While a much better technique, I think the major limitation is that specific species will not have these maps delineated yet. However, until MOL catches up, big picture questions can be addressed with a greater degree of accuracy. The talk also reminded me I need to learn more Point Process Poisson modeling

The other instance SDMs that I thought was extremely informative was by Leung discussing co-occurrence models for invasion. This models have strong similarities with our work except instead of testing how an invasive species co-occurs with native species, we are trying to determine how a facilitating benefactor species interacts with neighbouring species. The way this is done is either using a proxy measurement or by using multi-species models. The example Leung used for a proxy measurement was boat movement in Ontario as a function of invasibility for a particular non-native species. I though this was a great idea and something I will consider for my next SDM experiment. The multi-species models is something that was a bit more complicated and that I will need to explore further.

Species distributions

General

Overall ESA went well! The attendance appeared a bit lower than last year, but I felt I was still super busy. It was a great experience and I learned a lot more that the highlights I am listing here. We also received some great feedback on micronet on how to improve it and I go some ideas to develop an R package that hopefully satisfies everyone’s micro-environmental challenges. A full list of my participation at ESA below:

A test of the stress-gradient hypothesis including both abiotic stress and consumer pressure during an extreme drought year

How to Set Up Automated Sensors Arrays for Measuring Micro-Environmental Characteristics and Synthesize to Larger Scales

Microenvironmental change as a mechanism to study global change

The use of shrubs as a tool for re-establishing native annuals to an invaded arid shrub land

 

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Precipitation mediates the mechanism of facilitation in a Californian Desert

ESA 101 at Fort Lauderdale is coming up! I will be presenting on recent findings from an experiment we conducted over two years. I am extremely excited for both the presentation and the results! Here is the slide deck, statistical analyses and program outline.

https://afilazzola.github.io/water.consumer/

Background/Question/Methods
The stress gradient hypothesis original purposed the frequency of plant interactions along countervailing gradients of abiotic stress and consumer pressure. However, research to date has studied these two stressors in isolation rather than together, thereby potentially neglecting the interaction of these factors on plant composition. In the arid central valley of California, we artificially manipulated a soil moisture gradient and erected animal exclosures to examine the interactions between dominant shrubs and the subordinate annual community. We conducted this experiment in an extreme drought year (2014) and a year of above-average rainfall (2016).

Results/Conclusions

Shrubs positive affected the abundance and biomass of the annual community at all levels of soil moisture and consumer pressure. In the drought year, shrub facilitation and water addition produced similar positive effect sizes on plant communities; however, the shrub facilitation effect was significantly greater in watered plots. During the year with higher rainfall, there was no observed water or exclosure effect, but shrubs still significantly increased biomass of the subordinate plants. Shrubs and positive interactions maintain productivity of annual plant communities at environmental extremes despite reductions in droughts stress or consumer pressure and these positive effects are even more pronounced with water addition. The relationship between consumer pressure and abiotic stress on plant interactions is non-linear particularly since shrubs can facilitate understorey plants through a series of different mechanisms.

A funny story about external HD failures for #animalcamera and #pollinator imagery and videos

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Funny story on drive failures
I have had the external HD from Panoche Hills Ecological Reserve with records of background animal cam monitoring on my desk for about a month.  About to back up, had call with Ally, and she told me her nightmare experiences with external drive failures this season. Righteously, I held up this particular ‘x’ brand hard drive and said ‘ohya these are way better, never fail’.
After call, I am thinking, well time to use that unlimited google drive folder and back up these animal cam photos.  Plug in drive, opens up, spins for less than a minute, then promptly fails.  We do not have backup so this was only copy….
I am like are you kidding, here I am about to finally back up to cloud, and it crashes!!
Spoke with NCEAS informatics team.  Apparently, there are just two types of drives – those about to fail, those that have failed. Also, the failure rate for mechanical drives can be up to 45% when there many, many small files versus lower volume, larger files. Of course, we have exactly the worst case scenario (a million small file-sized animal pics from the Carrizo this season). Mechanical drives, in trying to read many little files, jump around a lot.
 #irony
Unknown
So, again, we need to shoot for this bare minimum rule.
Three backups of all video/animal cam raw imagery.
TWO external HDs in different places.
ONE cloud back up.
Workflow for archiving
1. Copy from external HD to HD of a local, dedicated lab machine (doing directly from external introduces too much lag).
2. Use ethernet not wifi to move to cloud drive.
3. Put in appropriate folder on drive with subfolders.
4. Google drive does not support folder dropping with Safari so use Chrome or Opera.
5. PUT a raw.imagery.data.csv or googlesheet file in same master folder as your raw imagery explaining folder and file names and replication so that ANYONE could go to that master folder and understand the raw imagery. Meta-data make the world go round and science reproducible, verifiable, and open.
Final note, publish imagery data to data journal before you write paper.  Taylor did this via GigaScience, but we could also try for Zooniverse or Nature Scientific Data.
After all, these data are precious.
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Ephedra can escape me, but I can’t escape Ephedra

Taking a short trip to the American southwest, I have discovered my study shrub occurs quite commonly. Although I normally examine Ephedra californica in the Mojave and San Joaquin deserts in my travels, I have found it i the Chihuahuan Desert, Sonoran Desert, Great Basin Desert, and Colorado Plateau.

Petrified Forest National Park

Petrified Forest National Park

Canyonlands National Park

Canyonlands National Park

White Sands National Monument

White Sands National Monument

Seeds different than the California species

Seeds different than the California species

Monument Valley

Monument Valley

Lizard Radio Tracking

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9 lucky blunted-nosed leopard lizards are enjoying their new necklaces.

Hoping to catch more lizards soon. Our goal is to have 12-15 animals collared by the end of the week.

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Chase and I have been spending lots of time with our new friends. We relocated the lizards several times a week, as well as doing hour-long behavior observations. By the end of the season we hope to have 4-5 hours of observation on each animal.

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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.

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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.

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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

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Herbivory? Check

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The hemi-parasitic Castilleja exserta, surrounded by Lasthenia