Articles by Daniel Hocking

High Resolution Figures in R

March 12, 2013 | Daniel Hocking

As I was recently preparing a manuscript for PLOS ONE, I realized the default resolution of R and RStudio images are insufficient for publication. PLOS ONE requires 300 ppi images in TIFF or EPS (encapsulated postscript) format. In R plots … Continue reading → [Read more...]

Building R packages: missing path to pdflatex

December 15, 2012 | Daniel Hocking

Recently whiling trying to build an R package for generalized estimating equation model selection (QICpack on github), I was getting an error related to latex creating the PDF package manuals. It seems like this is a relatively common problem on … Continue reading → [Read more...]

GEE QIC update

November 15, 2012 | Daniel Hocking

Here is improved code for calculating QIC from geeglm in geepack in R (original post). Let me know how it works. I haven’t tested it much, but is seems that QIC may select overparameterized models. In the code below, I … Continue reading → [Read more...]

Stan for Bayesian Analysis

October 23, 2012 | Daniel Hocking

Bayesian analysis has been growing in popularity among ecologists recently, largely due to accessible books such as Models for Ecological Data: An Introduction, Introduction to WinBUGS for Ecologists, and Bayesian Methods for Ecology. Most ecologists with limited programming background have … Continue reading → [Read more...]

Plotting 95% Confidence Bands in R

July 26, 2012 | Daniel Hocking

I am comparing estimates from subject-specific GLMMs and population-average GEE models as part of a publication I am working on. As part of this, I want to visualize predictions of each type of model including 95% confidence bands. First I had to ma...
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Model Validation: Interpreting Residual Plots

July 18, 2011 | Daniel Hocking

When conducting any statistical analysis it is important to evaluate how well the model fits the data and that the data meet the assumptions of the model. There are numerous ways to do this and a variety of statistical tests to evaluate deviations from model assumptions. However, there is little ...
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GLMM Hell

July 7, 2011 | Daniel Hocking

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 l...
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More on R-Studio

March 22, 2011 | Daniel Hocking

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.h...
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New R IDE

March 8, 2011 | Daniel Hocking

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 complete...
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Introductory R Books

January 31, 2011 | Daniel Hocking

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/
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R GUIs, IDEs, and text editors

January 18, 2011 | Daniel Hocking

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 highlightin...
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R Workflow

December 7, 2010 | Daniel Hocking

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 workf...
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JAGS – Bayesian Analysis

December 6, 2010 | Daniel Hocking

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 ...
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GLMM and R issues

December 4, 2010 | Daniel Hocking

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 n...
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