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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

 

#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

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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

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unlike the very green hills we observed earlier in the year

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