Articles by Peter Solymos

Introducing the bSims R package for simulating bird point counts

December 22, 2019 | 0 Comments

The bSims R package is a highly scientific and utterly addictive bird point count simulator. Highly scientific, because it implements a spatially explicit mechanistic simulation that is based on statistical models widely used in bird point count analysis (i.e. removal models, distance sampling), and utterly addictive because the implementation ...
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Fitting removal models with the detect R package

August 30, 2018 | 0 Comments

In a paper recently published in the Condor, titled Evaluating time-removal models for estimating availability of boreal birds during point-count surveys: sample size requirements and model complexity, we assessed different ways of controlling for point-count duration in bird counts using data from the Boreal Avian Modelling Project. As the title ...
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Fitting removal models with the detect R package

August 30, 2018 | 0 Comments

In a paper recently published in the Condor, titled Evaluating time-removal models for estimating availability of boreal birds during point-count surveys: sample size requirements and model complexity, we assessed different ways of controlling for point-count duration in bird counts using data from the Boreal Avian Modelling Project. As the title ... [Read more...]

Shiny slider examples with the intrval R package

March 8, 2018 | 0 Comments

The intrval R package is lightweight (~11K), standalone (apart from importing from graphics, has exactly 0 non-base dependency), and it has a very narrow scope: it implements relational operators for intervals — very well aligned with the tiny manifesto. In this post we will explore the use of the package in two ...
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Phylogeny and species traits predict bird detectability

February 9, 2018 | 0 Comments

It all started with this paper in Methods in Ecol. Evol. where we looked at detectability of many species. So we wanted to use life history traits to validate our results. But we had to cut the manuscript, and there was this leftover with some neat patterns, but without much ...
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PVA: Publication Viability Analysis, round 3

February 6, 2018 | 0 Comments

A friend and colleague of mine, Péter Batáry has circulated news from Nature magazine about the EU freezing innovation funds to Bulgaria. The article had a figure about publication trends for Bulgaria, compared with Romania and Hungary. As I have blogged about such trends in ecology before (here ... [Read more...]

The progress bar just got a lot cheaper

January 23, 2018 | 0 Comments

The pbapply R package that adds progress bar to vectorized functions has been know to accumulate overhead when calling parallel::mclapply with forking (see this post for more background on the issue). Strangely enough, a GitHub issue held the key to the solution that I am going to outline below. ... [Read more...]

What is new in the intrval R package?

January 26, 2017 | 0 Comments

An update (v 0.1-1) of the intrval package was recently published on CRAN. The package simplifies interval related logical operations (read more about the motivation in this post). So what is new in this version? Some of the inconsistencies in the 1st CRAN release have been cleaned up, and I ... [Read more...]

How to write and document %special% functions in R

November 26, 2016 | 0 Comments

I spend a considerable time 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 ... [Read more...]

Progress bar overhead comparisons

October 15, 2016 | 0 Comments

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. [Read more...]

How to add pbapply to R packages

September 16, 2016 | 0 Comments

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 ...
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What is the cost of a progress bar in R?

September 11, 2016 | 0 Comments

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 ... [Read more...]

How to add pbapply to R packages?

September 6, 2016 | 0 Comments

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 ...
[Read more...]

Trends in daily R package downloads

August 23, 2016 | 0 Comments

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 ... [Read more...]

Data set with all the conceivable errors

June 14, 2016 | 0 Comments

As I was preparing for an R intro course I came up with the idea of creating a fake data set that is stuffed full of all the conceivable errors one can imagine. Just in case my imagination falls short, I’d appreciate all the suggestions in the comments so ... [Read more...]

Timer progress bar added to pbapply package

March 4, 2016 | 0 Comments

pbapply is a lightweight R extension package that adds progress bar to vectorized R functions (*apply). The latest addition in version 1.2-0 is the timerProgressBar function which adds a text based progress bar with timer that all started with this pull request. [Read more...]

mefa4 R package update

March 2, 2016 | 0 Comments

The mefa4 R package is aimed at efficient manipulation of very big data sets leveraging sparse matrices thanks to the Matrix package. The recent update (version 0.3-3) of the package includes a bugfix and few new functions to compare sets and finding dominant features in compositional data as described in ... [Read more...]
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