R Weekly 2020-34 Best OS for R, lines of best fit, truncated distributions

24 Aug 2020

Release Date: 2020-08-24

This week’s release was curated by Miles McBain, with help from the RWeekly team members and contributors.

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

Highlight

• Best OS for R users

• Lines of best fit

• Generating data from a truncated distribution

Insights

• Why Package & Environment Management is Critical for Serious Data Science

• Simulate! Simulate! - Part 4: A binomial generalized linear mixed model

• Benford’s Law: Applying to Existing Data

• Best OS for R users

• Developing dittodb

• Taking Control of Plot Scaling

• Boundary corrected kernel density

• Make R Shiny Dashboards Faster with updateInput, CSS, and JavaScript

• Lines of best fit

• Generating data from a truncated distribution

R in the Real World

• Modeling the Pittsburgh City Boundary

R in Academia

• Thank you to our Speakers and Participants – COVID-19 Data Forum II

Resources

• More sample exams

• Graphics in R with ggplot2

• Awesome R Learning Resources

New Packages

📦 Go Live for More New Pkgs 📦

CRAN

• {hover} 0.1.0: CSS Animations for ‘shiny’ Button Elements

• {nimbleSCR} 0.1.0: Spatial Capture-Recapture (SCR) Methods Using ‘nimble’

• {fable.prophet} 0.1.0: Prophet Modelling Interface for ‘fable’

• {cyclomort} 1.0.2: Survival Modeling with a Periodic Hazard Function

• {HeterFunctionalData} 0.1.0: Test of No Main and/or Interaction Effects in Functional Data

• {fairmodels} 0.1.1: Flexible Tool for Bias Detection, Visualization, and Mitigation

• {bootComb} 0.2.0: Combine Parameter Estimates via Parametric Bootstrap

• {tgstat} 2.3.14: Amos Tanay’s Group High Performance Statistical Utilities

• {hiphop} 0.0.1: Parentage Assignment using Bi-Allelic Genetic Markers

• {faux} 0.0.1.4: Simulation for Factorial Designs

• {bomWater} 0.4.0: Download Australian Bureau of Meteorology Water Data

• {PO.EN} 1.0: An Elastic-Net Regularized Presence-Only Model

• {pdi} 0.4.1: Phenotypic Index Measures for Oak Decline Severity

• {eurlex} 0.2.1: Retrieve Data on European Union Law

• {ebmstate} 0.1.0: Empirical Bayes Multi-State Cox Model

• {textmatching} 0.1.0: Functions for Matching with Text-Based Confounding

• {weightedZdiff} 0.1.0: Calculation of z-Differences

• {twn} 0.1.0: Taxa Waterbeheer Nederland voor R

• {SmartMeterAnalytics} 1.0.3: Methods for Smart Meter Data Analysis

• {prt} 0.1.0: Tabular Data Backed by Partitioned ‘fst’ Files

• {pathmodelfit} 1.0.4: Path Component Fit Indices for Latent Structural Equation Models

• {BayesMRA} 1.0.0: Bayesian Multi-Resolution Gaussian Process Approximations

• {tTOlr} 0.2: Likelihood Ratio Statistics for One or Two Sample T-Tests

• {ProbReco} 0.1.0: Score Optimal Probabilistic Forecast Reconciliation

• {liver} 1.0: “Eating the Liver of Data Science”

• {DWBmodelUN} 1.0.0: Dynamic Water Balance a Hydrological Model

• {konfound} 0.2.2: Quantify the Robustness of Causal Inferences

• {ffscrapr} 1.0.0: API Client for Fantasy Football League Platforms

• {pdxTrees} 0.4.0: Data Package of Portland, Oregon Trees

• {edmdata} 1.0.0: Data Sets for Psychometric Modeling

• {BioInsight} 0.1.0: Filter and Plot RNA Biotypes

• {dpseg} 0.1.1: Piecewise Linear Segmentation by Dynamic Programming

• {ROCpsych} 1.3: Compute and Compare Diagnostic Test Statistics Across Groups

• {ResidentialEnergyConsumption} 1.0.1: Residential Energy Consumption Data

• {ER} 1.0.0: Effect + Residual Modelling

• {rasciidoc} 2.1.3: Create Reports Using R and ‘asciidoc’

• {goxygen} 1.0.3: In-Code Documentation for ‘GAMS’

• {glmbb} 0.4: All Hierarchical or Graphical Models for Generalized Linear Model

GitHub or Bitbucket

• {tinieR} 0.1.0: Shrink image filesizes with TinyPNG.com’s API

• Introducing {sourrr}: a dinky little package for generating sourdough recipes using baker’s percentage

• Introducing ‘cairobasic’ - an R6 wrapper around cairocore

• Introducing ‘cairocore’ - fast 2d drawing canvas backed by cairo

• Introducing ‘chipmunkcore’ - a wrapper for the chipmunk2d physics simulation c library

Galton board now working (in mysterious ways!)

Hoping to release {chipmunkcore} package soon - you'll be able to place your own segments and circular bodies for 2d rigid body physics sim.#RStats @carroll_jono pic.twitter.com/p5QkPQNOuU

— mikefc (@coolbutuseless) August 19, 2020

Updated Packages

• taxizedb: an update

• {nlme} 3.1-149: Linear and Nonlinear Mixed Effects Models

• {mgcv} 1.8-32: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

• {SNPassoc} 1.9-2.1: SNPs-based Whole Genome Association Studies

• {dplyr} 1.0.2: A Grammar of Data Manipulation

• {chron} 2.3-56: Chronological Objects which can Handle Dates and Times

• {Require} 0.0.7: Installing and Loading R Packages for Reproducible Workflows

• {reproducible} 1.2.1: A Set of Tools that Enhance Reproducibility Beyond Package Management

• {pbapply} 1.4-3: Adding Progress Bar to ‘*apply’ Functions

• {mlr3pipelines} 0.2.1: Preprocessing Operators and Pipelines for ‘mlr3’

• {hdf5r} 1.3.3: Interface to the ‘HDF5’ Binary Data Format

• {emmeans} 1.5.0: Estimated Marginal Means, aka Least-Squares Means

• {MASS} 7.3-52: Support Functions and Datasets for Venables and Ripley’s MASS

• {tidyLPA} 1.0.8: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software

• {rFerns} 4.0.0: Random Ferns Classifier

• {pcalg} 2.6-11: Methods for Graphical Models and Causal Inference

• {startR} 2.0.0: Automatically Retrieve Multidimensional Distributed Data Sets

• {StanHeaders} 2.21.0-6: C++ Header Files for Stan

• {Signac} 1.0.0: Analysis of Single-Cell Chromatin Data

• {DiffXTables} 0.1.1: Pattern Analysis Across Contingency Tables

Videos and Podcasts

• Shiny Developer Series Episode 11 - Eric Nantz is joined by package author and Shiny enthusiast Yoni Sidi to discuss the impact of Shiny in life sciences, origins of {ggedit}, and more.

• How to create an API for your R code

Gist & Cookbook

• 2019 NFL Team Ratings

• Voronoi portraits

R Internationally

• The impact of CDSB on me

Tutorials

• Loading and Visualizing OpenSky Network Flight Data in R (short)

• Buffer areas for nearest neighbours or national marine areas delineation

• R Package Integration with Modern Reusable C++ Code Using Rcpp - Part 4

• Spreadsheet workflows in R

• How to Extract Time from Datetime in R – with Examples

• Deepfake detection challenge from R

• Shiny in Production: App and Database Syncing

R Project Updates

Updates from R Core

Upcoming Events in 3 Months

Events in 3 Months:

• Join us at R/Medicine – Aug 27-29, 2020

• 88th TokyoR Virtual Meetup - September 19th, 2020

• VirtuEARL – EARL Conference online - October 2020

• A list of R conferences and meetings

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

Jobs

• Job Opportunities: Data Scientist and Engineer

Call for Participation

Your support will keep R Weekly team moving! 💡

Quotes of the Week

My hot take: I am loving Distill for sites where I want to be a babysitter but not a parent. Like, I just want to tend to them temporarily but then be able to stop watching them. I'll keep using Hugo for any site that requires more of a bespoke layout/styling.

— Alison Presmanes Hill (@apreshill) August 21, 2020

This is bioseq: a new #rstats package 📦 to work with biological sequences and which plays nicely with the #tidyverse.

... and yes you can have colored nucleotides! 🧬🌈💻#bioinformatics #DNA https://t.co/or0uZjZ0wt pic.twitter.com/SypsqLngvb

— Francois Keck (@FrancoisKeck) August 17, 2020

A tale of three Cities? Of wingers past, present, future?

Fully expecting Twitter to compress it so better res versions here - https://t.co/js869lriQp. DM for hi-res versions.

Can do a few requests if there is enough interest in specific players.#TidyTuesday #Rstats pic.twitter.com/6QmQ6VWBPX

— The Come On Man (@thecomeonman) August 18, 2020

I have updated the *Data Science Course in a Box* resources at https://t.co/N21dyees9Y. If you're teaching introductory data science with #rstats, take a look and feel free to use/adapt as you like. Source code for all materials are linked from the website and licensed CC BY-SA! pic.twitter.com/uw9HrzffkD

— Mine Çetinkaya-Rundel (@minebocek) August 21, 2020