Resources, software and data

Resources

• McMaster R users’ list info/subscription page (“A list for general help and discussion among R users at McMaster”) – intended as a friendly/low-stress channel for people to ask R questions of the campus community
• Bio data lunch mailing list (weekly lunchtime group discussions of specific data analysis problems)
• Notes on running R on HPC, especially Compute Canada

Software

I write a lot of software in R. Here are some R packages.

package	purpose	other authors	download percentile on CRAN	total downloads	first year posted
lme4	mixed models	Doug Bates, Martin Maechler	99.5	34.6M	2012
broom.mixed	“tidy” summaries of mixed models		97.4	843.4k	2018
glmmTMB	mixed models	Mollie Brooks, Kasper Kristensen	96.8	1.2M	2017
bbmle	maximum likelihood estimation		96.4	1.2M	2012
emdbook	utilities for “Ecological Models and Data in R”		94.3	536.6k	2012
R2admb	R interface to AD Model Builder		89.1	153.6k	2012
epigrowthfit	epidemic growth curve estimation	Mikael Jagan	29.2	1k	2024
fitode	general purpose ODE fitting via sensitivity equations	Sang Woo Park	12.6	4.4k	2022
cpcbp	common principal components analysis and size correction				NA
mixstock	analysis of “mixed stocks” (biological populations)				NA
macpan2	epidemic model calibration and forecasting	Steve Walker and others			NA
celebrate	goofy sound effects for statistical summaries				NA
glmmadmb	GLMMs with AD Model Builder				NA
cricketr	assessing stopping rules in cricket	Ahsan Batti			NA

• “Other authors” only includes authors who contributed significantly more to the package than I did. Check out the DESCRIPTION files or help(package="whatever") for the full lists of authors and contributors.
• Package ranks and download counts computed as of 08 Oct 2024. (These metrics differ in order because packages have been on CRAN for different lengths of time.)

Data and miscellaneous

• code for spatial moment equations
• measles data
• workshop notes and materials from workshops before the Ecology and Evolution of Infectious Disease (2005, 2008-2012)