Articles by R on Pablo Bernabeu

Avoiding knitting errors in (R) Markdown using knit-deleting-service-files()

December 17, 2021 | R on Pablo Bernabeu

The function knit-deleting-service-files() is designed to avoid (R) Markdown knitting errors caused by service files from previous knittings (e.g., manuscript.tex, ZHJhZnQtYXBhLlJtZA==.Rmd, manuscript.synctex.gz). The function first suggests deleti...

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Walking the line between reproducibility and efficiency in R Markdown: Three methods

November 13, 2021 | R on Pablo Bernabeu

As technology and research methods advance, the data sets tend to be larger and the methods more exhaustive. Consequently, the analyses take longer to run. This poses a challenge when the results are to be presented using R Markdown. One has to walk the line between reproducibility and efficiency. On ... [Read more...]

Tackling knitting errors in R Markdown

November 13, 2021 | R on Pablo Bernabeu

When knitting an R Markdown document after the first time, errors may sometimes appear. Three tips are recommended below. 1. Close PDF reader window When the document is knitted through the ‘Knit’ button, a PDF reader window opens to present the result. Closing this window can help resolve knitting errors. 2. Delete ... [Read more...]

A new function to plot convergence diagnostics from lme4::allFit()

October 20, 2021 | R on Pablo Bernabeu

Linear mixed-effects models (LMM) offer a consistent way of performing regression and analysis of variance tests which allows accounting for non-independence in the data. Over the past decades, LMMs have subsumed most of the General Linear Model, with a stead increase in popularity (Meteyard & Davies, 2020). Since their conception, LMMs have ...

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Parallelizing simr::powercurve() in R

July 23, 2021 | R on Pablo Bernabeu

The powercurve function from the simr package in R (Green & MacLeod, 2016) can incur very long running times when the method used for the calculation of p values is Kenward-Roger or Satterthwaite (see Luke, 2017). Here I suggest three ways for cutting down this time. Where possible, use a high-performance (or high-end) ...

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WebVTT caption transcription app

December 31, 2020 | R on Pablo Bernabeu

This open-source, R-based web application allows the conversion of video captions (subtitles) from the Web Video Text Tracks (WebVTT) Format into plain texts. For this purpose, users upload a WebVTT file with the extension .vtt or .txt (examples av... [Read more...]

R Markdown amidst Madison parks

August 13, 2020 | R on Pablo Bernabeu

This document is part of teaching materials created for the workshop ‘Open data and reproducibility v2.1: R Markdown, dashboards and Binder’, delivered at the CarpentryCon 2020 conference. The purpose of this specific document is to practise R Markdown, including basic features such as Markdown markup and code chunks, along with more ... [Read more...]

Web application for the simulation of experimental data

May 31, 2020 | R on Pablo Bernabeu

Purposes This open-source, R-based web application is suitable for educational and research purposes in experimental and quantitative sciences. It allows the creation of varied data sets with specified structures, such as between-group and within-participant variables, that can be categorical or continuous. These parameters can be set throughout the various tabs (...

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Data dashboard: Butterfly species richness in Los Angeles

December 31, 2019 | R on Pablo Bernabeu

Dashboard This dashboard presents open data (iNaturalist and BioScan) from Prudic, K.L.; Oliver, J.C.; Brown, B.V.; Long, E.C. Comparisons of Citizen Science Data-Gathering Approaches to Evaluate Urban Butte... [Read more...]

Data is present: Workshops and datathons

December 31, 2019 | R on Pablo Bernabeu

Enhanced data presentation using reproducible documents and dashboards Calendar Date Title Event and location Registration 26 Nov 2020 Mixed-effects models in R, and a new tool for data simulation New Tricks Seminars, Dept. Psychology, Lancaster University [online] 8 Oct 2020 Reproducibilidad en torno a una aplicación web Reprohack en español, LatinR Conference 2020 [... [Read more...]

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Articles by R on Pablo Bernabeu

Avoiding knitting errors in (R) Markdown using knit-deleting-service-files()

Walking the line between reproducibility and efficiency in R Markdown: Three methods

Tackling knitting errors in R Markdown

A new function to plot convergence diagnostics from lme4::allFit()

Parallelizing simr::powercurve() in R

WebVTT caption transcription app

R Markdown amidst Madison parks

Web application for the simulation of experimental data

Data dashboard: Butterfly species richness in Los Angeles

Data is present: Workshops and datathons

Articles by R on Pablo Bernabeu

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