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.

 

Microenvironmental change in Cuyama Valley 2017.2 goals

In 2016, we deployed micro-environmental data logger arrays to monitor global change dynamics at very fine scales. We also structured measurements to ensure we can infer and link to a biotic interaction signal between common plants within this region.

This is very important region to study for at least two reasons ecologically.

(1) Water issues with people, plants, and agricultural are critical here.

(2) Cuyama Valley is an excellent set of sites or mesocosm for the San Joaquin Valley at large. The San Joaquin Valley is still sinking (NASA report). We need to understand temperature, precipitation, and soil moisture availability patterns at many scales within the region.

This season, 2017, is a relative boom year in terms of precipitation. Here are the immediate sampling goals for this season.

1. April (mid). At peak flowering, count burrows, re-measure shrub sizes, sample annual vegetation, and collect biomass.
2. May (mid). Retrieve all logger units, download data, and check functionality. These data capture two growing seasons – one drought, one wet.
3. May (mid). Re-deploy and re-initialize loggers. Rationale – need data on shrub effects when it matters for animals like lizards and hoppers etc and when it is really hot.
4. Sept (end). Retrieve loggers and sensors, download data, end experiment.
5. Oct. Design and test a missing-data strategy to address missing sensor and logger failures. I will likely implement a within-site, resampling data strategy associated with central tendency measures to fill gaps.

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.