Publications by Daniel Hocking
Another boring blog
I recently decided to create two blogs as outlets for my research. The first (The Richness of Life) focuses more on the organisms I work with as an ecologist and my general interest as a student of natural history. This blog on Quantitative Ecology stems from my recent obsessive frustration with analyzing various data sets. I ha...
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GLMM and R issues
I have been trying to run a Generalized Linear Mixed Model (GLMM) for some count data with repeated measures on sub-sampled sites and fixed effects at the site level with covariates at both the sub-plot and time levels. Plus there are different numbers of sub-plots within each site and not all sub-plots are sampled the same number o...
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JAGS – Bayesian Analysis
JAGS is used for Bayesian analysis using MCMC and stands for Just Another Gibbs Sampler. It is an alternative to WinBUGS and can be accessed through R just like WinBUGS (via R2jags or RJags). It will work on a Mac unlike WinBUGS. The only problem is that most books include WinBUGS examples and not JAGS examples. However, much of the langu...
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R Workflow
When working with R you end up using a large number of datasets, packages, functions, objects, output files, workspaces, etc. It can get a bit overwhelming trying to keep everything organized. That is why a consistent, well-organized workflow is needed. I definitely do not have one yet. I’ll post more on script editors and IDEs another...
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Why use R
Here’s a link to a blog that lists some reasons to use Rhttp://blog.fosstrading.com/2010/12/why-use-r.html Related To leave a comment for the author, please follow the link and comment on their blog: Quantitative Ecology. R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics...
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R GUIs, IDEs, and text editors
When deciding what program to write your R code in it is important to consider a number of factors so you can keep organized and work efficiently. I found this article useful for getting started. Text editors include syntax highlighting and other useful features often including text auto-complete functions. Integrated Development Envi...
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Introductory R Books
Here’s a link to another blog compiling information and recommendations are introductory books on R (not statistics books that use R). I thought this might be useful for people.http://csgillespie.wordpress.com/2011/01/28/r-programming-books-updated/ Related To leave a comment for the author, please follow the link and comment on...
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New R IDE
I’m always looking for ways to improve my workflow and overall academic efficiency. I’ve tried a variety of text editors, GUIs, and integrated development environments (IDEs) for R. I have some preferences but I haven’t found anything that I’m completely happy with. I just heard about a new one from RStudio and am going to giv...
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More on R-Studio
Here’s a link to keyboard shortcuts for the RStudio IDE. RStudio has replaced EMacs, Aquamacs, Tinn-R, Bluefish, and even Komodo Edit as my preferred R IDE/editor.http://gettinggeneticsdone.blogspot.com/2011/03/rstudio-keyboard-shortcut-reference-pdf.html?showComment=1300836557238#c4651124233045895931 Related To leave a comment fo...
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GLMM Hell
I have been starting to analyze some data I have of repeated counts of salamanders from 5 plots over 4 years. I am trying to develop a predictive model of salamander nighttime surface activity as a function of weather variables. The repeated counting leads to the need for Generalized Linear Mixed Models (GLMM). Count data often result...
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