Cam trapping: ten simple steps to process all those amazing photos

Workflow

  1. Read some cam trap papers.
  2. Check camtrapR package and see what it does to decide if it suits your specific needs.
  3. Open folder for each site, each day, each rep.  Do a folder ‘get info’ to count # of total pics.  These are your ‘reps’ within reps, i.e. literally total number of snapshots (or use command line to get dir info for all your photo data).
  4. I would honestly just paste 0’s all the way down because many will be ‘false hits’.
  5. Then, open them all up and scroll through.
  6. Every time a positive hit, overwrite 0 in ‘animal.capture’ vector and in ‘animal’ vector record what it is.
  7. Also, copy all positive hits photos into a separate folder for additional analyses.  Use a folder structure or ID system that keeps track of the place and time that photo was from.  For instance, have a folder entitle positive-hits for each site, day, location, rep or aggregate into a single positive hit folder but use a mechanism to ensure we know where/when photo was taken. Do not cut and paste, copy. This is a backup mechanism for additional analyses and sharing data.
  8. We also want to know when animals are most active, or not; and hence, check timestamps and paste down in that column too. Ideal is actual time but morning, afternoon, night is absolutely adequate and more rapid if we cannot automate the scraping using R-package.
  9. If timestamp is incorrect, do a light-dark assessment to code as night or day – this is a very rapid process.
  10. Record observations if more than one animal or if the same animal was recaptured from previous instance. Record anything of note ecologically to calibrate the quantitatives and link photo-capture processing to data mapping/translation. The goal is to accurately map photos onto numbers that represent the dynamics of the system in study.

Outcomes

The goal is have to have both an evidence folder of positive hits and a dataframe that can then be wrangled to estimate relative efficacy of sampling, frequencies of different animals, spatiotemporal dynamics, and differences between structured treatments in the implementation of trapping.

Meta-data for manual processing spreadsheet workflow

Attribute is the column headers.

attribute description
year we have many years for Carrizo (evil laugh) so good to list here in a vector
region MNP for Mojave, CNM for Carrizo
site if you have more than one site, put name of site
calendar date dd-m-year
microsite larrea, buchhorn, ephedra or open depending on region
day this is census day, 1,2,3, to however many days sampled
rep if more than one rep per day
photo rep just cut and paste to total number of photos each cam took on one day, could be 10 to 10000
animal.capture binary 0 = false hit, 1 = animal present
animal list animal as ‘none’ if false hit, then animal name if one was there
timeblock with animal telemetry work, morning, afternoon, night is usually sufficient 6am to noon, noon to 6pm, them night time
night.day back up if timestamps are incorrect – just do by night and day using light and darkness in photos. very quick
filename.ID.positive.hits
optional depending on your filing system, copy all positive hits to a separate folder. somehow, keep track of positive locations and times for subsequent analyses
observations
record observations of anything ecological that pops such as if there was another animal in the photo OR if it was the same animal repeatedly recaptured

CSEE 2017 Highlights

This year the ecoblender lab attended CSEE 2017. The conference was great and covered four days of talks, workshops, and networking events. I attended a free workshop that taught some basics in mapping spatial data and different packages to use in R. There was also a wide range of talks that mostly seemed interdisciplinary. This included discussions of uncertainty in ecology, estimate the value of natural resources, and developing models of habitat selection. Here are some of the highlights I took away from the conference:

Modelling:

There was discussion over the usage and power of mechanistic vs. phenomenological models. This is a topic discussed often in ecology (see of that discourse here), but can be defined here as:

mechanistic: includes a process (physical, biological, chemical, etc) that can be predicted and described.

phenomenological: Is a correlative model that describes trends in associated data but not the mechanism linking them.

The discussion mostly described the relationship between phenomenological and Mechanistic models as not binary and rather a gradient of different models that describe varying amounts of a particular system. However, it did touch upon models such as GARP and MaxEnt that are often used for habitat selection or SDM but neglect the mechanism that is driving species occurrence. Two techniques I would like to learn more about are Line Search MCMC and HMSC which is a newly developed method for conducting joint species distribution models.

Camera traps:

There was also a morning session that described benefits and tools for using camera traps. These sessions are always great as they give a chance to see some wildlife without disturbance. Topics focus around deer over abundance harming caribou populations, how wildlife bridges do not increase predation through the Prey-Trap Hypothesis and techniques for using wildlife cameras or drones. One talk that was particularly interested used call back messages when triggered to see how animals respond to noises such as human’s talking or a mating call.

One of the more useful things I believe to have taken out of the session is how to estimate animal abundance and movement when the animals in your camera traps are unmarked. One modelling technique using Bayesian modelling and was found to be equivalent to genetic surveys of animal fur for estimating animal abundance. This is in contrast to the more frequent spatial capture-recapture (SCR) methods that either mark individuals or supplement camera trap data with other surveys. I also discovered there the eMammal project at the Smithsonian that is an Open Access project for the management and storage of camera trap data.

Ecology and climate change:

Climate change as always is a big topic at these conferences. There was a good meta-analysis out of the Vellend lab that show artificial warming of plant communities does not result in significant species loss. However, there was evidence that changes in precipitation does significant impact plant communities. The results are very preliminary, but I look forward to seeing more about it in the future. I also liked a talk that is now a paper in Nature that models networks in the context of climate change. The punchline of the results being that species composition in communities is dependent on dispersal, and high dispersal rates can maintain network structure although members of the community may change.

I presented results from our upcoming paper modelling positive interactions in desert ecosystems:

Overall I learned a lot from the CSEE 2017 conference and thought it was a health balance of size and events. Victoria was also a great city and made hosting the conference very easy. Next year it will in the GTA and I plan on connecting with the organization committee to potentially host an R workshop at the beginning of the conference. Until then!

Ecoblender hosting a workshop: An Introduction to R and Generalized Linear Models

Full details are provided here.
https://afilazzola.github.io//YorkU.GLM.2017-04-28/

General Information

The purpose of this workshop is to provide tools for a new/novice analyst to more effectively and efficiently analyse their data in R. This hands-on workshop will introduce the basic concepts of R and use of generalized linear models in R to describe patterns. Participants will be encouraged to help one another and to apply what they have learned to their own problems.

Who: The course is aimed at R beginners and novice to intermediate analysts. You do not need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 88 Pond Road, York University. Room 2114 DB (TEL). Google maps

Requirements: Participants should bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) with administrative privileges. If you want to work along during tutorial, you must have R studio installed on your own computer. However, you are still welcome to attend because all examples will be presented via a projector in the classroom. Coffees and cookies provided for free.

 

How we use a handheld soil moisture probe to supplement in situ plant ecology sampling

It is best to deploy loggers with appropriate sensors to capture an environmental signal within a set of study sites. Nonetheless, when actively sampling for plant-plant interactions dynamics,  an estimate of soil moisture at that particular point in time and space precisely is useful (at least as a covariate). We use the Delta-T SM-150 handheld unit to complement our long-term logging arrays.

Here is a brief summary of the settings/methodology we use.

Method

  1. Push right button to activate unit.
  2. Repeatedly depress right button to cycle through modes until you reach ‘organic’.
  3. Insert probe into ground and ensure that metal conductors are fully embedded in ground with ceramic/plastic unit flush with ground surface.
  4. Left button to measure. Typically, it should take only 1-2 seconds.
  5. Avoid rocks and voids in the ground when inserting probe.

Comments: Ranges you can expect at least in arid and semi-arid systems we have tested within California are between 1-40% but most frequently < 10%.  The unit is durable, and the control unit is ‘water resistant’. However, when the controller gets wet in the rain, it stops working until it drys out again (typically at least a day later). The cable is not that robust, and to be safe, we insert/push the sensors into the ground using the ceramic casing.

 

mini-reviews

Mini-reviews are shorter and more focused than traditional literature reviews. Their specific format varies between journals, however they all have a few things in common: They are topical, concise and specialized, rather than being exhaustive. They quickly bring the reader up to speed on current research in a field, particularly when there has been a major change in thinking. This is in contrast to major reviews, which provide a comprehensive overview of a subfield.

Mini-reviews often synthesize recent research, offering insight and new direction in an important emerging research area. They ideally propose new ideas and hypotheses that arise from the synthesis. Challenging current views in ecology and embracing a bit of controversy is welcome. Despite being called minor, these reviews may garner higher readership and impact than major reviews, due to their conciseness, readability and relevance. I think they are particularly suited to interdisciplinary synthesis, as they do not require writing an exhaustive background from each field, making it easier to communicate the interesting or important aspects of the crossover to a wider audience.

While only a handful of ecology journal explicitly provide guidelines for a mini-review, but quite a few impose a shorter word limit (< 3000 – 5000) and limit references to around 40, essentially requiring a mini-review. Other keywords I have noted are ‘topical’, ‘specialized’, ‘research reviews’, ‘briefings’ and ‘question-based’.

They following ecology-related journals either publish mini-reviews by name, have previously published mini-reviews or their submission guidelines strongly suggest that they welcome the format:

  • Journal of Ecology
  • Methods in Evolution and Ecology
  • New Phytologist
  • Annals of Botany (Botanical Briefings)
  • Frontiers in Ecology and the Environment
  • Global Ecology and Biogeography
  • Conservation Letters
  • PLoS Computational Biology
  • Insect Conservation and Diversity
  • Basic and Applied Ecology
  • Functional Ecology (question-based)
  • Ecosystems (invited only)

Mojave Desert Site Selection

I recently had the chance to spend a few days exploring in the Mojave National Preserve in California to select new study sites for my study of plant-plant-pollinator positive interactions. Sunset Cove, located in the UCNRS Sweeney Granite Mountains Desert Research Centre, is host to an incredible diversity of shrubs and cacti. The two foundational species I will be studying are creosote bush (Larrea tridentata) and buckhorn cholla (Cylindropuntia acanthocarpa), which are codominant in this site.

Annuals were germinating all over the site, however they are still incredibly tiny. Both creosote bush and buckthorn were showing facilitation, with higher abundances of germinants under the shrubs than in open areas. Finally, one cool observation was that 100% of the buckhorns surveyed were growing in close association with another codominant, but only 70% of creosote bush were growing with a codominant, suggesting cacti have some interesting interactions in this area. Finally, this area has been experiencing winter rainfall leading to optimism about flowering this spring.

 

 

Potential study species

The reproductive biology of Cactaceae is not well known – only approximately 2% of the 2000 or so species have been studied (Mandujano et al, 2010). Consequently, how they interact with neighbouring plants of different species for pollinators or what this means in a community context are both virtually unknown. In one of the few published experiments that explicitly tested these interactions, researchers focused on the highly invasive prickly-pear Opuntia stricta in coastal shrublands in Catalonia (Bartomeus 2008). Cacti in the Opuntia genus are primarily bee-pollinated; they have large, colourful bowl-shaped flowers and many species are rich in pollen and nectar (Mandujano et al, 2010), suggesting they are very attractive to pollinators. Plants that exhibit these characteristics can interact with other plants in two notable ways for pollinators – they may act as a magnet plant, increasing local abundances of shared pollinators and thus facilitating the pollination of their neighbours, or conversely, they may steal pollinators and reduce the fitness of their neighbours.

To determine the effects of the invasion on the native plant community, the researchers created plant-pollinator interaction networks for both invaded and uninvaded sites. They found that O. stricta acted as a super-generalist in its new range. It was visited by 31% of the insect taxa in the invaded sites and was outcompeting native plants for pollination services. Within the same study, they found that Carpobrotus, an invasive succulent, had the opposite interaction with the surrounding plant community; it facilitated the pollination of the native plants in the system. This highlights the species-specific and context-dependent aspects of these interactions. There are a few species of Opuntia common in the Mojave Desert, and I hope to discover if and how they are interacting with other plants, particularly shrubs and their annual understory.

Attribution Stan Shebs [GFDL (http://www.gnu.org/copyleft/fdl.html), CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or CC BY-SA 2.5 (http://creativecommons.org/licenses/by-sa/2.5)], via Wikimedia Commons

Bartomeus, I., Vilà, M., & Santamaría, L. (2008). Contrasting effects of invasive plants in plant–pollinator networks. Oecologia, 155(4), 761-770.

del Carmen Mandujano, M., Carrillo-Angeles, I., Martínez-Peralta, C., & Golubov, J. (2010). Reproductive biology of Cactaceae. In Desert plants (pp. 197-230). Springer Berlin Heidelberg.

Waiting for the rain

Rainfall updates

The growing season of 2015-2016 has come and gone with disappointing results from the supposed El Niño year. The 2016-2017 season is approaching and a few had feared that it would just continue the current pattern of drought. I was especially fearful having battling drought four years in a row in my study of plant interactions. It would be nice to have a chance with at least “average” precipitation amounts. Half way through the rain season and this year looks promising. Areas of California have been seeing some pretty significant precipitation including some potential floods. While this is great news in terms of drought relief for coastal cities and the Sierra Nevada snow pack, I wonder what the consequences will be for the deserts? In particular, the Mojave always seems to be in the unluckiest of rain shadows, missing most of the precipitation that the rest of the state experiences. I took a snap shot of the rainfall and average temperatures since seeding at the end of October. Here are the results:

Interpretation

The right combination of rain, temperature, and timing are absolutely crucial in desert ecosystems in regards to how the plant composition will respond. In an older paper by Beatley (1974) is a description of how these three variables determine plant composition. From this and my own experience, the absolute minimum rain to see any annual vegetation on the ground is 2.5 cm. However, these plants usually die within a month if there is no subsequent rain. I have seen this occur in multiple years where Halloween rain is not followed by any other precipitation until mid-January. The result? Many dead plants, and a new representation for plant communities. The Mojave has seen enough rain to begin germination and this rain has all occurred within the last 3 weeks. This, plus continued cold temperatures, should encourage the persistence of annuals for at least another month. If at least one other major rain storm passes through in that time I would expect to see these plants make it to flowering. On the more westerly side of the state, my sites have been seeing fairly consistent rain. This is great news for my Panoche Hills site that likely has passed its precipitation threshold that guarantees emerged plants to flowering.

Fingers crossed as always!