Statistical computing meets biodiversity conservation and natural resource management

How to write and document %special% functions in R

I spend a considerable portion of my working hours with data processing where I often use the %in% R function as x %in% y. Whenever I need the negation of that, I used to write !(x %in% y). Not much of a hassle, but still, wouldn’t it be nicer to have x %notin% y instead? So I decided to code it for my mefa4 package that I maintain primarily to make my data munging time shorter and more efficient. Coding a %special% function was no big deal. But I had to do quite a bit of research and trial-error until I figured out the proper documentation. So here it goes.

Effects of industrial sectors on species abundance in Alberta

Transformation of native habitat by human activity is the main cause of global biodiversity loss. Humans have visibly transformed 27% of Alberta to date. The effects of these changes depend on the species, and the nature and extent of the human activities in question. Teasing apart these factors in a cumulative effects framework are of the focus of several initiatives and organizations in Alberta. The Alberta Biodiversity Monitoring Institute (ABMI) collects data and produces information that helps attributing the effects of human activities on species to different industrial sectors, or as we call them, sector effects.

Progress bar overhead comparisons

As a testament to my obsession with progress bars in R, here is a quick investigation about the overhead cost of drawing a progress bar during computations in R. I compared several approaches including my pbapply and Hadley Wickham’s plyr.

How to add pbapply to R packages

As of today, there are 20 R packages that reverse depend/import/suggest (3/14/3) the pbapply package. Current and future package developers who decide to incorporate the progress bar using pbapply might want to customize the type and style of the progress bar in their packages to better suit the needs of certain functions or to create a distinctive look. Here is a quick guide to help in setting up and customizing the progress bar.

What is the cost of a progress bar in R?

The pbapply R package adds progress bar to vectorized functions, like lapply. A feature request regarding progress bar for parallel functions has been sitting at the development GitHub repository for a few months. More recently, the author of the pbmcapply package dropped a note about his implementation of forking functionality with progress bar for Unix/Linux computers, which got me thinking. How should we add progress bar to snow type clusters? Which led to more important questions: what is the real cost of the progress bar and how can we reduce overhead on process times?

My first blog post was a guest post

The title says it all. I wrote this piece about Publication Viability Analysis pondering about a pattern that I observed while looking at Hungarian ecologists publication output through time using the Web of Science database (the original post is in Hungarian).

Trends in daily R package downloads

This post was prompted by this blog about using the cranlogs package by Gabor Csardi. But my own interest as long time package developer dates back to this post by Ben Bolker. I like to see that my packages are being used. So I thought why stop at counting downloads and plotting the past. Why not predict into the future?


Yip, D. A., Bayne, E. M., Sólymos, P., Campbell, and Proppe, J. D., 2016. Sound attenuation in forested and roadside environments: implications for avian point count surveys. Condor, xx:xx–xx. —  journal website.

Dénes, F., Sólymos, P., Lele, S. R., Silveira, L., and Beissinger, S., 2016. Biome scale signatures of land use change on raptor abundance: insights from single-visit detection-based models. Journal of Applied Ecology, xx:xx–xx. —  journal website.

Ball, J. R., Sólymos, P., Schmiegelow, F. A. K., Haché, S., Schieck, J., and Bayne, E. M., 2016. Regional habitat needs of a nationally listed species, Canada Warbler Cardellina canadensis, in Alberta, Canada. Avian Conservation and Ecology, 11(2):10. —  journal website fulltext PDF.

Nordell, C. J., Haché, S., Bayne, E. M., Sólymos, P., Foster, K., Godwin, C. Krikun, R., Pyle, P., and Hobson, K. A., 2016. Within-site variation in feather stable hydrogen isotope (δ2Hf) values of boreal songbirds: implications for assignment to molt origin. PLoS ONE, 11(11):e0163957. —  journal website fulltext PDF.

Mahon, C. L., Holloway, G., Sólymos, P., Cumming, S. G., Bayne, E. M., Schmiegelow, F. K. A., and Song, S. J., 2016. Community structure and niche characteristics of upland and lowland western boreal birds at multiple spatial scales. Forest Ecology and Management, 361:99–116. —  journal website.