2024 LLMs/genAI + R roundup
Tools and packages for working with LMMs in R.
All Posts
2024
Descargar, procesar, y acomodar imágenes en un mosaico hexagonal interactivo
Mosaicos hexagonales en HTML con múltiples imágenes desde un directorio.
Download, batch process, and tile images
Hexagonal html tiles with all the images in a folder.
New packages - hexsession & forgts
Recent releases
Filenames to variables
Putting information recorded in filenames into the data rectangle
Formatted spreadsheets can still work in R
Tackling problematic spreadsheets
Cleaning tables with merged cells
Tidying data with problematic line breaks
Plotting phylogenies with collapsed and labeled nodes
Iteration made easy with purrr
You ‘tidyr::complete()’ me
Complete sequences from start and end values stored in separate columns
2023
What are people commenting about their loaded packages?
Exploring code comments about R package calls on GitHub
2022
Fixing broken and irregular column headers
Useful function from unheadr for data cleaning
Waffle charts with svg images
Creating waffle charts with ggsvg
annotater 0.2.0
Annotate R code with details on the packages being loaded
NBA player names in hip hop lyrics
Tidy text manipulation and plotting.
2021
Sharing nice code with addins and IDE tools
Five tools to make R code cleaner and more reproducible.
Plotting model-based clusters of population genetic structure
Plotting Structure, DAPC, or Admixture results with ggplot2.
Mapas tridimensionales en R
Utilizando el paquete rayshader para generar mapas fotorealistas a partir de objectos ggplot.
Rendering thematic maps in 3D
Using rayshader to render ggplot2 maps in 3D.
Filter data before reading with awk and R
Command line tools + R to read large Global Fishing Watch data efficiently.
Data Cleaning with R
New Course Available - Clean your data more quickly and efficiently than ever before
Raster calculations on stars objects
Using R as a GIS - raster calculation (reclass, sum) and plotting.
SIG con R - Objetos stars
Análsis espaciales con R - suma, reclasificación y visualización de rasters.
2020
Classifying rodent diets
New publication
Intersecting consecutive pairs of list elements in R
An example with NBA postseason data.
PCA with Age of Empires II data
Data cleaning, Principal Component Analysis, and visualization of AoE2 data.
Bold indicates negative
Flattening spreadsheet cell formatting to usable character strings.
Dog breed popularity bump chart
Plotting how popularity rankings for dog breeds change through time, (p)updated for 2020.
High-latitude maps
Plotting seal observations in Antarctica with R and ggplot2.
Mapas de altas latitudes en R
Ilustrando la distribución de dos especies de focas antárticas con R y ggplot2.
annotater
RStudio addins to annotate R code with details on the packages being loaded
SIG con R - Actualización
Extraer valores de uno o más raster a partir de coordenadas xy usando R.
Tidying formatted spreadsheets with unheadr
Rectangling formatted spreadsheet data
2019
Merging rows in R
Verb-like function to identify and merge rows
Formatted spreadsheets in R
Import and work with formatted spreadsheet data
Extracting raster values into polygon attributes using R
Getting or calculating the values from an underlying raster using stars and sf
ggplot2 visualization of conditional inference trees
Plotting conditional inference trees with dichotomous responses in R, a grammar of graphics implementation
Data Rectangling Resource Roundup
Links to material on Data Rectangling.
Dog breed popularity chart
Plotting how popularity rankings for dog breeds change through time, (p)updated for 2019.
Plots for model-based clustering of ancestral populations
Plot models of population structure with ggplot for arbitrary values of K.
Quantifying point overlap for NBA shot chart data
Find the most and least similar shot patterns for basketall players.
Shot distances and court locations for NBA games
Follow up post - Download, plot, and animate per-game shooting data.
Animate shot distances for NBA games
Download, plot, and animate per-game shooting data.
2018
Riqueza de especies usando R y sf
Alternativas a los SIG para calcular riqueza de especies con una cuadrícula.
Species richness analysis with R and sf
Quantify and plot spatially-intersecting features.
From photo to tibble
Digitizing and rectangling a restaurant menu.
Less bar charts with error bars please
ggplot2 alternatives to dynamite plunger plots
PDF to PPT via RMarkdown
How was this not a thing already?
Crisp spatial figures with R, ggplot2, and sf
Pretty plotting of point and polygon features.
Mapas nítidos con R, ggplot2 y sf
Figuras espaciales con puntos y polígonos.
Spreadsheet hijinks
The results from crowd-sourcing a suitable term for a common spreadsheet practice.
Unnesting unsplittable strings
Tidyng human-readable data by inserting suitable separators.
More on extracting data from PDFs
Cleaning data from the US Financial Disclosure Reports featured in the A.B. Tran and H. Wickham live data challenge.
Get top values by group (animated)
Animated explanation of dplyr::top_n() and code to create the gif.
Animate your data wrangling
Using gganimate to animate the data-munging process.
unheadr
A package to handle awkwardky-structured data with multiple header rows or values broken across multiple rows.
Unbreaking values with R
Wrangling grouped data with broken values and NA/empty rows per variable per group.
New publication: Arboreal rodent movement ecology
Tracking two species of Neotropical cloud forest rodents in three dimensions.
This is what happens when you encode data as cell formatting in Excel
Extracting and wrangling data encoded as text formatting in multi-sheet Excel files.
Dog breeds bump chart
Plotting how popularity rankings for dog breeds change through time.
Tidyeval meets PDF table hell
Using tidy evaluation to fix values broken up across rows.
Set the breaks!
Omitting items from legends in ggplot2.
2017
The tRee of dog bReeds (version 2)
Manipulate and visualize data describing dog breeds and how they are related.
Apply functions to grouped data and write each element to disk
Split a table by a grouping variable, apply functions to each element, and export to separate files.
Comparing dog and cat ratings
Downloading, comparing, and visualizing Twitter ratings for dogs and cats.
Limpiando datos en R
Algunos pasos para reacomodar tablas con columnas repetidas, encabezados que no pertenecen, y notas al pie de página.
Reshaping and tidying data from awkward spreadsheet formats
Wrangle duplicated variable names, weird header rows, and footnotes.
Jumping dogs and density plots
Plotting density distributions with the underlying data as a point swarm.
Using Tidy Evaluation to untangle header rows
An R function to put interspersed header rows into their own column.
Tidy tables for collections-based research (Part 2)
Wrangling commonly-used data formats. Part 2 - Compound values.
Tidy tables for collections-based research (Part 1)
Wrangling commonly-used data formats. Part 1 - GenBank accession tables.
Matrix Indexing
Recoding binary dummy variables into factors. Includes tidyverse and base R approaches.
Novedades en la literatura mastozoológica, abril 2017
Resumen del seminario mensual de actualización en literatura científica del grupo de Mastozoología, MZFC-UNAM.
The tRee of dog bReeds
Working with data describing dog breeds and how they are related.
Good dogs (and their names)
Extracting dog names from tweets by WeRateDogs.
What’s in a name?
Text analysis applied to mammalian common names.
ggpup: place two random dog images next to any ggplot object
Using web scraping, raster objects and gridExtra to add images to your plots.
Novedades en la literatura mastozoológica, marzo 2017
Resumen del seminario mensual de actualización en literatura científica del grupo de Mastozoología, MZFC-UNAM.
More on diverging stacked bar plots
My take on the SkepticalScience global warming figure using ggplot, includes R code and data.
Making sense of trees
Extracting edge lengths from R phylo objects.
Visualizando pares de variables independientes
Graficando dos variables independientes sin usar ejes duales.
Who is Who?
Matching taxonomic names; joint post with Manuela González-Suárez.
Rongeurs
La morphologie permet de prédire le régime alimentaire et mode de locomotion des rongeurs.
Rodent ecomorphology in a phylogenetic context
Summary of our new publication ‘Morphology captures diet and locomotor types in rodents’.
The world’s primates are in trouble
Brief updates on our new publication reviewing the primate extinction crisis.
Valore máximos y mínimos para datos agrupados
Cómo identificar los valores máximos o mínimos de una variable para datos agrupados utilizando R y dplyr.
Top and bottom values for groups
Using R and dplyr to extract minimum or maximum (or both) variable values within groups.
2016
Diverging bar plots
Making diverging stacked bar plots in R using ggplot.
Grouping points
Four ways to draw polygons around groups of points using ggplot2.
Agrupando Puntos
Cuatro maneras de agrupar puntos en dos dimensiones con ggplot.
Measuring point overlap
Measuring spatial overlap with point data.
Science Is Global
Emoji flags, international research, and tweet analysis in R.
R para tareas espaciales
Extraer valores de uno o más raster a partir de coordenadas xy usando R.
Basic biodiversity data-wrangling operations
Manipulating variables and content in biodiversity datasets using base R and dplyr.
pls don’t do this :(
Easy changes to make before sharing tabular data with others.
Labeled barplots in ggplot2
Visualizing grouped values using labeled side-by-side bars in ggplot2.
Presentations section and Biotweeps
Brief updates, March 2016
2015
Research patterns in new species of mammals
Summary and visualization of research effort for recently described species of terrestrial mammals. Includes R code and data.
Extinction risk research in mammals
Trends and patterns in mammal extinction risk research, and thoughts on writing a sole-author paper.
Mapping local and cross-boundary conservation research
Mapping spatial patterns in conservation research using R and ICCB 2011 presentation data.
Getting elevation data for point occurrences in R using rgbif
Using R to fetch elevation for lat/long data through an API.
Section lengths in scientific papers
How long is the average section in a research article? Includes code for downloading and plotting data for five journals.
Plotting conditional inference trees
Example code for visualizing binary trees with dichotomous responses in R, focused on extinction risk modeling.
If you present will you publish?
Why study the publication rates of presentations at ecology, evolution, and conservation conferences.
Trends in mammal research in Mexico 1991-2012
Summary of research presented at scientific meetings of the Mexican Mammalogy Society (AMMAC) 1991-2012.
Postdoc!
Update on my upcoming position and thoughts on the job hunt.
Ordinal extinction risk models
Modeling IUCN Red List data as an ordered response variable. A reproducible #rstats example for terrestrial carnivores.
Lagomorph research
Inaugural blog post, May 2015. Summary of recent research on Lagomorpha (rabbits, hares, pikas).