noamross.net

Git Hosting for the Distraught and the Restless

Noam Ross — Sun, 15 Dec 2019 00:00:00 +0000

It’s generally impossible to only use services, private or government, that perfectly align with one’s values, so one must opt to choose one’s battles. The controversy over GitHub’s contract with U.S. Immigration and Customs Enforcement is the latest such battle in the open-source software world. GitHub employees and users are trying to pressure GitHub to drop the contract, as a way to place greater pressure on ICE and the U.S. government to curtail crimes and human rights abuses.

A letter to GitHub signed by many open-source maintainers has raised the profile of this campaign. It stops short of calling for users to abandon GitHub, but many users concerned about this issue are searching for alternatives and considering how much they are locked in to GitHub’s ecosystem. I realize that I’m fairly locked in myself, in both personal and professional projects. While I’m not prepared to leave GitHub entirely, I wanted to see how hard it would be to set up a system where I have greater control. So here is documentation of setting up a git hosting service with using Gitea and nearlyfreespeech.net.

Job Posting: Research Software Engineer at EcoHealth Alliance

Noam Ross — Wed, 04 Dec 2019 00:00:00 +0000

I’m recruiting a Research Software Engineer to join my team at EcoHealth Alliance in New York. Details and how to apply can be found at https://www.ecohealthalliance.org/career/research-software-engineer.

Drake, Docker, and Gitlab-CI

Noam Ross — Tue, 24 Sep 2019 00:00:00 +0000

For a number of reasons I’ve been trying out GitLab as a replacement for for both GitHub and various continuous integration systems, and have been exploring configurations useful for model-fitting pipelines. I turned one of these into an example repository that shows how to use GitLab together with the Rocker Docker images and the drake build system to reproducibly run a project pipeline, using the cacheing functionality across all three tools to make things reasonably speedy and enable both local and remote builds.

A New Website

Noam Ross — Fri, 09 Aug 2019 00:00:00 +0000

For me, the task of building a personal website is fraught with so many of my technical, aesthetic, and personal hangups that I hadn’t updated mine since mid-graduate school. Thanks to consistent pestering by Maëlle, though, I finally got around to re-building this one using a modern toolkit. Hopefully I can keep it up to date.

Here are some of the pieces that I used to build it:

Questions for Jonathan Cornelissen, Dieter De Mesmaeker, Martijn Theuwissen, and Stephen LeSieur (the DataCamp Board), and Anurima Bhargava

Noam Ross — Tue, 30 Apr 2019 00:00:00 +0000

See my original post for background and updates. I was glad to see the announcement from the DataCamp Board that, after a long period of silence and inaction, the company is taking seriously an incident of sexual misconduct and re-examining its approach to the issue and its relationship with concerned instructors. The CEO’s leave of absence and the engagement of Ms. Bhargava indicate a turn in the right direction.

Don't Take My DataCamp Course, There Must be Consequences for Sexual Assault

Noam Ross — Fri, 12 Apr 2019 00:00:00 +0000

Please note there are MANY updates below, and a separate post following DataCamp’s April 24th announcement.

Last week (April 4, 2019) DataCamp published a blog post stating that “one of DataCamp’s executives danced inappropriately and made uninvited physical contact with another employee,” an action meeting many definitions of sexual assault. While the post makes the claim that DataCamp does not condone this behavior, it also makes clear that the disciplinary actions against the executive were limited to “sensitivity training, personal coaching, and a strong warning.”

Adventures in Polyglot Packaging

Noam Ross — Mon, 19 Mar 2018 00:00:00 +0000

I made a little demo package to experiment with the use of WebAssembly to use compiled code from R packages and htmlwidgets. More here: https://noamross.github.io/wassa/inst/doc/adventures-in-webassembly.html.

Bah! Humbug: Some scRoogery and Forecasting

Noam Ross — Mon, 20 Nov 2017 00:00:00 +0000

I had to go shopping for a family birthday and new apartment stuff this past weekend. I entered the big, bright department store and froze, with instant regret and dread, because I heard the foreboding sounds of this phenomenon: Now I don’t know about other countries, but in America the tinsel-laden commercial Christmas season stretches starts the day they break down the pop-up Halloween shops and eventually consumes all of popular culture for two months.

A smooth, differentiable, pulse function

Noam Ross — Thu, 12 Nov 2015 00:00:00 +0000

This function feeds a high-amplitude sine function through a logit, offsetting so as to have the pulse start and stop at arbitrary times. It has an integral of one per period for large $L$. \[f(t) = \frac{c}{a - b} \frac{1}{1 + e^{L \left(sin(2\pi((t-a)/c + \xi)) - sin(2\pi\xi)\right)} }\] where \[\begin{aligned} t &= \text{time} \\ a &= \text{time at start of pulse} \\ b &= \text{time at end of pulse} \\ c &= \text{period length} \\ a &< b < c \\ L &= \text{an arbitrarily large number} \\ \xi &= \frac{3}{4} - \frac{b - a}{2c} \\ \end{aligned}\]

Qualitative Text Analysis in R with RQDA

Noam Ross — Thu, 28 May 2015 09:00:00 +0000

Last Friday at the Davis R Users’ Group, Mallory Johnson gave a presentation on RQDA, an R-based GUI tool for doing coding on documents for use in qualitative text analysis. Here’s the video, and you can view the slides here. [Sorry about reverb in the video] Resources The RQDA home page More RQDA instructional videos

First Steps with Structural Equation Modeling

Noam Ross — Wed, 20 May 2015 11:30:00 +0000

Last Friday at the Davis R Users’ Group, Grace Charles gave a presentation on structural equation modeling in R using the Lavaan package. Here’s the video and her slides. We’ve also posted Grace’s script from the presentation as a gist here. More resources that Grace mentioned in her talk below. Resources Jim Grace’s website at USGS A Lavaan tutorial vingette by Yves Rosseel Materials from Jarret Byrnes’ short course

Visualizing fits, inference, implications of (G)LMMs with Jaime Ashander

Noam Ross — Wed, 29 Apr 2015 14:00:00 +0000

Last Fr Davis R Users’ Group, Jaime Ashander gave a presentation on and visualizing and diagnosing (G)LMMs in R. Here’s the video: Jaime also wrote up the notes from his talk, including all the code, on his blog here (with the raw R Markdown file on github here). The material in the blog post is expanded and improved upon from the original talk, though this means the video and posted code don’t match exactly.

Back to basics: High quality plots using base R graphics

Noam Ross — Fri, 24 Apr 2015 11:50:00 +0000

Today at the Davis R Users’ Group, Michael Koontz gave tour de force lesson in using R’s base graphics capabilities to plot data. Here’s the video: Get Michael’s excellent annotated script, which covers much more than we got to during our tutorial, here.

An introduction to ggplot with Myfanwy Johnston

Noam Ross — Sun, 15 Mar 2015 14:36:00 +0000

Last week at the Davis R Users’ Group, Myfanwy Johnston gave an introduction to the powerful and ubiquitous ggplot2 package for plotting in R. See below for the screencast and her particularly enlightening figure of how ggplot’s syntax and conceptual approach. Myfanwy also placed all her slides, code, and links to more ggplot resources in this GitHub repository. (In a D-RUG first, there was an actual small fire that occurred between ~23:10 - 25:40.

Making Maps in R with Ryan Peek and Michele Tobias

Noam Ross — Fri, 20 Feb 2015 14:31:00 +0000

Today at the Davis R Users’ Group, Ryan Peek and Michele Tobias gave an introduction to making maps in R. Here’s the webcast: (Pardon the little scuffle at the beginning and as we switched computers halfway through. Still getting the hang of hangouts.) Resources: Download all of Ryan’s code and HTML files here. See Michele’s slides on Slideshare here. Code for Michele’s example maps in her GitHub. repository.

Carl Boettiger on accessing online data with ROpenSci

Noam Ross — Fri, 30 Jan 2015 12:40:00 +0000

*Today, Carl Boettiger gave a tutorial on the ROpenSci project and how to use their many packages to connect to online data repositories to retrieve and up deposit data. Here’s our screencast of the talk. All the code from this talk is available at this github repository, and you can download it as a *.zip file here. Thanks to Carl for for a great session and the ROpenSci team for their work!

Tim Bowles on multivariate stats with vegan

Noam Ross — Tue, 09 Dec 2014 19:01:00 +0000

Today, Tim Bowles gave this presentation on the vegan package to the Davis R Users’ Group. The screencast and slides are below. You can also download Tim’s RStudio project with all the code, data, figures, and slides presented here. Thanks to Tim for a great session!

More ESA 2014 Program Text-Mining: Topics as Communities

Noam Ross — Fri, 22 Aug 2014 16:07:42 +0000

In my first pass at text analysis of the ESA program, I looked at how the frequency of words used in the ESA program differed from last year to this year. There are much more sophisticated ways at looking at word use in text, though, and I began to dive into the text-mining literature to find other ways to draw insight from ESA abstracts. One method I found is topic modeling using latent Dirichlet allocation (LDA).

ESA 2014: Don't Know Much About History...

Noam Ross — Tue, 05 Aug 2014 08:14:11 +0000

After my last post text-mining ESA Annual Meeting abstracts, Nash Turley was interested in the presence of the term “natural history” in ESA abstracts. I decided to collect a little more data by including programs back to 2010, giving a five-year data set. Thankfully the program back to 2010 remains in mostly the same format, so it’s easy to pull the data for these additional years. Now, not all talks that include natural history concepts will include the term “natural history”1 in their abstracts, but it’s frequency may be an indicator of importance, and variation in use of the term is may yield some insights.

What shall we talk about at ESA?

Noam Ross — Thu, 24 Jul 2014 01:45:15 +0000

ESA is just around the corner, and many of us are gearing up and trying to figure out a schedule to cover all the talks and people we can pack in. ESA is a big conference and there’s far too much for any one person to see. In the end, everyone experiences a different part of the elephant. However, I thought it would be interesting to take a look at the big picture, and examine the ESA program as a whole to see what could be learned from it.

Vectorization in R: Why?

Noam Ross — Wed, 16 Apr 2014 11:05:35 +0000

Here are my notes from a recent talk I gave on vectorization at a Davis R Users’ Group meeting. Thanks to Vince Buffalo, John Myles White, and Hadley Wickham for their input as I was preparing this. Feedback welcome! Beginning R users are often told to “vectorize” their code. Here, I try to explain why vectorization can be advantageous in R by showing how R works under the hood. Now, remember, premature optimization is the root of all evil (Knuth).

ESA 2014 Abstract: Modeling forest disease using a macroparasite framework

Noam Ross — Thu, 27 Feb 2014 13:17:19 +0000

I just submitted the abstract below to the ESA 2014 meeting. Can’t wait! I’m also organizing an oral session with Richard Cobb: “Ecosystem and Community Effects of Native and Invasive Diseases.” Click through for more details. It’s gonna be a good year! I haven’t been to ESA since 2008. Modeling forest disease using a macroparasite framework Noam Ross, UC Davis Graduate Group in Ecology Background/Question/Methods: Forest pathogens are typically modeled using variants of SI models, in which the infection states of trees are binary.

Using Dates and Times in R

Noam Ross — Mon, 10 Feb 2014 15:09:57 +0000

Today at the Davis R Users’ Group, Bonnie Dixon gave a tutorial on the various ways to handle dates and times in R. Bonnie provided this great script which walks through essential classes, functions, and packages. Here it is piped through knitr::spin. The original R script can be found as a gist here. Date/time classes Three date/time classes are built-in in R, Date, POSIXct, and POSIXlt. Date This is the class to use if you have only dates, but no times, in your data.

Ryan Peek on Creating Shiny Apps

Noam Ross — Tue, 28 Jan 2014 09:41:36 +0000

Yesterday at the Davis R User’s Group1, Ryan Peek gave a talk about using the shiny package to create interactive web apps with R. Here are his slides. Ryan includes a bunch of links to examples and tutorials, as well as his own thermohydrographs app: Thanks to Revolution Analytics for another year of sponsorship!↩

Dynamic Optimization in An Equation-Free Framework

Noam Ross — Wed, 22 Jan 2014 09:46:27 +0000

Many ecological processes are best represented by individual-based models (IBMs), where processes at the scale of individual scale of organisms and their actions are modeled explicitly. Such processes can pose a problem for management or control; our observational scale, control levers, or management goals may be limited to coarser scales than the individual. IBMs suffer from the curse of dimensionality. The number of possible states of the system, which consists of the possible states and combinations thereof of all individuals, is enormous.

How to format plots for publication using ggplot2 (with some help from Inkscape)

Noam Ross — Wed, 20 Nov 2013 19:51:47 +0000

The following is the code from a presentation made by Rosemary Hartman to the Davis R Users’ Group. I’ve run the code through the spin function in knitr to produce this post. Download the script to walk through here. First, make your plot. I am going to use the data already in R about sleep habits of different animals. It’s the same one Noam used for his intro to ggplot.

MBI Meeting Poster: Optimal Control of Forest Disease

Noam Ross — Thu, 07 Nov 2013 22:20:40 +0000

For the past week I’ve been at the Mathematical Biosciences Institute at Ohio State, attending the Workshop on Sustainable Management of Living Natural Resources. It’s been an absolutely top-notch meeting. I need to get myself to more of these small workshops. I brought a poster describing some of my work in progress on managing Sudden Oak Death. Here it is, and it’s archived over at Figshare.

Some analytics: Does age structure matter for disease spread?

Noam Ross — Fri, 21 Jun 2013 13:58:39 +0000

My first crack at an age-structured disease model with multiple infections yielded the interesting result that one could observe differences in disease rates across age without any actual differences in the biology between old and young individuals. Today I’m trying to answer a different question analytically: does age structure matter for the course of the disease in the whole population? Here’s the model. There are two minor changes: I no longer scale $J$ and $A$ with $K$ in the third and fourth equations; there’s no reason the encounter rate should be tied to carrying capacity.

Printing R help files in the console or in knitr documents

Noam Ross — Tue, 18 Jun 2013 10:57:22 +0000

Yesterday, I was creating a knitr document based on a script, and was looking for a way to include content from an R help file. The script, which was a teaching document, had a help() command for when the author wanted to refer readers to R documentation. I wanted that text in my final document, though. There’s no standard way to do this in R, but with some help from Stack Overflow and Scott Chamberlain, I figured out I needed some functions hidden in the depths of the tools package.

Dave Harris on Maximum Likelihood Estimation

Noam Ross — Mon, 17 Jun 2013 15:11:17 +0000

At our last Davis R Users’ Group meeting of the quarter, Dave Harris gave a talk on how to use the bbmle package to fit mechanistic models to ecological data. Here’s his script, which I ran throgh the spin function in knitr: # Load data library(emdbook) ## Loading required package: MASS Loading required package: lattice library(bbmle) ## Loading required package: stats4 data(ReedfrogFuncresp) plot(ReedfrogFuncresp, xlim = c(0, 100), xaxs = "i") Statistical models are stories about how the data came to be.

The null model for age effects with overdispersed infection

Noam Ross — Wed, 12 Jun 2013 17:32:30 +0000

How does overdispersion of infections affect the behavior of the multiple-infection model? I redefine the model to account for overdispersion, assuming the same overdispersion occurs in both age classes. The parameter $k$ varies inversely with the degree of overdispersion. Again, the classes are demographically identical, and infection affects mortality but not growth: \[\begin{aligned} \frac{dJ}{dt} &= A f_A \left(1 - \frac{J+A}{K} \right) + J \left(f_J \left(1 - \frac{J+A}{K} \right) - d_J - g\right) - \alpha P_J \\ \frac{dA}{dt} &= J g - A d_A - \alpha P_A \\ \frac{dP_J}{dt} &= \lambda \frac{J}{K} (P_J + P_A) - P_J \left(d_J + \mu + g + \alpha \left(1 + \frac{(k+1)P_J}{kJ} \right) \right) \\ \frac{dP_A}{dt} &= \lambda \frac{J}{K} (P_J + P_A) + P_J g - PA \left(d_A + \mu + \alpha \left(1 + \frac{(k+1)P_A}{kA} \right) \right) \end{aligned}\]

A Null Model for Age Effects in Disease with Multiple Infections

Noam Ross — Tue, 11 Jun 2013 17:32:30 +0000

Here’s a little thought exercise I did that has caused me to go back and restart my Sudden Oak Death modeling in a new framework. Feedback welcome. I’m especially interested in relevant literature – I haven’t found many good examples of macroparasite/multiple infection models with age structure. Introduction Cobb et al. (2012) develop two models of forest stand demography in the face of Sudden Oak Death. The first, a statistical survival model, estimated the rates of infection and time-to-mortality as functions of density of infected trees and tree size.

Early Warning Signals: the Charted and Uncharted Territories

Noam Ross — Thu, 30 May 2013 09:18:42 +0000

Carl Boettiger, Alan Hastings and I have a new review out on early warning signals and regime shifts. It’s about an idea that Carl and I have been kicking around for a couple of years and finally got around to writing up for a special issue of Theoretical Ecology. There has been a lot of excitement in the past six years or so about early warning signs - statistical signals that indicate that an ecosystem is near a dramatic shift, like the collapse of a fishery or a switch from grassland to desert.

Robert Hijmans on Spatial Data Analysis

Noam Ross — Thu, 23 May 2013 13:08:43 +0000

Last week at the Davis R Users’ Group Robert Hijmans gave a talk about spatial data analysis in R. Robert is a professor of biogeography at UC Davis and the author of the raster (analysis of gridded data), dismo (species distribution modeling), and geosphere (spherical trigonometry), packages. Robert’s presentation spanned topics including basic geographical data and geostatistics concepts, his raster package and its usage, and some great examples of visualization and other resources.

Improved R Profiling Summaries

Noam Ross — Thu, 02 May 2013 16:48:01 +0000

In my last post I mentioned that I had improved on R’s summaryRprof() function with a custom function called proftable(). I’ve updated proftable() to take advantage of R 3.0.0’s ability to record line numbers while profiling. I’ve put it on github – you can get it there or below. proftable reads in a file generated by Rprof() and creates an easy-to read table of the most time-consuming calls in your code, ordered from most time-consuming to least.

FasteR! HigheR! StrongeR! - A Guide to Speeding Up R Code for Busy People

Noam Ross — Thu, 25 Apr 2013 14:49:34 +0000

This is an overview of tools for speeding up your R code that I wrote for the Davis R Users’ Group. First, Ask “Why?” It’s customary to quote Donald Knuth at this point, but instead I’ll quote my twitter buddy Ted Hart to illustrate a point: I’m just going to say it.I like for loops in #Rstats, makes my code readable.All you [a-z]*ply snobs can shove it! — Ted Hart (@DistribEcology) March 12, 2013 Code optimization is a matter is a matter of personal taste and priorities.

Setting up Automated Reprint Requests in Gmail

Noam Ross — Wed, 24 Apr 2013 17:37:22 +0000

I recently wrote about my first peer-reviewed publication and lamented that it’s behind a $1500 paywall. I am not allowed to post the file to my website, but I am able to distribute the paper by e-mail, so I’ve set up a system to automate requests for the paper. Michael McCarthy wrote a similar post this fall for people using Outlook e-mail. My method is similar but is meant for Gmail.

My first peer-reviewed publication: Economics and Ecology of Open-Access Fisheries

Noam Ross — Wed, 24 Apr 2013 10:57:21 +0000

My first peer-reviewed publication is an encyclopedia article written with colleagues in economics in UC Davis: Economics and Ecology of Open-Access Fisheries K. Fuller, D. Kling, K. Kroetz, N. Ross and J.N. Sanchirico (2013) In: Shogren, J.F., (ed.) Encyclopedia of Energy, Natural Resource, and Environmental Economics, Vol. 2 Encyclopedia of Energy, Natural Resource, and Environmental Economics p.39-49. Amsterdam: Elsevier. http://dx.doi.org/10.1016/B978-0-12-375067-9.00114-5 Abstract In open-access fisheries, participation and harvest by fishermen are unregulated.

Debugging Tools in R with Michael Hannon

Noam Ross — Thu, 18 Apr 2013 13:44:59 +0000

Today at Davis R Users’ Group, Michael Hannon gave a great talk on how to use R’s native debugging functions. Here are his notes and code. Introduction This is a discussion of debugging techniques in R. It is based on a paper by Roger Peng, now at Johns Hopkins University (http://www.biostat.jhsph.edu/~rpeng/docs/R-debug-tools.pdf) Focus on five functions: traceback debug browser trace recover Severity level R mainly uses two ways of reporting a problem:

Demographic analysis using the `popbio` library and some other fun stuff

Noam Ross — Thu, 04 Apr 2013 11:16:55 +0000

This week at the Davis R Users’ Group we had a great presentation by Kara Moore O’Leary on using the popbio package to examine rare plant demographics. The following is her script run through knitr. You can download the original script and associated data here. Find out more about Kara and her work at her website here Demographic analysis using the popbio library and some other fun stuff A population viability type analysis for a rare herbacious perennial plant, Penstemon albomarginatus, for its only remaining California population

Model Selection and Multi-Model Inference

Noam Ross — Wed, 20 Feb 2013 17:14:43 +0000

At D-RUG this week Rosemary Hartman presented a really useful case study in model selection, based on her work on frog habitat. Here is her code run through ‘knitr’. Original code and data are posted here. (yes, I am just doing this for the flying monkey) Editor’s note: we’re giving away flying monkey dolls from our sponsor, Revolution Analytics, to all our D-RUG presenters. So, let’s say you want to find out where things are and why they are there.

Mason Earles on interfacing R with the Forest Vegetation Simulator

Noam Ross — Wed, 13 Feb 2013 15:06:42 +0000

Mason Earles gave a great presentation this week at Davis R Users’ Group about linking R with the Forest Vegetation Simulator (FVS). FVS is a model developed by the US Forest Service to simulate forest growth over time. It’s written in FORTRAN and has been around since the 1970s. FVS has recently gone open-source (its repository is on google code), and now has an alpha-level API which can be called from R.

Ryan Peek on using xts and ggplot for time-series data

Noam Ross — Wed, 06 Feb 2013 15:44:25 +0000

At Davis R Users’ Group today, Ryan Peek gave a presentation on how he takes data from his field instruments and visualizes it in R. Here are his notes. The original *.Rmd file and data can be found here SHORT HOW-TO ON USING XTS AND GGPLOT FOR TIME SERIES DATA XTS is a very helpful package when working with time series data. I work with temperature and flow data frequently, so the ability to work with timeseries, and particularly to shift intervals (from 15 min to hourly or daily) can be very handy.

A Draft Dissertation Proposal: Forest Disease Dynamics and Management

Noam Ross — Sun, 27 Jan 2013 19:37:16 +0000

A first draft, just out to my committee. Feedback welcome! A modifiable souce version can be found on github here Abstract Forest disease spreads through plant communities structured by species composition, age distribution, and spatial arrangement. I propose to examine the consequences of the interaction of these components of population structure Phytophthora ramorum invasion of California redwood forests. First, I will compare the dynamic behavior of a series of epidemiological models that include different combinations of population structure.

I try to figure out when many trees will die together

Noam Ross — Thu, 17 Jan 2013 14:49:49 +0000

The amazing UpGoer5 text editor only allows you to use the 1000 most commonly used words in the english language. Here is my research described using only those words: Sometimes many trees get sick and die very quickly. I look at how death moves between different kinds of trees and how groups of different trees change how fast death moves. I try to figure out when many trees will die together, and the type of things we need to know in order to figure this out ahead of time.

Steve Culman on the `plyr` Package

Noam Ross — Thu, 17 Jan 2013 10:11:48 +0000

At Davis R Users’ Group yesteray, Steve Culman gave us an introduction to the plyr package and how to use it to manipulate data. Here’s his presentation, and the accompanying demonstration script: Steve’s talk is based on this paper by Hadley Wickham in the Journal of Statistical Software. A lot of useful related resources are at Hadley Wickham’s plyr website. We had a quick exchange about using plyr for parallel processing.

Don't R alone! A guide to tools for collaboration with R

Noam Ross — Mon, 07 Jan 2013 09:10:36 +0000

This a brief guide to using R in collaborative, social ways. R is a powerful open-source programming language for data analysis, statistics, and visualization, but much of its power derives from a large, engaged community of users. This is an introduction to tools for engaging the community to improve your R code and collaborate with others. (Am I missing anything? Let me know in the comments and I’ll update this guide.

Quals Reading: Sudden Oak Death

Noam Ross — Mon, 07 Jan 2013 00:07:16 +0000

My study system is Sudden Oak Death (SOD) in California Forests, so my examiner [David Rizzo] has given me plenty of readings on the subject. There’s too much for a pithy summary here, but some highlights about the disease’s biology: SOD is caused by Phytophthora ramorum, a water mold in the same family as brown algae. It’s origin is unknown, but 3 lineages are known, two dominant in California and one in Europe.

Quals Reading: Modeling Philosophy

Noam Ross — Sun, 23 Dec 2012 07:44:27 +0000

My examiner on theoretical ecology, Marissa Baskett, suggested that I return to some basic literature on the why of mathematical modeling in ecology. Here are notes on three papers: Summary Modeling purpose must be clearly defined, as this determines whether to focus on generality, realisms, and/or precision Complexity is as often obfuscating as illuminating When prediction is a desired goal, separating calibration from validation is essential Must test robustness of models against different mathematical assumptions, structures, and parameters Many of these assumptions relate to the need to model at a simpler level than reality Disclosure, clarity, and reproducibility in publication are required to justify model use for prediction and policy Model precision is irrelevant if the model fails to address a question of relevance.

Quals Reading: Four Reviews of Forest Epidemiology

Noam Ross — Fri, 21 Dec 2012 12:02:48 +0000

Here’s the first of my quals reading summaries, this landscape forest pathology. David Rizzo will be examining me on this topic. Summary Much of our knowledge of pathology is at the organismal level (host-pathogen interactions), but actual management occurs at stand, forest, and regional levels. To understand and manage forest diseases at this scale, we need appropriate epidemiological and landscape ecology tools and frameworks. Gilbert and Hubbell (1996) discusses the differences between traditional, agriculturally-focused plant pathology and pathology at the forest community level, with conservation management goals.

Qualifying Exam Reading List

Noam Ross — Mon, 17 Dec 2012 16:20:45 +0000

My qualifying exams are on March 5, 2013. 78 days away! I’ll be trying to blog my reading as well as the development of my proposal here and in a github repository. Today - my topics and reading list. Forest Landscape Pathology Landscape-level disease management Sudden Oak Death Model Construction and Theory Approaches to building and using models SIR epidemiological models Population structure in disease dynamics Plant-specific applications Confronting Models with Data Fitting time-series data with iterative filtering Model Comparison Natural Resource Economics Forest rotation models Age-structured harvest models Insect control References Forest Landscape Pathology Examiner: David Rizzo

Lauren Yamane on Matrix Population Models in R

Noam Ross — Fri, 30 Nov 2012 10:11:17 +0000

Last week in Davis R Users’ Group, Lauren Yamane showed us how she created and analyzed a stochastic age-structured population in R. Her examples are below. Her original scripts can be found as *.Rmd files here A note to UC Davis students: This topic and others will be covered by Marissa Baskett and Sebastian Schreiber in their course this winter, Computational methods in population biology (ECL298) A discrete time, age-structured model of a salmon population (semelparous) that can live to age 5, with fishing and environmental stochasticity Parameter values

A multi-species, age-structured model for forest disease

Noam Ross — Wed, 28 Nov 2012 18:00:20 +0000

This is a description of the model I’ve implemented in the SODDr package, which I prepared for a presentation for the Hastings lab meeting on November 29, 2012. Background Sudden Oak Death (SOD) is a disease that threatens tanoak populations in California. It’s cause is an introduced pathogen, Phytophthora ramorum. Phytophthora is a water mold that spreads by wind-blown rain and fog as well as through human transport (e.g., transportation of plants).

A quick function for editing CSV files in R

Noam Ross — Mon, 19 Nov 2012 13:47:25 +0000

I’ve been hunting for a lightweight CSV editor for OSX so I could to make fixes to data files and not need to fire up Excel. While you can edit a CSV file in any text editor, it’s a pain to navigate the files without a spreadsheet-like interface. Unfortunately there doesn’t seem to be a good, free option out there. Today I remembered R has a native XCode editor for editing data frames, and I realized I could write a function that would load the CSV as a data frame, let me edit it, then close and save it in CSV format again.

Simulating Sudden Oak Death Dynamics

Noam Ross — Fri, 16 Nov 2012 10:22:42 +0000

I am working on a project with the Rizzo Lab examining the dynamics of Sudden Oak Death (SOD). I really have to write more about this, but today I’m just going to post the results of an initial exercise. Here I attempt to replicate model results from Cobb et al. (2012). The model in that paper simulates the spread of disease and resulting tree mortality and stand dynamics in a mixed system of tanoak, bay laurel, and redwood.

Jordi Bascompte on Mutualistic Networks

Noam Ross — Thu, 15 Nov 2012 16:09:23 +0000

Jordi Bascompte gave a Storer Lecture at UC Davis on November 15, 2012. Here are my rough notes: Biodiversity as the set of interactions between species, rather than accounting of species Most research in mutualism in evolution focus on bilateral interactions (e.g., Darwin’s orchids and moths) Jordi’s goal is to use network theory to represent mutualism in ecological communities and generalize about them. Three Using data sets on man mutualistic communities (pollinators, frugivores),

Ecological Stoichiometry: Population Dynamics

Noam Ross — Tue, 13 Nov 2012 10:05:03 +0000

Lauren Yamane talked about Andersen et al. (2004) in our Ecological Stoichiometry course today. Here are her slides, and below, my rough notes on the paper: Notes on the Paper Stoichiometry is a way of representing food quality - there is evidence that consumers have preference for high quality (e.g., low C:N) food. There is often a mismatch between composition of prey (autotrophs) and needs of consumers. Autotrophs have variable C:N ratios, consumers are more constrained.

Exploring GAMs with Rosemary Hartman

Noam Ross — Fri, 09 Nov 2012 12:49:25 +0000

Today at Davis R Users’ Group, Rosemary Hartman took us through her work in progress fitting general additive models to organism presence/absence data. Below is her presentation and script. You can get the original script and data here Also, check the comments below for some discussion of other options for this type of analysis, such as boosted regression trees. ## GAMs using mgcv and amphibian presence/absence dataset ## code and data by Rosemary Hartman (rosehartman at gmail dot com) ## First, load the mgcv package (Simon Wood) library(mgcv) ## Now, attach your data set (or my data set) fishlakes <-read.

Dynamics of Coupled Nutrient Cycling and Acclimation: 3 Modeling Papers

Noam Ross — Mon, 05 Nov 2012 19:47:23 +0000

Tomorrow in my stoichiometry seminar I’ll be talking about the dynamics of growth under multiple nutrient limitation and acclimation. Here are my notes: Rastetter and Shaver (1992) In this paper, Rastetter and Shaver introduce a model of plant growth on multiple nutrients, with the goal of understanding the conditions under which single- and multiple-nutrient limitation arise, the difference between short- and long-term behavior, and the role of organism-environment feedbacks. It’s not entirely clear whether this is on the scale of a single or a population.

Ryan Peek on Customizing Your R Setup

Noam Ross — Fri, 02 Nov 2012 11:37:00 +0000

Ryan Peek showed us how to use an .Rprofile file to customize your R setup. Here are his instructions and script: For Windows To change profile for R, go here: C:\Program Files\R\R-2.15.1\etc (or whatever version you are using) Edit the “Rprofile.site” file Restart R For Macs Create your Rprofile file. -use TextEdit or another editor to create a file called Rprofile.txt In a terminal window, type:

Chris Hamm on using plot.new() for better combined plots

Noam Ross — Fri, 26 Oct 2012 10:41:35 +0000

At DRUG today, Chris Hamm (email) showed us an easier way to combine multiple figures into one plot using plot.new, rather than par(mfrow=...) Here’s his script: .knitr.inline { background-color: #f7f7f7; border:solid 1px #B0B0B0; } .error { font-weight: bold; color: #FF0000; }, .warning { font-weight: bold; } .message { font-style: italic; } .source, .output, .warning, .error, .message { padding: 0em 1em; border:solid 1px #F7F7F7; } .source { background-color: #f7f7f7; } .

Ecological Stoichiometry: The Perils of Famine and Plenty

Noam Ross — Mon, 22 Oct 2012 19:55:56 +0000

Pretty raw notes this week from a discussion about how food webs respond to nutrient starvation and excess. Whalen on consumption in Food Webs Boersma and Elser (2006) - fitness cost of excessive P. Implications for models - but what about competition as a more likely limiting factor? Not sure about the “food left on the table” argument. What about the metabolic costs? Not mentioned in the paper. Nonlinearity in P-growth relationship could be coexistence mechanism Raubenheimer and Simpson (2004) - Fitness and body composition can be affected by food quality.

Stella Copeland's Intro to Mixed Models in R

Noam Ross — Fri, 19 Oct 2012 10:26:56 +0000

In D-RUG today, Stella Copeland gave a quick introduction to mixed models in R. Here’s the script that she presented: Get the data file for this script here Stella also recommends this paper by Ben Bolker as a quick introduction to the topic.

A Science-based Voter's Guide

Noam Ross — Fri, 19 Oct 2012 09:43:28 +0000

The Davis Chapter of the Society for Conservation Biology sent along this great voter guide for upcoming California propositions: SCB voter’s guide Nov 2012 ballot measures relevant to conservation Prop 37 Mandates labeling of genetically modified food. Prohibits such food from being labelled as “natural”. However, this law would exempt foods that are certified organic, foods unintentionally produced with genetically modified material, meat of animals fed genetically modified food but that are not genetically modified themselves, alcoholic beverages, and food sold in restaurants.

Ecological Stoichiometry: Back to Basics with Elser

Noam Ross — Mon, 15 Oct 2012 10:36:30 +0000

Our ecological stoichiometry course kicked off today. My initial training is in this area, which I called “ecosystem biogeochemistry”, but it was very much a geologically focused, big systems approach. It’s interesting to approach this material from a more organism- and population-centric perspective that most Davis ecologists have. Today, Alison started us off with some first principles of nutrient constraints on ecology. Drawing a lot from Sterner and Elser (2002), but noting that a lot of these principles go all the way back to Lotka (1925).

A quick introduction to ggplot()

Noam Ross — Fri, 05 Oct 2012 12:05:10 +0000

I gave a short talk today to the [Davis R Users’ Group] about ggplot. This what I presented. Additional resources at the bottom of this post ggplot is an R package for data exploration and producing plots. It produces fantastic-looking graphics and allows one to slice and dice one’s data in many different ways. Comparing with base graphics (This example from Stack Overflow) First, get the package: install.packages("ggplot2") library(ggplot2) Let’s say we wanted to plot some two-variable data, changing color and shape by the sub-category of data.

Forest Ecology Journals

Noam Ross — Wed, 03 Oct 2012 09:26:45 +0000

This week I pinged the Davis Forest Biology Students’ Association and my twitter friends for recommendations for forest-specific journals. Here are their responses: Forest Ecology and Management Canadian Journal of Forest Research Journal of Forestry Tropical Ecology (not forest specific, but heavy on tropical forest research) Biotropica (ditto) The first two on the list got the most votes. I was actually surprised that there weren’t more. Sometimes I read The Forestry Chronicle, but that’s more of a manager’s trade journal.

Seminar in Ecological Stoichiometry: Day 1

Noam Ross — Tue, 02 Oct 2012 10:57:18 +0000

My advisor Alan Hastings and colleague Alison Marklein have put together a great seminar this quarter on theoretical appraoches to nutrient flows and ecological stochiometry. I’m excited because this bridges my own current work, in population modeling, with my undergraduate training in ecosystem- and biogiochemical-based ecology. I’ll try to blog about the papers we read as we go, and I’ve created a public Mendeley Group where I’ll be posting the readings.

Multiple Goals in Floodplain Restoration - Workshop Notes

Noam Ross — Mon, 01 Oct 2012 15:08:48 +0000

Panelists at the floodplains workshop. Left to right: Ron Unger, Dave Shpak, Richard Howitt, Petrea Marchand, Elizabeth Andrews, Paul Brunner, and J. D. Wikert. See below for affiliations and titles We had a fantastic workshop on Floodplain Restoration on September 14 as part of our work with UC Davis’ REACH IGERT program. Here are my notes: Geologist and prolific floodplain-er Jeff Mount introduced the day with an overview of the scale of changes in the Central Valley and the types of challenges that had to be overcome to produce functioning floodplains.

Melinda D. Smith: Divergence in grassland responses to Fire and Grazing in N. America and S. Africa

Noam Ross — Thu, 27 Sep 2012 16:01:02 +0000

Melinda D. Smith of Colorado State spoke this week at Davis’s Ecology and Evolution seminar. These are my rough notes from the talk. Any errors or misrepresentations are my own. Also, a shorter version of the talk is available as a PDF here Melinda’s general framework: Ecological implications of global change. How human caused global changes (climate, biochemical modification, land use), ultimately change community structure and function. Grasslands (inc. steppe, tundra, savanna, and scrublands) cover 40% of earth’s surface.

An R Users' Group in Davis

Noam Ross — Mon, 24 Sep 2012 11:05:27 +0000

I’m excited to share that we’ve started a new R users’ group at UC Davis! Right now our main purpose is to run weekly 2-hour work/hack sessions where R users can get together to work through problems together. More info here

Regime Shifts in Forest Ecosystems

Noam Ross — Mon, 02 Jul 2012 14:43:01 +0000

As I begin to put together material for my thesis proposal, I’m collecting literature on regime shifts in forest ecosystems. I’m interested in the time scale of regime shifts, and how they compare with the time scale of stand dynamics (typically decades), which are the dominant time scale in forestry economics. Here is a preliminary set of examples and citations. I’ve also created a Mendeley group with the papers I’m collecting for this topic.

Trade-Offs and Synergies in Floodplain Management - A Historical-Ecological Approach

Noam Ross — Fri, 01 Jun 2012 00:00:00 +0000

I’m pretty pleased that my IGERT team’s work has garnered both Judge’s Choice and Community Choice awards in the IGERT video and poster competition. IGERT (Integrative Graduate Education and Research Traineeship) is a National Science Foundation program to foster interdisciplinary research at the graduate level. Here at UC Davis, our team includes ecologists and a historian, and we have been looking at how floodplain restoration can be shaped by both bioeconomic constraints and historical legacies.

Carl Walters on Surprises in Adaptive Management at the Grand Canyon

Noam Ross — Fri, 25 May 2012 00:00:00 +0000

Carl Walters of UBC came to UC Davis for our seminar in adaptive management. Carl was also kind enough to permit us to post the pre-print of the paper which he was presenting, which you can download here. These are my rough notes from the talk. Any errors or misrepresentations are my own. Central tenet of adaptive management is that policies should be treated as experimental treatments with uncertain outcomes.

Jo Albers on Invasive Species in a River Network

Noam Ross — Tue, 15 May 2012 00:00:00 +0000

Jo Albers of OSU visited UC Davis’ Agricultural and Resource Economics department to speak about her work on optimal management on invasive species management. The work is also part of Kim Hall’s dissertation research and was completed in conjunction Majid Taleghan, Tom Dietterich, and Mark Crowley from OSU Engineering. These are my rough notes from Dr. Albers’ talk talk. Any errors or misrepresentations are my own. Economics of invasive species Need to bring the biology back into bioeconomic modeling.

Holly Doremus on Adaptive Management

Noam Ross — Fri, 20 Apr 2012 00:00:00 +0000

Holly Doremus, J.D., Ph.D., visited Davis on 4/20/2012 as part of a seminar series on interfaces between ecology, economics and policy. Dr. Doremus is at the UC Berkeley School of Law, but has Ph.D. in Plant Physiology from Cornell. She is former former UCD Faculty. These are my notes from Dr. Doremus’s lecture. Any errors or misrepresentations are my own. Adaptive Management – Knowing When to Say When Adaptive management is thought of as a solution to two problems:

Displaying Math in RSS feeds

Noam Ross — Wed, 04 Apr 2012 11:02:57 +0000

The equations in this blog are rendered using MathJax, which creates beautiful math from $\LaTeX$-style markup. However, the math doesn’t appear in RSS feeds, because RSS doesn’t allow Javascript. While I have a total of 12 RSS followers, this is how my closest collaborators, and my most math-y readers, are likely to read my posts, so I’ve been looking for a way to produce readable equations in the RSS feed.

Exploring Pollen Data

Noam Ross — Mon, 02 Apr 2012 15:06:18 +0000

I wrote a few functions to grab data and from the Global Pollen Database: source("~/code/_Pollen/pollendatafuntions.R") ## Loading required package: stratigraph ## Loading required package: grid ## Loading required package: graphics ## Loading required package: stats billys <- getpctAP("billys", plot = TRUE) ## Number of taxa: 105 ## Number of levels: 77 Arboreal Pollen over time at Billy’s Lake Clearly, there’s are trends at different time scales. The trouble with using S-Maps on this is that there are uneven sampling intervals.

A New, Shiny Website!

Noam Ross — Sun, 01 Apr 2012 17:27:15 +0000

I’ve finally got this new website built using Jekyll and migrated my old content over. I’ve been looking to move to a new system for a while - one that would fit with my workflow and help me keep a blog as an open lab notebook. Squarespace was a great place to start a blog, but a Jekyll site hosted on Github is (A) faster, (B) free, (C) more customizable.

Links and Resources

Noam Ross — Sun, 01 Apr 2012 16:44:09 +0000

(Material migrated over from my old website) Blogs and News Sources Grist, especially David Roberts’ sharp political commentary Resilience Science, by Garry Peterson. See also the Resilience Wiki and the Resilience Alliance Conservation Bytes, a blog on conservation science by C.J. Bradshaw Ecosystem Marketplace, the Katoomba Group’s excellent portal for ecosystem markets and finance. Worldchanging, showing models for a bright green future EcoTone, the blog of the Ecological Society of America GreenBiz, Joel Makower’s hub of all green business news Environmental Economics at Ohio State University Fast Company’s Ethonomics Blog Researchblogging is a community of blogs covering peer-reviewed scientific literature.

Notes on S-maps and regime shifts

Noam Ross — Tue, 31 Jan 2012 00:00:00 +0000

General Problem and Approach Shifts between "states" in ecological systems are shifts between dynamical regimes, or between different attractors within a dynamical regime. The warning signals approach attempts to detect characteristics of a system undergoing a transition between dynamical regimes. This transition may have common properties in many systems [#Scheffer2009;], but not all systems [#Hastings2010;]. Another approach would be to characterize the properties of the dynamic regime over a period of time, and attempt to detect if those properties change, irrespective of whether the change takes the particular form.

Jan 17

Noam Ross — Wed, 18 Jan 2012 00:00:00 +0000

Pollen Met with Alan to discuss the conceptual model for regime shift. His suggestion was to look at Sugihara's method of prediction by looking at the difference paths of different systems - useful for when we have lots of data, even if it's sparse for individual sites. Some papers to look at are : http://www.jstor.org/stable/10.2307/76859 - "Distinguishing Error from Chaos in Ecological Time Series" http://www.jstor.org/stable/10.2307/54223 - "Nonlinear Forecasting for the Classification of Natural Time Series"

January 10, 2012

Noam Ross — Wed, 11 Jan 2012 00:00:00 +0000

Class: Theoretical Ecology First class meeting with Alan - see notes Readings (See notes): Hastings (2008) "Editorial – an ecological theory journal at last" Kareiva (1989) "Renewing the dialogue between theory and experiments in population ecology" Scheiner and Willing (2008) A general theory of ecology Process - Kintr Installed and learned the knitr package. Looks like a great way to write literate code more easily Easy enough to process Multimarkdown, but if processing MMD to Latex/PDF, want to put knitr between the LaTeX and PDF for better processing.

Back in the Saddle January 9, 2012

Noam Ross — Tue, 10 Jan 2012 00:00:00 +0000

Letter Submitted public university funding letter to Frontiers in Ecology and Environement. Follow up in a week.January 9, 2012 Warning signals Read Bel et. al. (2012) "Gradual regime shifts in spatially extended ecosystems." and discussed with Carl. Interesting. Shows a simple model of transition between spotted spatial patterning and uniform landscapes, describes the "snaking" bifurcation pattern between the two. Might be applicable to pollen stuff below. Pollen Read Williams et.

Forest Pest Outbreaks - A Bibliography

Noam Ross — Tue, 06 Dec 2011 00:00:00 +0000

For the seminar I organized on forest pests this quarter, we generated a bibliography of all the papers read or referred to for the various topics. It can be found here: http://goo.gl/ya7a6

Extinction debt, dark diversity, and how things are much worse than they look

Noam Ross — Mon, 28 Nov 2011 00:00:00 +0000

I discovered this unpublished post today, originally written in the Spring: A while ago I wrote a wikipedia article on extinction debt. Frankly, researching this topic scared the hell out of me. Extinction debt began as a fairly obscure theoretical concept that emerged out of mathematical modeling exercises in ecology that showed that it could take tens or even hundreds of years for species to go extinct (Timan et al. 1994).

Monday, November 28, 2011

Noam Ross — Mon, 28 Nov 2011 00:00:00 +0000

Pollen Data for Williams (2010) List of sources of data, but not data, is in a table in the supplementary material Most records are from North American Pollen Database (NAPD) Just browsing through the datasets from this, it looks like a challenge may be that there isn't much data preceding most of the abrupt shifts - there may not be anything resembling a baseline.

Pollen project sources

Noam Ross — Mon, 28 Nov 2011 00:00:00 +0000

Met with Stephen Pacala last week, who suggested we look into records of pollen sediments in lakes (varves) as potential data sources for early warning signals. Some potential sources: A paper reviewing regime shifts in the pollen records: Drying period in N. American midwest look promising Williams, J. W., J. L. Blois, and B. N. Shuman. 2011. Extrinsic and intrinsic forcing of abrupt ecological change: case studies from the late Quaternary.

Can Novel Ecosystems Do the Job of "Natural" Ones?

Noam Ross — Thu, 01 Sep 2011 00:00:00 +0000

This week in Science, Shahid Naeem reviews two books (paywall) about modern, "novel" ecosystems, which humans have created by mixing together species that never evolved together. He wonders, are such systems Frankensteins? Modern ecosystems that are haphazardly assembled from the remains of human development are unpredictable and fragile. With one billion people hungry, two billion poor and three billion in desperate need of water, the hopes of humanity rest on conserving, restoring and sustainably managing the services that nature provides.

Climate Change and Credit Risk in the Chemicals Sector

Noam Ross — Tue, 22 Feb 2011 00:00:00 +0000

WRI continues the march of environmentally-driven credit analyses with a new report on the chemical sector and how climate regulation could effect industry's ability to borrow. WRI looks at both congressionally- and EPA-driven scenarios for greenhouse gas regulation and maps how different chemical sub-sectors will be affected in each. Differences between cap-and-trade legislation and EPA-implemented regulation are interesting and not entirely intuitive. For instance, based on previous attempts at cap-and-trade, legislation will probably provide free emissions permits to emissions-intense sectors for the first decade or so, leaving medium emitters the most exposed.

Delving into the Green Economy Report

Noam Ross — Mon, 21 Feb 2011 00:00:00 +0000

UNEP published the Green Economy Report (GER) today. I've been looking forward to reading this as it comes from the team that produced the impressive Economics of Ecosystems and Biodiversity Study (TEEB). TEEB aimed to be the "Stern report" for biodiversity, but it was very different piece of work. GER, on the other hand, does something very similar to Stern - it lays out contrasting scenarios for global investment and explores their consequences.

Of Billabongs, Weevils, and Alternative Stable States

Noam Ross — Thu, 03 Feb 2011 00:00:00 +0000

I've heard the song "Waltzing Matilda" many times but I only learned today the meaning of the word billabong - a long lake formed by a river jumping its bed. (In America we call them oxbow lakes.) The billabongs of Australia's Kakadu National Park are the site of a revealing ecological phenomenon reported today in Nature by Anthony Ives and colleagues. Kariba weed, an invasive fern, arrived in the lakes in 1983, but has been kept somewhat in check through the deliberate introduction of the silvinia weevil.

Tipping Points and the Precautionary Principle

Noam Ross — Mon, 24 Jan 2011 00:00:00 +0000

Many ecological systems have tipping points - thresholds where small changes in impacts can have very large effects on on ecosystem functioning, often in a bad way. Lakes, for example, might show little impact from nutrient pollution until a threshold level is reached, and then massive algal blooms form that choke off many other species growth. In the absence of knowledge of exactly how far one can push a system before reaching a tipping point, many invoke the precautionary principle, which states that in the face of uncertainty, one should take the most conservative approach.

George Sugihara on Early Warnings

Noam Ross — Mon, 17 Jan 2011 00:00:00 +0000

In SEED Magazine, theoretical biologist George Sugihara writes about early warning signals for collapses in complex systems: A key phenomenon known for decades is so-called “critical slowing” as a threshold approaches. That is, a system’s dynamic response to external perturbations becomes more sluggish near tipping points. Mathematically, this property gives rise to increased inertia in the ups and downs of things like temperature or population numbers—we call this inertia “autocorrelation”—which in turn can result in larger swings, or more volatility.

My article on rural abandonment and ecosystem services at GOOD

Noam Ross — Mon, 17 Jan 2011 00:00:00 +0000

I have an article up at GOOD magazine about the abandoned rural lands and how to manage them for ecosystem services: Brazil has had a declining rural population since 1990. Even as loggers and farmers cut and burn ancient rainforest in the south, emigrants leave northern farmlands fallow. In China, between just 2000 and 2008, the countryside lost 86 million people. The United Nations projects that the world’s total rural population will begin to decline in the 2020s.

Jellyfish and Ocean Tipping Points

Noam Ross — Sat, 15 Jan 2011 00:00:00 +0000

Over at Yale Environment 360, Richard Stone has an interesting article about ongoing work examining recent blooms of jellyfish populations. Anecdotal evidence suggests that jellyfish populations have been on the rise, and it is possible that some marine systems are entering alternate stable states that are jellyfish- rather than fish-dominated: By removing a curb on jellyfish population growth, overfishing “opens up ecological space for jellyfish,” says Anthony Richardson, an ecologist at CSIRO Marine and Atmospheric Research in Cleveland, Australia.

REDD+ and Financial Resilience for Conservation

Noam Ross — Fri, 07 Jan 2011 00:00:00 +0000

This month's Conservation Letters has a Policy Perspective on the risks of relying REDD+ funding for conservation projects. REDD+ (Reducing Emissions from Deforestation and Degradation, with the "+" standing for biodiversity and social benefits), is a mechanism for transferring funds to developing countries for forest preservation and restoration. REDD+ financing is eventually supposed to flow primarily from the private sector, and it is one of the few parts of an international climate agreement that has been uncontentious in negotiations.

Preparing for unexpected opportunities in Borneo

Noam Ross — Sun, 02 Jan 2011 00:00:00 +0000

Conservation Letters has an article about a situation in Borneo that illustrates how sudden, unpredictable events in ecology are not always bad. In the past year, the island's forests have undergone an ecosystem-wide event known as "general flowering," where trees of many species produce seeds and fruit in massive amounts. These events occur rarely (the last was 12 years ago), and in the years in between few seeds are produced and few new trees take root.

Tackling investor risk in forest restoration

Noam Ross — Tue, 21 Dec 2010 00:00:00 +0000

Ecosystem Marketplace posted an interesting document today on Global Forest Carbon Financial Risk Management Best Practices. Produced as part of a workshop of forest investors and lawyers, it outlines the risks in the forest carbon offset market and practices to manage these risks. Given the growth potential of forest carbon offset markets (not to mention other ecosystem service markets), the risk management tools for offset transactions are underdeveloped. The authors document 25 different categories of risk that need to be addressed in order to develop the market.

Managing New Invasion Risks from Biofuel Crops

Noam Ross — Thu, 16 Dec 2010 00:00:00 +0000

The search for new biofuels has effectively created an entire new category of agriculture, along with which comes a host of new management risks. The cycles of crop growth and failure may be less well known than those of more familiar food crops, and they may be affected by new pests and disease. A particularly worrisome area of risk associated with biofuel crops is the possibility that the crops themselves may become noxious pests in countries to which they are imported.

Good environmental management lowers cost of borrowing

Noam Ross — Mon, 06 Dec 2010 00:00:00 +0000

Today the RiskMetrics Group ESG Blog highlights new research showing that companies with better environmental performance are viewed as lower risk in bond markets and pay a lower cost of borrowing. The researchers, Rob Bauer and Daniel Hann, won the Moskowitz Prize for research in socially responsible investing. I found this the most interesting finding: ...the link between environmental risk and debt costs has strengthened over time. To test this, Bauer and Hann divided their 1995-2006 data sample into two parts, and performed the same tests on data from the 1995-2001 and 2001-2006 periods.

Fishing for metrics

Noam Ross — Sat, 20 Nov 2010 00:00:00 +0000

In 1998, Dan Pauly et al. of the University of British Columbia published a classic paper called "Fishing Down Marine Food Webs." They reported that humans were steadily depleting oceans of the top predators in the food web and working our way down the food web as the fish ran out. Pauly measured a value called "Mean Tropic Level," (MTL), essentially the average place in the food web that our fish come from, finding that it had declined in fisheries globally since the 1970s.

Apparently, there's nothing left to learn about ecosystem services

Noam Ross — Wed, 17 Nov 2010 00:00:00 +0000

In a new paper in Ecological Economics, Mark Sagoff criticizes ecologists for trying to find general, broadly applicable values for ecosystem services. Real values, Sagoff argues, are "dispersed, contingent, particular, local, transitory, and embedded in institutions and practices." He cites an example of citrus growers in the San Joaquin valley of California. While pollinators have been held up by many ecologists as providers of a valuable ecosystem services, pollinators are a pest to these farmers:

PricewaterhouseCoopers gets into the ecosystem services game

Noam Ross — Sun, 14 Nov 2010 00:00:00 +0000

I've noticed a rise lately in the frequency of times I see the name PricewaterhouseCoopers pop up in research about ecosystem services and economics. Most recently they have produced a series of reports with the United Nations Development Program on habitat banking in Latin America and the Carribean. Habitat banking is an ecosystem service market in which habitat "developers" protect or restore ecosystems to generate credits that can be bought by other developers as part of a requirement to mitigate damage caused by construction projects.

What do we do with forecasts of the future?

Noam Ross — Thu, 28 Oct 2010 00:00:00 +0000

Via Garry Peterson I discovered this post by Simon Donner about forecasts of this year'smassive coral bleaching event in the Caribbean. Donner and colleagues published a paper in PNAS in 2007 in which they calculated that heat waves that cause massive coral bleaching, like a previous event in 2005, had gone from being 1-in-1000-year events to a probability of once every 10-50 years during the 1990s, and by the 2030s will occur every 1-2 years.

Thinking about TEEB

Noam Ross — Sat, 23 Oct 2010 00:00:00 +0000

I've been reading the latest report from The Economics of Ecosystems and Biodiversity (TEEB) study, which was released this week at the meeting for the Convention for Biological Diversity. I've been skeptical as to the utility of the project, which was billed as a "Stern Report for Biodiversity" when it was begun three years ago. Nicholas Stern's report on the economic impact of climate change could be reduced to a few numbers - the cost of mitigation, and the cost of action, tons of carbon released and its concentration in the atmosphere.

New approaches to looking at water-related financial risks

Noam Ross — Thu, 21 Oct 2010 00:00:00 +0000

There's an article in the Times today about risks that utilities face due to water shortages. The story is based on a new report from Ceres and PricewaterhouseCoopers which claims that bond ratings agencies haven't adequately incorporated these risks into their ratings, causing an over-valuation of bonds issued by cities and public utilities. Ceres and PwC base their analyses on future projections of water supply and demand, which in turn are predicted from demographic and climate predictions.

Reading philosophy can get you down

Noam Ross — Mon, 18 Oct 2010 00:00:00 +0000

Reading Lawrence Hinman's "Ethics, a Pluralistic Approach to Moral Theory," I came across this quote in a discussion of valuing utility to future generations: ...they do not yet exist - and, depending on our actions, they may never exist. I stared at this for a long time.

Saving more than species at Nagoya

Noam Ross — Sat, 16 Oct 2010 00:00:00 +0000

There's been a whole lot of interesting stuff coming out this week related the Conference of the Parties (COP 10) for the Convention on Biological Diversity (CBD) going on in Nagoya, Japan right now. CBD's goal was to slow the loss of biodiversity loss by 2010, but that goal was not achieved, and nations are hammering out how to revive the CBD with new goals for 2020. At a prepatory meeting in May, governments agreed on 20 more specific draft targets, which aim to be “SMART” - specific, measurable, ambitious, realistic, and time-bound.

Why the carbon market needs ecologists

Noam Ross — Sat, 16 Oct 2010 00:00:00 +0000

Last week the Journal of Applied Ecology had an article titled, "How can ecologists help realize the potential of payments for carbon in tropical forest countries?" It outlined ways that ecologists could make themselves useful in Reducing Emissions from Deforestation and Degradation (REDD). The article was aimed at ecologists, but I'm going to give the authors' insights a different twist. In the interest of the welfare of my colleagues, I'd like to point out to the carbon community that ecological expertise is worth some money.

Does ecology tell us that some species are worth more than others?

Noam Ross — Mon, 11 Oct 2010 00:00:00 +0000

I just read a great paper by Michael Soulé et. al. discussing the management implications some ideas in ecology that have outpaced environmental policy. The authors, a mix of ecologists and conservationists, argue that some species, which they call "strongly interacting species," deserve higher priority in conservation because of their unique roles in ecosystems. These species have gone by many names in the ecological literature, including "keystone species," and "ecosystem engineers.

Liability for stolen ecosystem services

Noam Ross — Mon, 11 Oct 2010 00:00:00 +0000

In Wasior, Papua New Guinea, flash floods have killed well over 100 people. Conservation groups blame illegal logging activities in the Wasior area for exacerbating the flooding, and the Indonesian government is investigating this possibility. While this case is still uncertain, it is clear that deforestation leads to increased flood risk. CJA Bradshaw and colleagues published an article in Global Change Biology showing that at 10% increase in deforestation leads to a 4%-28% increase in flood frequencies in developing countries.

Measuring resilience to climate-change driven crop failure

Noam Ross — Fri, 08 Oct 2010 00:00:00 +0000

A number of news outlets have picked up on a new article in Environmental Research Letters by Andy Challinor and a team at the University at Leeds. The standard headline is "Crop Failures to Increase With Climate Change," but I think the much more interesting part of the research is the author's creation of a vulnerability index based on the historical crop data in China. Essentially, they looked at periods of drought in the past, and examined how well farmers were able to mitigate the drought's effects through additional labor or technology:

In honeybee collapse, cure the patient, not just the disease.

Noam Ross — Thu, 07 Oct 2010 00:00:00 +0000

My first published article examined implications of the massive collapse of honeybee populations on business, so I feel compelled to comment on the latest development in the hunt for the cause of colony collapse disorder (CCD). There is a new article out on the subject by a team led by University of Montana researchers and the US Army Chemical Biological center. Using proteomic sequencing, they found two culprits in the bodies of dead bees: invertebrate iridescent virus (IIV), a long-stranded DNA virus, and Nosema, a fungal spore.

Rapid evolution as a warning sign

Noam Ross — Sat, 02 Oct 2010 00:00:00 +0000

One of the emerging themes of my course in rapid environmental change is how humans have accelerated natural processes to a pace never seen before in earth's history. For instance, climate change has in the past occurred at scales of tens of thousands of years or longer, but man-made climate change in happening at the pace of decades or centuries. Less well-known is the effect we can have on the speed of evolution.

Harmful algal blooms highlight risks from cascading ecological collapse

Noam Ross — Fri, 01 Oct 2010 00:00:00 +0000

Harmful algal blooms (HABs) are scary things. The occur when populations of algae explode in coastal environments. The algae suck up the oxygen and release neurotoxins into the water, and even the local air. Fisheries and beaches have to be shut down. People have been killed. HABs aren't predictable, but its clear that they more damaging and more common than they were in the past due to nutrient pollution in coastal areas.

Payments for ecosystem services are great, unless we do them enough to make a difference

Noam Ross — Thu, 30 Sep 2010 00:00:00 +0000

The usually excellent Mongabay ran the scare headline, "Could industrial interests ruin payments for environmental services?" on a piece in Tropical Conservation Science. Thankfully the authors of the paper being reported on, "Upscaling Payments for Environmental Services (PES): Critical issues" are a little less alarmist. Nonetheless, I think that that their concern about large companies getting involved in ecosystem service markets is overwrought. PES have traditionally been conceived and applied in contexts where the providers of the service are populations (as opposed to industrial companies) – fishermen, farmers, forest dwellers.

A species is priceless - does that mean that it is worth nothing or everything?

Noam Ross — Mon, 27 Sep 2010 00:00:00 +0000

Richard Conniff has an eloquent piece up at Yale Environment 360 discussing how we place economic value on species and biodiversity in general. He tells the story of how farmers in India inadverdantly killed 99% of the country's vultures by feeding their cattle anti-inflamatory drugs. The drugs caused renal failure in vultures feeding on the carcasses. With the vultures gone, India's feral dog population skyrocketed, and the feral dogs gave many people rabies.

Risk, Insurance, LUST, and Fish

Noam Ross — Fri, 24 Sep 2010 00:00:00 +0000

Two papers crossed my desk yesterday highlighting the role insurance can play in mitigating environmental risk. The first, by Yin et. al. in Risk Analysis, discusses three appoaches to mitigating the risk of leaking underground storage tanks (a problem with the fantastic acronym LUST). Large fines for spills, as it turns out, are not a particularly efficient enforcement tool, as most LUSTs are owned by small businesses like gas stations that would likely go bankrupt before paying all the fines and cleanup costs.

Money Quote

Noam Ross — Thu, 23 Sep 2010 00:00:00 +0000

Pavan Sukhdev, Head of the UNEP Green Economy Initiative, and previously Managing Director in the Global Markets Division at Deutsche Bank, has some remarkably lucid things to say about fisheries in this month's Frontiers in Ecology and Environment: "Economics is the science of scarce resources. What is scarce here as a resource is not fishing capacity – in which every year we invest more, as a result of the subsidies that are targeted largely at the bigger fleets and the trawler fleets.

In the News: Hysteresis in Coral Reefs

Noam Ross — Tue, 21 Sep 2010 00:00:00 +0000

As this is my first crack at an explanatory post, I'd appreciate feedback on both the level and quality of the writing. Thanks! One of the things I plan to do on this blog is delve a little deeper into ecological stories that arise in the news. A great opportunity popped up today in a front-page story in the New York Times about coral reef bleaching. It seems that record temperatures this year are causing one of the largest coral die-offs in history.

Species in a Bucket

Noam Ross — Fri, 17 Sep 2010 00:00:00 +0000

I am not really a wildlife person. My own work and perspective is systemic; I study global biogeochemical cycles, mathematical systems theory, and other large, shapeless, abstract ideas. I am terrible at recognizing and remembering the names of plants and animals in the field. Also, while I enjoy an aesthetic and spiritual connection to nature, my own brand of environmentalism leans towards saving ourselves - nature for nature's sake has usually taken second place in my mind.

Michael Levy on Data Manipulation using dplyr

Noam Ross — Mon, 01 Jan 0001 00:00:00 +0000

Editor’s Note: This is a repost of Michael’s original post at his own site. Here is the dplyr talk that I recently gave to the Davis R Users’ Group. dplyr is an R library that does basic data manipulation extremely well. It is designed to make the data handling tasks that we all do over and over as easy as possible. It produces highly readable syntax that is low cognitive overhead to write.

Ongoing learning with user groups

Noam Ross — Mon, 01 Jan 0001 00:00:00 +0000

Work sessions: We have weekly, 2-hour co-work sessions where users come to work on their own projects and get help. Talks and tutorials: About every other week, the first half of our work sessions is dedicated to a presentation. These are mainly tutorials on tools in R. Sometimes they are “show-and-tell” where a user presents an analysis for feedback. Most speakers walk through a script on a large screen, and Q & A takes up half of the time.