R Weekly 2023-W03 Testing with shinytest2 and reproducibility with R!

16 Jan 2023

• How to have (my) content shared by R Weekly?

This week’s release was curated by Batool Almarzouq, with help from the R Weekly team members and contributors.

Highlight

• End-to-end testing with shinytest2 Part 2

• MRAN is getting shutdown - what else is there for reproducibility with R, or why reproducibility is on a continuum?

Insights

• progressr 0.13.0: cli + progressr = ♥

• One Fewer Dependency of knitr

R in the Real World

• Deploying R with kubernetes

• MRAN is getting shutdown - what else is there for reproducibility with R, or why reproducibility is on a continuum?

• RTutor: Public Infrastructure Spending and Voting Behaviour

• The Falling of ARK Innovation ETF: Forecasting with Boosted ARIMA Regression Model

• Asia Against Dollar: Forecasting with Modeltime

• Where should my family meet?

R in Organizations

• Expanding our Community through Multilingual Publishing

• How a UseR! 2014 Experience Led to the Development of a 1,700-member R Community in Budapest

Resources

• R Crash Course for Biologists

• Statistical Programming Paradigms and Workflows (BSPH 140.840)

New Packages

📦 Go Live for More New Pkgs 📦

CRAN

• {symphony} 0.1.0: Efficient and Precise Single-Cell Reference Atlas Mapping

• {chatgpt} 0.1.4: Interface to ‘ChatGPT’ from R

• {autoGO} 0.9: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

• {usedthese} 0.1.0: Summarises Package & Function Usage

• {scenes} 0.1.0: Switch Between Alternative ‘shiny’ UIs

• {loadeR} 1.1.1: Load Data for Analysis System

• {roxytest} 0.0.2: Various Tests with ‘roxygen2’

• {pkgmaker} 0.32.7: Development Utilities for R Packages

• {timeLineGraphics} 1.0: HTML with Horizontal Strips Symbolizing Events in a Person’s Life

• {plantTracker} 1.0.1: Extract Demographic and Competition Data from Fine-Scale Maps

• {zoomr} 0.1.1: Connect to Your ‘Zoom’ Data

• {scROSHI} 1.0.0.0: Robust Supervised Hierarchical Identification of Single Cells

• {options} 0.0.1: Simple, Consistent Package Options

• {paramGUI} 2.2.0: A Shiny GUI for some Parameter Estimation Examples

• {packagefinder} 0.3.4: Comfortable Search for R Packages on CRAN, Either Directly from the R Console or with an R Studio Add-in

• {mdsr} 0.2.7: Complement to ‘Modern Data Science with R’

GitHub or Bitbucket

• whatarelief

Updated Packages

🔍 Search on R-universe 🔍

• {reproducer} 0.5.0: Reproduce Statistical Analyses and Meta-Analyses - diffify

• {biomod2} 4.2-2: Ensemble Platform for Species Distribution Modeling - diffify

• {starry} 0.1.2: Explore Data with Plots and Tables - diffify

• {spsurvey} 5.4.1: Spatial Sampling Design and Analysis - diffify

• {mikropml} 1.5.0: User-Friendly R Package for Supervised Machine Learning Pipelines - diffify

• {landsepi} 1.2.4: Landscape Epidemiology and Evolution - diffify

• {FAIRmaterials} 0.2.0: Make Materials Data FAIR - diffify

• {dbplyr} 2.3.0: A ‘dplyr’ Back End for Databases - diffify

• {anipaths} 0.10.2: Animation of Multiple Trajectories with Uncertainty - diffify

• {DiceView} 2.1-0: Methods for Visualization of Computer Experiments Design and Surrogate - diffify

• {ngramr} 1.9.3: Retrieve and Plot Google n-Gram Data - diffify

• {geomorph} 4.0.5: Geometric Morphometric Analyses of 2D and 3D Landmark Data - diffify

• {shiny.i18n} 0.3.0: Shiny Applications Internationalization - diffify

• {doRNG} 1.8.6: Generic Reproducible Parallel Backend for ‘foreach’ Loops - diffify

• {this.path} 1.2.0: Get Executing Script’s Path, from ‘Rgui’, ‘RStudio’, ‘VSCode’, ‘source()’, and ‘Rscript’ (Shells Including Windows Command Line / / Unix Terminal) - diffify

• {schtools} 0.4.0: Schloss Lab Tools for Reproducible Microbiome Research - diffify

• {mlflow} 2.1.1: Interface to ‘MLflow’ - diffify

• {pak} 0.4.0: Another Approach to Package Installation - diffify

• {dataverse} 0.3.12: Client for Dataverse 4+ Repositories - diffify

• {edeaR} 0.9.2: Exploratory and Descriptive Event-Based Data Analysis - diffify

• {gdtools} 0.3.0: Utilities for Graphical Rendering and Fonts Management - diffify

• {ggspectra} 0.3.10: Extensions to ‘ggplot2’ for Radiation Spectra - diffify

• {collapse} 1.9.0: Advanced and Fast Data Transformation - diffify

• {r2resize} 1.4: In-Text Expandable and Resizable Containers, Images and Data Tables in ‘Shiny’, ‘Markdown’ and ‘Quarto’ Documents - diffify

• {styler} 1.9.0: Non-Invasive Pretty Printing of R Code - diffify

• {tidyquery} 0.2.4: Query ‘R’ Data Frames with ‘SQL’ - diffify

• {explore} 1.0.2: Simplifies Exploratory Data Analysis - diffify

• {SCpubr} 1.1.1: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data - diffify

• {RNAsmc} 0.8.0: RNA Secondary Structure Module Mining, Comparison and Plotting - diffify

• {KMunicate} 0.2.3: KMunicate-Style Kaplan–Meier Plots - diffify

• {shapviz} 0.4.1: SHAP Visualizations - diffify

Videos and Podcasts

• Listen to the R-Weekly Highlights Podcast

Tutorials

• SQL and noSQL approaches to creating & querying databases

• End-to-end testing with shinytest2 Part 2

• git and GitHub in R for the casual user

R Project Updates

Updates from R Core:

Upcoming Events in 3 Months

Events in 3 Months:

• A list of R conferences and meetings

• This week’s local R-User and applied stats events

• {targets} in Action

• Weekly R Workshops for Ukraine

• Feb 23: Making Beautiful And Effective Maps In R

• March 15-17: ShinyConf 2023

• SatRdays London 2023

rtistry

library(tidyverse)
seq(from=-10, to=10, by = 0.05) %>%
expand.grid(x=., y=.) %>%
ggplot(aes(x=(x+pi*sin(y)), y=(y+pi*sin(x)))) +
geom_point(alpha=.1, shape=20, size=1, color="black")+
theme_void()#rstats #maths #generativeart #ggplot2 pic.twitter.com/Iq4bSeNAD4

— Antonio Sánchez Chinchón (@aschinchon) January 15, 2023

Quotes of the Week

Fun yet cruel #rstats #R pic.twitter.com/zei1hsfp4f

— Racha (@Racha_R_G) January 16, 2023

A good number of requests for a population density map of Pakistan so here's one! #rayshader adventures, an #rstats tale pic.twitter.com/4LXBiKL7nm

— terence fosstodon (@researchremora) January 13, 2023