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Science Research Weekly

Science Research Weekly

By Mark R Williamson

A weekly overview of helpful scientific research topics and the successor of the podcast Statistics Weekly. Every week, I will cover 3 topic areas: Research Articles, Research Tools, and Research Funding. Science On.
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Episode 9: Boxes and Babies

Science Research WeeklyMay 27, 2022

00:00
10:09
Episode 9: Robot Parade!

Episode 9: Robot Parade!

Get ready for self-healing soft robots, modular NASA robots, Shiny recaps, Statistical Rethinking training, statistical kindergarten, and the NIH Pioneer Award Program. Science On. References: Optical tweezers throw and catch single atoms The connectome of an insect brain A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes A self-healing electrically conductive organogel composite Engineering breakthrough in softbotics Mix-and-match kit could enable astronauts to build a menagerie of lunar exploration bots The Young Supernova Experiment Data Release 1 (YSE DR1) Observation of a critical charge mode in a strange metal 6 predictions for AI and data in health care and life sciences Use the metalog distribution in SAS R 4.2.3 is released ShinyConf 2022 – Short Recap Statistical Rethinking (2023 Edition) Introduction to data analysis with {Statgarten}. WebR IS HERE! NIH: Director’s Pioneer Award Program NIH: Entry-Level Modules for Training the Genomics Research Workforce NIH: Enhancement of external environmental exposure assessment for cancer epidemiology research Falk Medical Research Trust: Catalyst Awards Program CRI: Immuno-Informatics Postdoctoral Fellowship ACS: Early Career Postdoctoral-Faculty Bridge Grant Other Articles: LEXpander: Applying colexification networks to automated lexicon expansion Surface changes observed on a Venusian volcano during the Magellan mission Why is Pumas-QSP So Fast? Some Insights Into Differentiable Simulation Performance R-packages: pharmaverse: Navigate 'Pharmaverse' toweranNA: A Method for Handling Missing Values in Prediction Applications waspasR: Tool Kit to Implement a W.A.S.P.A.S. Based Multi-Criteria Decision Analysis Solution
Mar 17, 202309:36
Episode 8: Flash Grants in the Pan

Episode 8: Flash Grants in the Pan

Get ready for technological tribology, tingible translational cell biology, flipping fossils, Volume 14/4 of the R Journal, ebook tips and tricks, and flash grants to fixate on.  Science On. References: Novel friction stabilization technology for surface damage conditions using machine learning Crevasse refreezing and signatures of retreat observed at Kamb Ice Stream grounding zone Apoptotic cell fragments locally activate tingible body macrophages in the germinal center Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart An abundant sea anemone from the Carboniferous Mazon Creek Lagerstӓtte, USA Paleontologists flip the script on anemone fossils Python 3.12.0 alpha 6 released The R Journal Volume 14/4 7 New books added to Big Book of R What I’ve learned making an .epub Ebook with Quarto DOD: DEPSoR - Research Collaboration DOD: Ovarian Cancer CTR Award DOD: Ovarian Cancer Clinical Trial Award NHBLI: Research Project Grants in Valvular Heart Disease NHBLI: Integrative Omics Analysis of NHLBI TOPMed Data HHS: Small R01s for Clinical Trials Targeting Diseases for NIDDK Biogen: Sponsorships AHR: Strategically Focused Research Networks CRI: Technology Impact Award IAFNS: Live Dietary Microbe Intake and Health Outcomes NC Life Sciences: Flash Grants R-packages: BayesFluxR: Implementation of Bayesian Neural Networks lorem: Generate Lorem Ipsum Text HDRFA: High-Dimensional Robust Factor Analysis guildai: Track Machine Learning Experiments aihuman: Experimental Evaluation of Algorithm-Assisted Human Decision-Making
Mar 10, 202310:22
Episode 7: Life, the R-Universe, and Everything

Episode 7: Life, the R-Universe, and Everything

Get ready for an exploration of the R-Universe, simulated octopus tentacles, effects of Vitamin D and exercise on health, fossil wings and fins, statistical conferences to set your calendar by, and a very special 23rd birthday.  Science On. References: Energy-shaping control of a muscular octopus arm moving in three dimensions Injury primes mutation-bearing astrocytes for dedifferentiation in later life Origin of the propatagium in non-avian dinosaurs Effectiveness of physical activity interventions for improving depression, anxiety and distress: an overview of systematic reviews MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data 3D printing of living structural biocomposites Network expansion of genetic associations defines a pleiotropy map of human cell biology A shape-shifting nuclease unravels structured RNA Systematics and Phylogenetic Interrelationships of the Enigmatic Late Jurassic Shark Protospinax annectans Woodward Vitamin D supplementation and incident dementia: Effects of sex, APOE, and baseline cognitive status JuliaHub Newsletter February 2023 Bioconductor Conference 2023 PhyloPic R 4.2.3 R-universe January 2023: “Top 40” New CRAN Packages Happy 23rd Birthday R! NIH: Translational Research in Maternal and Pediatric Pharmacology and Therapeutics (R01) NIH: Translational Research in Maternal and Pediatric Pharmacology and Therapeutics (R21) NIH: Genomic Community Resources (U24) CDC: Clinical and Applied Research Strategies for the Prevention and Control of Fungal Diseases USDA: USDA-ARS Postdoctoral Fellowship in Spatial Statistics for Continental-Scale Soil Health Modeling TSC Alliance: 2023 Grant Cycle CHEST: COPD Research Grant CHEST: Young Investigator Research Grant R-packages: aihuman: Experimental Evaluation of Algorithm-Assisted Human Decision-Making reactCheckbox: Checkbox Group Input for 'Shiny' treediff: Testing Differences Between Families of Trees rutledge: Real-Time PCR Data Sets by Rutledge et al. (2004)
Mar 03, 202311:07
Episode 6: Boss-Level Antibiotics

Episode 6: Boss-Level Antibiotics

Get ready for better arsenic detection, broad-spectrum antibiotics, model-breaking massive galaxies, Julia and Python working in harmony, a hard-to-pronounce R-package on Gaussian mixture models, and Department of Defense lung cancer grants aplenty.  Science On. References: Scalable selective absorber with quasiperiodic nanostructure for low-grade solar energy harvesting Toward surface-enhanced Raman scattering using electroless substrate for trace arsenic detection and speciation Site-specific encoding of photoactivity and photoreactivity into antibody fragments Complete Genome Sequence of the Lysogenic Pseudomonas Bacteriophage Fyn8 A broad-spectrum synthetic antibiotic that does not evoke bacterial resistance Discovery of massive early galaxies defies prior understanding of the universe Julia and Python better together DOD: Multidisciplinary Research Program of the University Research Initiative (MURI) DOD: Lung Cancer, Concept Award DOD: Lung Cancer, Translational Research Award DOD: Lung Cancer, Idea Development Award DOD: Lung Cancer, Career Development Award NASA: Early Career Faculty FDA: Natural History and Biomarker Studies of Rare Neurodegenerative Diseases LCRF: Leading Edge Research Grant Program UMDF: Research Grant Program R-packages: dataMojo: Reshape Data Table ggmapinset: Add Inset Panels to Maps bubbleHeatmap: Produces 'bubbleHeatmap' Plots for Visualising Metabolomics Data gmmsslm: Semi-Supervised Gaussian Mixture Model with a Missing-Data Mechanism rWCVP: Generating Summaries, Reports and Plots from the World Checklist of Vascular Plants
Feb 24, 202305:16
Episode 5: A Bouquet of Space ROSEs

Episode 5: A Bouquet of Space ROSEs

Get ready for exoplanetary systems, missing Neptunes, a Dungeons & Dragons R package, GIFs for top R packages, Tidvyverse functions to save your day, and a whole host of NASA grant announcements.  Science On. References Framework for the architecture of exoplanetary systems RNA's 'joints' play key role in our gene expression Help! Our Neptune-sized exoplanets are missing The ins and outs of an undergrad-run journal the difference between the bernoulli and binomial distributions Top 9+ Interesting R Project Ideas To Try In 2023 10 Tidyverse functions that might save your day Putting the top 100 R packages into a GIF NSF: Plant Genome Research Program NSF: Computer and Information Science and Enginering Core Programs NIH: HEAL Initative NIH: Aging Research NIH: IDeA Networks of Biomedical Research Excellence (INBRE) DOD: Ovarian Cancer Early-Career Investigator Award DOD: Ovarian Cancer Investigator-Initiated Research Award DOD: Ovarian Cancer Pilot Award NASA: Research Opportunities in Space and Earth Science (ROSES) 2023 R-packages HanStat: Package for Easy Interpretation of Statistical Methods hidecan: Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results dndR: Dungeons Dragons Functions for Players and Dungeon Masters
Feb 17, 202306:12
Episode 4: To Err in R is Human

Episode 4: To Err in R is Human

Get ready for the top 10 errors in R, self-assembling peptides, microbiome mishaps, a theory-defying dwarf planet ring system, and a chance to save tiny hearts.  Science On. References The virtual microbiome: A computational framework to evaluate microbiome analyses A dense ring of the trans-Neptunian object Quaoar outside its Roche limit 3D Printing of Self-Assembling Nanofibrous Multidomain Peptide Hydrogels This one-atom chemical reaction could transform drug discovery logitr: Fast Estimation of Multinomial and Mixed Logit Models with Preference Space and Willingness-to-Pay Space Utility Parameterizations Python 3.11.2, Python 3.10.10 and 3.12.0 alpha 5 are available How to use Git to share SAS programs Top 10 errors in R and how to fix them NIH: Using Multimodal Biomarkers to Differentially Diagnose ADRDs for Clinical Trials NSF: Accelerating Research Translation Saving Tiny Hearts Society: Research Grants R packages deFit: Fitting Differential Equations to Time Series Data synMicrodata: Synthetic Microdata Generator animate: A Web-Based Graphics Device for Animated Visualisations formatBibtex: Format BibTeX Entries and Files
Feb 10, 202305:21
Episode 3: The Ocean that Snuck up on Me

Episode 3: The Ocean that Snuck up on Me

Get ready for heart-attack healing hydrogels, super rare supernovas, volumes of viroid sequences, stealth oceans, finding hex logos and packages by topic in CRAN, and NASA funding for exobiology.  Science On. References This groundbreaking biomaterial heals tissues from the inside out A high-mass X-ray binary descended from an ultra-stripped supernova Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs Tracking the Evolution of an Ocean Within Mimas Using the Herschel Impact Basin Journal of Statistical Software Volume 105 Annual Julia Growth Statistics - January 2023 Tips for organizing your R code December 2022: “Top 40” New CRAN Packages NASA: Exobiology- Living Systems Science NIH: Data Harmonization, Curation and Secondary Analysis of Existing Clinical Datasets DOD: Peer Reviewed Medical, Discovery Award DE-FOA: 2023 Exploratory Research for Extreme Scale Science NIH NOSI: Development of Functional Assay Sites to Evaluate Candidate -Omics Variants Associated with Heart, Lung, Blood, or Sleep Disease NIH NOSI: Revision Applications to add a Curation and Informatics Component to existing Animal and Biological Material Resource Centers R-packages hexFinder: Find Hex Logos for CRAN Packages vvsculptor: Apply Manipulations to Data Frames findPackage: Find 'CRAN' Package by Topic
Feb 03, 202305:40
Episode 2: What Double Teeth You Have

Episode 2: What Double Teeth You Have

Get ready for new deep sea bacterial phyla, extra ancient caecilian fossils, R Journal Volume 14/3 JuliaHub 6.0, visualizing star maps in R, and an IceCube neutrino competition!  Science Research Weekly covers 3 topic areas: Research Articles, Research Tools, and Research Funding.  Science On. References Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits Chem-map profiles drug binding to chromatin in cells Study offers first glimpse of how many suffer from previously unknown illness Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin Triassic stem caecilian supports dissorophoid origin of living amphibians The R Journal Volume 14/3 Star Map with R Show all data in the background of your faceted ggplot Fitting robust non-Gaussian models in Stan and R-INLA JuliaHub 6.0 Features Released Kaggle Competition: IceCube - Neutrinos in Deep Ice NSF: Molecular Foundations for Biotechnology NSF: Expanding Capacity in Quantum Information Science and Engineering DE: Scientific Machine Learning for Complex Systems AFOSR: Fiscal Year 2023 Science, Technology, Engineering and Mathematics (STEM) Program R-packages neatR: Neat Data for Presentation polyglotr: Translate Text clarify: Simulation-Based Inference for Regression Models poolHelper: Simulates Pooled Sequencing Genetic Data vDiveR: Visualization of Viral Protein Sequence Diversity Dynamics
Jan 27, 202307:49
Episode 1: An Explosive Beginning

Episode 1: An Explosive Beginning

Welcome to Science Research Weekly, the successor to my first podcast, Statistics Weekly.  This abbreviated trial run of an episode includes: a research article on microbes from a volcanic island, the largest stellar catalogue to date, Arduino project ideas for 2023, and NSF Research and Development grants. References: The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga A high-quality Ixodes scapularis genome advances tick science Haplotype-aware pantranscriptome analyses using spliced pangenome graphs The molecular evolution of genes previously associated with large sizes reveals possible pathways to cetacean gigantism The Dark Energy Camera Plane Survey 2 (DECaPS2): More Sky, Less Bias, and Better Uncertainties Volume 105 of the Journal of Statistical Software 12 blog posts from 2022 that deserve a second look Top 15 Stunning Arduino Project Ideas For 2023 Some R Conferences for 2023 Web scraping in R Imputation in R: Top 3 Ways for Imputing Missing Data FDA: Fellowship in Understanding Pathogenesis and Improving Detection of Flaviviruses NSF: Future Manufacturing NSF: Division of Environmental Biology NSF: Division of Molecular and Cellular Biosciences Core Programs NSF: Division of Integrative Organismal Systems Core Programs NIH NOSI: Research on the Etiology, Early Detection, Screening and Prevention of Early-Onset Colorectal Cancer NIH NOSI: Computational and Statistical Methods to Enhance Discovery from Health Data R packages: ggplate: Create Layout Plots of Biological Culture Plates and Microplates glmmrOptim: Approximate Optimal Experimental Designs Using Generalised Linear Mixed Models shiny.benchmark: Benchmark the Performance of 'shiny' Applications blindreview: Blind Review Using Forward Search Procedures metabias: Meta-Analysis for Within-Study and/or Across-Study Biases evoTS: Analyses of Evolutionary Time-Series OssaNMA: Optimal Sample Size and Allocation with a Network Meta-Analysis
Jan 25, 202307:48
Science Research Weekly Trailer

Science Research Weekly Trailer

Welcome to Science Research Weekly.  This is the successor to my first podcast, Statistics Weekly.  Every week, I will cover 3 topic areas: Research Articles, Research Tools, and Research Funding.  Check out the accompanying blog at: https://scienceresearchweekly.wordpress.com/
Jan 24, 202300:60
Episode 40: The Close of 2022

Episode 40: The Close of 2022

Take the poll to weigh in on the future of Statistics Weekly.
Dec 30, 202201:01
Episode 39: Last Stat Before Christmas

Episode 39: Last Stat Before Christmas

In this episode, I pondered the problem of false positives in publications, rotated around the JuliaHub, machinated over machine learning projects, and put R package ‘drawCell’ to the test. References: Are most published research findings false in a continuous universe? Principal component analysis A no-free-lunch theorem for multitask learning JuliaHub Signal-to-noise ratio and statistical tests Large Enough Sample Condition Top 11 Interesting Machine Learning Project Ideas For 2023 Code longevity of the R programming language {drawCell} – R package and Shiny app for drawing cell structures R-packages: colorRamp2: Generate Color Mapping Functions rworkflows: Test, Document, Containerise, and Deploy R Packages MetChem: Chemical Structural Similarity Analysis panelsummary: Create Publication-Ready Regression Tables with Panels arf: Adversarial Random Forests
Dec 23, 202204:58
Episode 38: Ho, Ho, Holiday Statistics Projects

Episode 38: Ho, Ho, Holiday Statistics Projects

In this episode, I marched through machine learning abstractions, brought home the BQN, discovered statistics projects to work on over Christmas, and found the Gosling that lays the golden egg, References: Quantifying uncertainty of machine learning methods for loss given default Evaluating the performance of memory type logarithmic estimators using simple random sampling A fast kernel independence test for cluster-correlated data Autoencoders for sample size estimation for fully connected neural network classifiers [R-pkgs] onetime 0.1.0: Run Code Only Once 🚧 WIP 🚧 From Julia to BQN Using SAS to score a test Using the cspade action to find frequent gene sequences The easygoing relationship between computer scientists and null hypothesis significance testing Top 11+ Coding Projects for Beginners (2023 Edition) Gosling: Interactive Genomics Charts in R Shiny Gosling Main Page R-packages: POMS:  Phylogenetic Organization of Metagenomic Signals macroBiome: A Tool for Mapping the Distribution of the Biomes and Bioclimate reservr: Fit Distributions and Neural Networks to Censored and Truncated Data NPCox: Nonparametric and Semiparametric Proportional Hazards Model
Dec 16, 202206:28
Episode 37:  Hexadecimal Codes of Christmas

Episode 37: Hexadecimal Codes of Christmas

In this episode, I got into the spirit of Sinterklaas with Python, jumpstarted Julia learning, cleared up confusion between ANOVA and regression results, and color paletted the night away. References: Estimation of population variance under ranked set sampling method by using the ratio of supplementary information with study variable 10 Simple Reasons to Learn the Julia Programming Language (in 2023) Python 3.11.1, 3.10.9, 3.9.16, 3.8.16, 3.7.16, and 3.12.0 alpha 3 are now available Art in SAS: Christmas wrapping paper when the results of your anova table and regression coefficients disagree Select colours from an image in R with {eyedroppeR} How to make your own #RStats Wrapped! R-packages: HodgesTools: Common Use Tools for Genomic Analysis DependencyReviewer: Tool Suite to Investigate Other Packages gmvjoint: Joint Models of Survival and Multivariate Longitudinal Data r2social: App Inclusion of Social Sharing and Connect Buttons lterpalettefinder: Extract Color Palettes from Photos and Pick Official LTER Palettes jackknifeR: Jackknife Linear Regression and Correlation POMADE: Power for Meta-Analysis of Dependent Effects HTT: Hypothesis Testing Tree
Dec 09, 202205:39
Episode 36: Curb your Stats-thusiasm

Episode 36: Curb your Stats-thusiasm

In this episode, I picked the choicest R journal articles, served up a digital poker hand in SAS, and tried not to let a defective R-package get me down. References: brolgar: An R package to BRowse Over Longitudinal Data Graphically and Analytically in R shinybrms: Fitting Bayesian Regression Models Using a Graphical User Interface for the R Package brms R-miss-tastic: a unified platform for missing values methods and workflows Bias reduction in the logistic model parameters with the LogF(1,1) penalty under MAR assumption A simulation study: Using dual ancillary variable to estimate population mean under stratified random sampling Multi-omics peripheral and core regions of cancer Efficient and automated bandwidth selection in SAS PROC KPCA Simulate poker hands in SAS Covariates: Definition & Uses Our First Peer-Reviewed Statistical R Packages! Navigating folders in RStudio: a beginner’s guide October 2022: “Top 40” New CRAN Packages R-packages: HTT: Hypothesis Testing Tree boxfilter: Filter Noisy Data ggpcp: Parallel Coordinate Plots in the 'ggplot2' Framework StatTeacherAssistant: An App that Assists Intro Statistics Instructors with Data Sets tidyclust: A Common API to Clustering
Dec 02, 202205:36
Episode 35: Turkey v. Tukey

Episode 35: Turkey v. Tukey

In this episode, I skimmed over a dimension estimator, skipped past a piecewise linear curve, and slipped by the launch of a simple data science ebook. References: The generalized ratios intrinsic dimension estimator The area under a piecewise linear curve Adapted Randomization confusing statistical term #13: missing at random and missing completely at random When to Use plotly? PCA for Categorical Variables in R How to combine Multiple Plots in R RObservations #42: Using the jinjar and tidyRSS packages to make a simple newsletter template Ebook launch – Simple Data Science (R) R-packages: ASRgenomics: 'ASReml-R' Genomics Tools flashr: Create Flashcards of Terms and Definitions scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale
Nov 24, 202202:31
Episode 34: Genomics, My Dear Watson

Episode 34: Genomics, My Dear Watson

In this episode, I dusted off my genomic gloves with the HCLC-FC and CLIMB methods, waxed poetic with Python’s latest alpha release, and solved plotting mysteries with R-package ‘sherlock’. References: Regression discontinuity threshold optimization Explaining predictive factors in patient pathways using autoencoders HCLC-FC: A novel statistical method for phenome-wide association studies Uncertainty-aware mixed-variable machine learning for materials design Closed-form continuous-time neural networks New statistical method improves genomic analyzes synr: Analyze stimulus-color consistency test data Profile plots in SAS Optimal linear profile plots in SAS Python 3.12.0 alpha 2 released What is Interactive Analytics? Top 9 Highest Paying Programming Languages (2023) How to Analyze Likert Scale Data? Top 10 Data Visualisation Tools Every Data Science Enthusiast Must Know Open source is a hard requirement for reproducibility R-packages: exactLTRE: An Exact Method for Life Table Response Experiment (LTRE) Analysis sherlock: Graphical Displays to Aid Structured Problem Solving and Diagnosis cipheR: Encryption and Decryption with Text Ciphers rjtools: Preparing, Checking, and Submitting Articles to the 'R Journal' commafree: Call Functions Without Commas Between Arguments
Nov 18, 202206:17
Episode 33: Healthy Heaping of Free Stats

Episode 33: Healthy Heaping of Free Stats

In this episode, I took advantage of more than one free data science course, mused over mappings for R, and helped myself to a heap of helper functions with R package ‘mlmhelpr’. References: The Hybrid Model of Autoregressive Integrated Moving Average and Fuzzy Time Series Markov Chain on Long Memory Data Predicting prediction: A systematic workflow to analyze factors affecting the classification performance in genomic biomarker discovery A supervised topic embedding model and its application Shrinkage estimators of large covariance matrices with Toeplitz targets in array signal processing SAS® Fast-KPCA: An efficient and innovative nonlinear principal components method TDApplied version 2.0.0 Issues While Switching R to UTF-8 and UCRT on Windows Datacamp Free Access Week Map any region in the world with R – Part II: Obtaining the coordinates R ggmap – How to Visualize Spatial Data in R R-packages: cauchypca: Robust Principal Component Analysis Using the Cauchy Distribution nett: Network Analysis and Community Detection pwrss: Power and Sample Size Calculation Tools SASdates: Convert the Dates to 'SAS' Formats planningML: A Sample Size Calculator for Machine Learning Applications in Healthcare mlmhelpr: Multilevel/Mixed Model Helper Functions ExomeDepth: Calls Copy Number Variants from Targeted Sequence Data
Nov 10, 202205:35
Episode 32: Spooky Scary Statistics

Episode 32: Spooky Scary Statistics

In this episode, I waved my hand across several financial data journal articles,  took advantage of free data science tutorials, learned how to run a dev   environment from a flash drive, and did a double take at a seeming CRAN package duplication. References: Analyzing Intraday Financial Data in R: The highfrequency Package A Practitioner's Guide and MATLAB Toolbox for Mixed Frequency State Space Models spsur: An R Package for Dealing with Spatial Seemingly Unrelated Regression Models Bias reduction in the logistic model parameters with the LogF(1,1) penalty under MAR assumption The Annals of Statistics Volume 50 Issue 5 R 4.2.2 is released Call for proposals to organize a hybrid useR! in 2023 or 2024 A trick to combine and split strings 365 Data Science courses free until November 21 A Linux Live USB as a statistical programming dev environment Top 5 Shiny UI Add-On Packages September 2022: “Top 40” New CRAN Packages R-packages: ExomeDepth: Calls Copy Number Variants from Targeted Sequence Data minsample1: The Minimum Sample Size minsample2: The Minimum Sample Size palaeoverse: Prepare and Explore Data for Palaeobiological Analyses SAP: Statistical Analysis and Programming tidyfit: Regularized Linear Modeling with Tidy Data robustbetareg: Robust Beta Regression
Nov 04, 202207:24
Episode 31: Awash in Acronyms

Episode 31: Awash in Acronyms

In this episode, I tried to keep my acronyms straight, dealt with big and tall (data), poked the ribs of SPSS, and contrasted the PIC with the AIC (more acronyms on the march!) References: Fast Penalized Regression and Cross Validation for Tall Data with the oem Package synthACS: Spatial Microsimulation Modeling with Synthetic American Community Survey Data BGVAR: Bayesian Global Vector Autoregressions with Shrinkage Priors in R Facilitating time series classification by linear law-based feature space transformation Severe testing with high-dimensional omics data for enhancing biomedical scientific discovery Visualize dependencies of missing values Formatting your Microsoft Excel output using ODS Excel How to use the image function in R How to create a heatmap in R The pheatmap function in R SAS or R-Yould Should Know! Understanding ShinyApps R-packages: worrrd: Generate Wordsearch and Crossword Puzzles picR: Predictive Information Criteria for Model Selection
Oct 28, 202206:31
Episode 30: The GitHub Secret Sauce

Episode 30: The GitHub Secret Sauce

In this episode, I spilled the secret sauce behind my research methods, predicted extreme events, pursued plots off the beaten ggplot path, and added another simulation-based power analysis tool to my belt. References: Statistics Weekly Research GitHub Repository Flexible time-to-event models for double-interval-censored infectious disease data with clearance of the infection as a competing risk Predicting the data structure prior to extreme events from passive observables using echo state network SCpubr: Generate high quality, publication-ready plots of single-cell transcriptomics data Concordances the difference between chi square tests of independence and homogeneity How to create a ggalluvial plot in R? How to create a Sankey plot in R? Understanding the Basics of Package Writing in R R-packages: VIGoR: Variational Bayesian Inference for Genome-Wide Regression ggstats: Extension to 'ggplot2' for Plotting Stats mlpwr: A Power Analysis Toolbox to Find Cost-Efficient Study Designs ARIMAANN: Time Series Forecasting using ARIMA-ANN Hybrid Model makeunique: Make Character Strings Unique
Oct 21, 202206:06
Episode 29: Business or Bust

Episode 29: Business or Bust

In this episode, I contributed to the Python Developers Survey, wiped a sweaty brow over the Isoband Incident, and booted up package 'bupaverse' for business process analytics. References: The R Journal Volume 14/1 gsDesign 3.4.0 is released Improvements in handling bytes encoding Join the Python Developers Survey 2022: Share and learn about the community Who rotated my cookie?  CRAN and the Isoband Incident – Is Your Project at Risk and How to Fix It Map any region in the world with R – Part I: The basic map R-packages: dfms: Dynamic Factor Models precmed: Precision Medicine RobustANOVA: Robust One-Way ANOVA Tests under Heteroscedasticity and Nonnormality bakR: Analyze and Compare Nucleotide Recoding RNA Sequencing Datasets nestedmodels: Tidy Modelling for Nested Data powRICLPM: Perform Power Analysis for the Random Intercept Cross-Lagged Panel Model bupaverse: Easily Install and Load the 'bupaverse'
Oct 14, 202206:20
Episode 28:  Everything’s Coming Up Machine Learning

Episode 28: Everything’s Coming Up Machine Learning

In this episode, I netted new ways to knock neural networks out of the park, let R do my calculus calculations for me, garnered gentle overviews to many   machine learning topics, and made sure my phylogenic trees were publication ready with the R package ‘CancerEvolutionVisualization'. References: Pathogen.jl: Infectious Disease Transmission Network Modeling with Julia calculus: High-Dimensional Numerical and Symbolic Calculus in R Deep Image Prior for medical image denoising, a study about parameter initialization On Physics-Informed Neural Networks for Quantum Computers Not frequentist enough. ggradar: radar plots with ggplot in R Mastering Debugging in R Understanding leaf node numbers when using rpart and rpart.rules A Gentle Introduction to using Support Vector Machines for Classification Boosting in Machine Learning: A Brief Overview Algorithm Classifications in Machine Learning R-packages: pirouette: Create a Bayesian Posterior from a Phylogeny CancerEvolutionVisualization: Publication Quality Phylogenetic Tree Plots odetector: Outlier Detection Using Partitioning Clustering Algorithms stats4teaching: Simulate Pedagogical Statistical Data camcorder: Record Your Plot History openxlsx2: Read, Write and Edit 'xlsx' Files
Oct 07, 202205:47
Episode 27: Statistical Models on the Quick

Episode 27: Statistical Models on the Quick

In this episode, I kept it quick with appropriate microbial resistance data procedures, using a TI 83 calculator for statistics, and hoping for an easy entry to NEON data wrangling with package ‘neonOS’. References: Statistical Network Analysis with Bergm ParMA: Parallelized Bayesian Model Averaging for Generalized Linear Models AMR: An R Package for Working with Antimicrobial Resistance Data new version of package declared 3 ways to enhance productivity with AI TI 83 for Statistics: Easy Steps for Common Problems Hazard Ratio: Interpretation & Definition Writing Functions in R August 2022:  “Top 40” New CRAN Packages R-packages: easydb: Easily Connect to Common Types of Databases neonOS: Basic Data Wrangling for NEON Observational Data getpublist: Obtain a List of Publications from 'PubMed' and 'Google Scholar' adjustedCurves: Confounder-Adjusted Survival Curves and Cumulative Incidence Functions
Sep 30, 202204:54
Episode 26: Random Learning on the Short

Episode 26: Random Learning on the Short

In this episode, I kept it short and sweet with a new statistical journal reference, data science job scraping, and random learning for R-packages. References: Generalized resilience and robust statistics Stochastic continuum-armed bandits with additive models: Minimax regrets and adaptive algorithm Generate random ID values for subjects in SAS Linear Regression Equation Explained An Example of Specifying Within-Subjects Factors in Repeated Measures Designing Online Data Science Training for the Modern Age Optimizing my search for Data scientist jobs by scraping Indeed with R Seeking Inspiration from Random Learning R-packages: BiOFI: Feature Identification Between Metabolome and Microbiome in Disease and Health glmmrBase: Specification of Generalised Linear Mixed Models REDCapTidieR: Extract 'REDCap' Databases into Tidy 'Tibble's verbaliseR: Make your Text Mighty Fine betaSandwich: Robust Confidence Intervals for Standardized Regression Coefficients DynForest: Random Forest with Multivariate Longitudinal Predictors roBTT: Robust Bayesian T-Test alqrfe: Adaptive Lasso Quantile Regression with Fixed Effects recurrentpseudo: Creates Pseudo-Observations and Analysis for Recurrent Event Data alkahest: Pre-Processing XY Data from Experimental Methods
Sep 23, 202204:01
Episode 25: Machine Learning vs. Magic

Episode 25: Machine Learning vs. Magic

In this episode, I found that Bambi (Bayesian Model Building Interface) is more than a little deer, rooted for the round-robin operator for genetic algorithms, and had my convictions that machine learning is not magic reinforced. References: HighFrequencyCovariance:  A Julia Package for Estimating Covariance Matrices Using High Frequency Financial Data Bambi: A Simple Interface for Fitting Bayesian Linear Models in Python Spbsampling: An R Package for Spatially Balanced Sampling plot3logit: Ternary Plots for Interpreting Trinomial Regression Models Learning Base R (2nd Edition) Python and R for the Modern Data Scientist Genetic algorithm with a new round-robin based tournament selection: Statistical properties analysis Healthcare researchers must be wary of misusing AI New method to identify symmetries in data using Bayesian statistics Python 3.11.0rc2 is now available Complex Layouts using the SG Procedures Factor Analysis Guide with an Example How to Choose Appropriate Clustering Method for Your Dataset How to Apply AI to Small Data Sets? The R Consortium Needs Your Help with satRdays Visualizing OLS Linear Regression Assumptions in R R-packages: TPCselect:  Variable Selection via Threshold Partial Correlation historicalborrow:  Non-Longitudinal Bayesian Historical Borrowing Models historicalborrowlong:  Longitudinal Bayesian Historical Borrowing Models kgp:  1000 Genomes Project Metadata DBIsqldf:  Manipulate R Data Frames Using SQL latentFactoR:  Data Simulation Based on Latent Factors TSdeeplearning:  Deep Learning Model for Time Series Forecasting
Sep 16, 202208:05
Episode 24: The Way of the R Warrior

Episode 24: The Way of the R Warrior

In this episode, I chose mediation analysis over a hospital heist, gained additional sample size calculation insights, memorized machine learning methods, and battled my way up a text-based tower using package ‘rwarrior’. References: Hierarchical Clustering with Contiguity Constraint in R Blang: Bayesian Declarative Modeling of General Data Structures and Inference via Algorithms Based on Distribution Continua Robust Mediation Analysis: The R Package robmed A Software Tool For Sparse Estimation Of A General Class Of High-dimensional GLMs bayesanova: An R package for Bayesian Inference in the Analysis of Variance via Markov Chain Monte Carlo in Gaussian Mixture Models blindrecalc - An R Package for Blinded Sample Size Recalculation Power and Sample Size for Longitudinal Models in R – The longpower Package and Shiny App RFpredInterval: An R Package for Prediction Intervals with Random Forests and Boosted Forests Alternative stopping rules to limit tree expansion for random forest models gMCPLite: Lightweight Graph Based Multiple Comparison Procedures pkglite 0.2.1 is released Python releases   3.10.7, 3.9.14, 3.8.14, and 3.7.14 are now available Ordinal Data: Definition, Examples & Analysis How the Population Distribution Influences the Confidence Interval Talks to watch at the RSS International Conference How to Avoid Overfitting? Beneath and Beyond the Cox Model (www.r-bloggers.com/2022/09/beneath-and-beyond-the-cox-model/) What are the algorithms used in machine learning? (www.r-bloggers.com/2022/09/what-are-the-algorithms-used-in-machine-learning/) 23 New books added to Big Book of R (www.r-bloggers.com/2022/09/23-new-books-added-to-big-book-of-r/) R Warrior Leader Board (www.r-bloggers.com/2022/08/r-warrior-leader-board/) R-packages: oceanexplorer: Explore Our Planet's Oceans with NOAA OneArm2stage: Optimal One-Arm Two-Stage Phase II Design with Survival Endpoint rwarrior: R Warrior - An AI Programming Game manymome: Mediation, Moderation and Moderated-Mediation After Model Fitting voice: Tools for Voice Analysis, Speaker Recognition and Mood Inference shinylight: Web Interface to 'R' Functions
Sep 09, 202210:09
Episode 23: Biting Off More Statistics Than I Can Chew

Episode 23: Biting Off More Statistics Than I Can Chew

In this episode, I bite off more journal articles than I could chew, bookmarked how to reorder SGPLOT bars, was underwhelmed by R surprises, and muddled through the meta-package ‘easystats’. References: On the Programmatic Generation of Reproducible Documents Automatic Identification and Forecasting of Structural Unobserved Components Models with UComp exuber: Recursive Right-Tailed Unit Root Testing with R The R Journal Volume 14/1 A unified Framework for analyzing complex systems: Juxtaposing the (Kernel) PCA method and Graph Theory Grand Challenges in Mathematical Biology: Integrating Multiscale Modelling and Data CohensdpLibrary: Compute Cohen's d and its confidence interval in any experimental design Two types of syntax for the SELECT-WHEN statement in SAS Order the bars in a bar chart with PROC SGPLOT Top 10 online data science programs How to handle Imbalanced Data? July 2022: “Top 40” New CRAN Packages Surprising Things You Can Do With R SAS vs R  Programming: Which to Choose and How to Switch R-packages: easystats: Framework for Easy Statistical Modeling, Visualization, and Reporting once:  Execute Expensive Operations Only Once snSMART: Small N Sequential Multiple Assignment Randomized Trial Methods tidyplus: Additional 'tidyverse' Functions transPlotR: Visualize Transcript Structures in Elegant Way
Sep 02, 202211:30
Episode 22: Python with a Side of Waffles

Episode 22: Python with a Side of Waffles

In this episode, I grabbed the tools to conduct mobility data analysis and interactive plots in Python, detected outliers in spherical data, considered the next programing language to learn, and readied the statistical syrup for waffle plots using package ‘baffle’. References: scikit-mobility: A Python Library for the Analysis, Generation, and Risk Assessment of Mobility Data spNNGP R Package for Nearest Neighbor Gaussian Process Models Feller-Pareto and Related Distributions: Numerical Implementation and Actuarial Applications A new outlier detection method for spherical data Confidence bands in survival analysis How to stagger labels on an axis in PROC SGPLOT Experimental Design: Definition and Types The Difference Between R-squared and Adjusted R-squared Top 5 Python Libraries for Data Science (2023) Edition Base-R and Tidyverse Code, Side-by-Side R Design Patterns, Base-R vs. Tidyverse With a view toward the teaching of R beginners Hello Shiny Python Which programming language should I learn? R Markdown Tips: Code, Images, Comments, Tables, and more Is Data Science a Dying Profession? R-packages: evalR Evaluation of Unverified Code goldfish Statistical Network Models for Dynamic Network Data baffle Make Waffle Plots with Base Graphics ggDoE Modern Graphs for Design of Experiments with 'ggplot2' jjAnno An Annotation Package for 'ggplot2' Output multinomialLogitMix Clustering Multinomial Count Data under the Presence of Covariates IntLIM Integration of Omics Data Using Linear Modeling scrutiny Error Detection in Science shinyHugePlot Efficient Plotting of Large-Sized Data ctmva Continuous-Time Multivariate Analysis ggcoverage Visualize Genome Coverage with Various Annotations
Aug 26, 202207:31
Episode 21: Behind the Statistical Software Curve

Episode 21: Behind the Statistical Software Curve

In this episode, I played catch-up with the Journal of Statistical Software, schemed how to snag a top spot in the XP Learning Challenge, and roared alongside the R-package ‘TRexSelector’. References: modelsummary: Data and Model Summaries in R stringi: Fast and Portable Character String Processing in R evgam: An R Package for Generalized Additive Extreme Value Models Julia 1.8 Highlights The Box-Cox transformation for a dependent variable in a regression TDApplied: Machine Learning and Inference for Topological Data Analysis Some project opportunities for Ph.D. students! Learn data skills, earn points and win money prizes daily with Datacamp! Designing #TidyTuesday visualisations for mobile (with Quarto) Find out which data skills are most in demand? R-packages: ctmva: Continuous-Time Multivariate Analysis ggcoverage: Visualize Genome Coverage with Various Annotations TRexSelector: T-Rex Selector: High-Dimensional Variable Selection FDR Control countdown: A Countdown Timer for HTML Presentations, Documents, and Web Apps TDApplied: Machine Learning and Inference for Topological Data Analysis brassica: 1970s BASIC Interpreter
Aug 19, 202208:37
Episode 20:  The Count of Monte Carlo

Episode 20: The Count of Monte Carlo

In this episode, I browsed yet more Monte Carlo simulation papers, introduced myself to various structural equation models, championed base R, and went neural to neural with the R package ‘cito’. References: A kernel mixing strategy for use in adaptive Markov chain Monte Carlo and stochastic optimization contexts Bootstrap-based inferential improvements to the simplex nonlinear regression model Python 3.10.6 is available Stanine Score: Definition, Examples, How to Convert The Four Models You Meet in Structural Equation Modeling Downstream Bioinformatics Analysis of Omics Data with edgeR Simulating data from a non-linear function by specifying a handful of points RObservations #36: Opinions on RStudio’s name change. A Bayesian approach with Stan Base-R Is Alive and Well R-packages: cito Building and Training Neural Networks cbioportalR Browse and Query Clinical and Genomic Data from cBioPortal gtreg Regulatory Tables for Clinical Research diffdfs Compute the Difference Between Data Frames fake Flexible Data Simulation Using the Multivariate Normal Distribution seeker Simplified Fetching and Processing of Microarray and RNA-Seq Data ympes Collection of Helper Functions
Aug 12, 202205:44
Episode 19: Get Python Not Sleep

Episode 19: Get Python Not Sleep

In this episode, I didn’t get a lot of sleep. But I did get a lot of quirky Python, classy SAS, and ridiculous R. References: A systematic review of statistical methodology used to evaluate progression of chronic kidney disease using electronic healthcare records Statistical inference for a constant-stress partially accelerated life tests based on progressively hybrid censored samples from inverted Kumaraswamy distribution Python 3.11.0b5  is now available How to reveal new connections in a knowledge graph with link prediction https://blogs.sas.com/content/iml/2022/08/01/examples-monte-carlo-simulation.html 5 pillars for a successful DataOps strategy June 2022: “Top 40” New CRAN Packages Bioinformatics Analysis of Omics Data with the Shell & R Script monkey! Getting fun with ggdogs, ggcats and gganimate R-packages: gganimate
Aug 05, 202204:34
Episode 18: The Software Formerly Known as RStudio

Episode 18: The Software Formerly Known as RStudio

In this episode, RStudio gets a Posit-tively new name, SAS estimates area with  Monte Carlo simulation, and I take in the view of package ‘P2C2M.Skyline.’ References: Progressive censoring schemes for marshall-olkin pareto distribution with applications Assessing model adequacy for Bayesian Skyline plots using posterior predictive simulation Testing for Benford’s Law in very small samples: Simulation study and a new test proposal Inferring the underlying multivariate structure from bivariate networks with highly correlated nodes R Can Use Your Help: Translating R Messages Monte Carlo estimates of area effectsize: A new Python package for computing effect sizes / standardized differences Hoeffding’s Inequality Exogenous and Endogenous Variables in Structural Equation Modeling Announcing Quarto, a new scientific and technical publishing system RStudio is becoming Posit Posit– Why Rstudio is changing its name How to Create an Interaction Plot in R? How to Standardize Data in R? R code snippet : Transform from long format to wide format Programming a simple minimax chess engine in R R-packages: P2C2M_Skyline
Jul 29, 202207:53
Episode 17:  Tidal Waves of R Packages

Episode 17: Tidal Waves of R Packages

In this episode, I pared down three important -omics data considerations, coded my way into wave of new R packages, boasted about the Big Book of R, and havered over the ‘dots’ package. References: Editorial: Statistical Data Science - Theory and Applications in Analyzing Omics Data Introducing riskCommunicator: An R package to obtain interpretable effect estimates for public health On the mixed Kibria–Lukman estimator for the linear regression model Rejection Region (Critical Region) for Statistical Tests Join rstudio::conf(2022) Virtually ggdensity: A new R package for plotting high-density regions R Color Generalized Linear Models, Part I: The Logistic Model Part 1 of 3: 300+ milestone for Big Book of R Part 2 of 3: 300+ milestone for Big Book of R Part 3 of 3: 300+ milestone for Big Book of R R-packages: htmcglm:  Hypothesis Testing for McGLMs nextGenShinyApps:  Advanced Tools for Building the Next Generation of 'Shiny' Applications and Dashboards robustmeta:  Robust Inference for Meta-Analysis with Influential Outlying Studies lnmCluster:  Perform Logistic Normal Multinomial Clustering for Microbiome Compositional Data binaryTimeSeries:  Analyzes a Binary Variable During a Time Series codebookr:  Create Codebooks from Data Frames dots:  Dot Density Maps ggpackets:  Package Plot Layers for Easier Portability and Modularization trouBBlme4SolveR:  Troubles Solver for 'lme4'
Jul 22, 202206:40
Episode 16: The Wizard of Stats

Episode 16: The Wizard of Stats

In this episode, I clued in on the claims that Linear Programming Discriminant analysis is effective, mused on the methods of PROC SQL in SAS, and fired up a virtual machine to use for package ‘vmr’. References: moreThanANOVA: A user-friendly Shiny/R application for exploring and comparing data with interactive visualization LPDA: A new classification method based on linear programming Speedups in operations with regular expressions Why learn SQL? Correlated Errors in Confirmatory Factor Analysis Network Graphs in R vmrPoster R-packages: htmldf: Simple   Scraping and Tidy Webpage Summaries gpboost: Combining   Tree-Boosting with Gaussian Process and Mixed Effects Models vmr: Virtual   Machines for R
Jul 15, 202204:50
Episode 15: Data Synthetic and the Multiverse of Modeling

Episode 15: Data Synthetic and the Multiverse of Modeling

In this episode, I assessed applications for AI-generated synthetic data, read up on the radical R tutorial rflow, and stepped into the ‘multiverse’ package to manage reporting on many different statistical analyses. References: Machine learning techniques for forecasting agricultural prices: A case of brinjal in Odisha, India The risk of bias in denoising methods: Examples from neuroimaging Bayesian model averaging for nonparametric discontinuity design AI-generated Synthetic Data, easy and fast access to high quality data? Use functions in a WHERE statement to filter observations Cronbach’s Alpha: Definition, Calculations & Example Updated Comparison of R Graphical User Interfaces A Major Contribution to Learning R R-packages: multiverse: 'Explorable Multiverse' Data Analysis and Reports
Jul 08, 202205:60
Episode 14:  Outliers from the Reaches of Sample Space

Episode 14: Outliers from the Reaches of Sample Space

In this episode, I explored model selection methods for fending off invading   outliers, marveled at May’s Top 40 CRAN packages, refreshed my suppositions on samples space, and rallied up to replace words in text using package ‘rflashtext’. References: Robust model selection using the out-of-bag bootstrap in linear regression Data-informed deep optimization Compute the multivariate t density function Sample Space Examples and The Counting Principle Cohens D: Definition, Using & Examples Statistical Inference: Definition, Methods & Example Replace NA with Zero in R May 2022: “Top 40” New CRAN Packages R-packages: sciRmdTheme: Upgraded 'Rmarkdown' Themes for Scientific Writing rflashtext: FlashText Algorithm for Finding and Replacing Words
Jul 01, 202205:14
Episode 13: Funny-Looking Bioinformatics

Episode 13: Funny-Looking Bioinformatics

In this episode, I broadened up my bioinformatics background, found that the latest R-release was a Funny-Looking Kid, and extracted lobster species using package ‘OpenTreeChronograms’.  References: A New Tobit Ridge-Type Estimator of the Censored Regression Model with Multicollinearity Problem Selecting predictive biomarkers from genomic data COBREXA.jl: constraint-based reconstruction and exascale analysis Partial leverage plots R 4.2.1 is released {CIPerm}: Computationally-Efficient Confidence Intervals for Mean Shift from Permutation Methods When Linear Models Don’t Fit Your Data, Now What? SVG to PNG How to Find Unmatched Records in R Create new variables from existing variables in R R-packages: OpenTreeChronograms: Open Tree of Life Chronograms phacking: Sensitivity Analysis for p-Hacking in Meta-Analyses RCTS: Clustering Time Series While Resisting Outliers MakeYourPalette: Make Your Palette ontologics: Code-Logics to Handle Ontologies CIPerm: Computationally-Efficient Confidence Intervals for Mean Shift from Permutation Methods
Jun 24, 202207:09
Episode 12: Bayesian Fire Engine

Episode 12: Bayesian Fire Engine

In this episode, I tackled ‘omics’ data with a Bayesian fire engine, soared over a timeline of statistical ideas, and decreased statistical bias by increasing bias understanding. References: A Survey of Statistical Methods for Microbiome Data Analysis PyCon US: Successful Return to In-Person in 2022 PUSH, POP, and reset options for ODS graphics Using Bayesian Additive Regression Trees for Flexible Outcome Modeling R 4.2.1 scheduled for June 23 Bias in Statistics: Definition, Selection Bias & Survivorship Bias X-MR (X-Moving Range) Chart From Anna Menacher: A timeline of the most important statistical ideas of the past 50 years useR! 2022 – all virtual – is next week! R-packages: bnClustOmics: Bayesian Network-Based Clustering of Multi-Omics Data starticles: A Generic, Publisher-Independent Template for Writing Scientific Documents in 'rmarkdown'
Jun 17, 202205:11
Episode 11: Putting the Meta in Meta and Drooling Over Donut Plots

Episode 11: Putting the Meta in Meta and Drooling Over Donut Plots

In this episode, I learned there are both good and bad R books, umbrella reviews are meta on top of meta, flowcharts can be fashioned in ggplot2, and package ‘ggpie’ is more than mere fluff. References: Monotone Regression: A Simple and Fast O(n) PAVA Implementation Pro Data Visualization Using R and JavaScript: Analyze and Visualize Key Data on the Web Doing Meta-Analysis with R - A Hands-On Guide Convergence analysis and approximate optimal temporal step sizes for some finite difference methods discretising Fisher’s equation Early warning signals of financial crises using persistent homology and critical slowing down: Evidence from difference correlation tests Methodological approaches for assessing certainty of the evidence in umbrella reviews: A scoping review Python 3.10.5 is available Weights for residuals in robust regression The effect of weight functions in a robust regression method Considerations for generating time-accurate animation with SAS Extra! Extra! Read all about how SAS is leading in analytics! Bug BBQ What Is Specification Error in Statistical Models? Becoming an R developer: the workshop Creating flowcharts with {ggplot2} R-packages: clinicalsignificance: Determine the Clinical Significance in   Clinical Trials mlrpro: Stepwise Regression with Assumptions   Checking ggpie: Pie, Donut and Rose Pie Plots gTestsMulti: New Graph-Based Multi-Sample Tests plnr: A System for Planing Analyses holiglm: Holistic Generalized Linear Models
Jun 10, 202208:41
Episode 10: Multiple Last Names and Growing a Backbone

Episode 10: Multiple Last Names and Growing a Backbone

In this episode, I chained together multiple scientific last names, found heaps of PLOS ONE journal articles, and learned how to grow a backbone in R using package ‘backbone’. References: Event History Regression with Pseudo-Observations: Computational Approaches and an Implementation in R More on Multidimensional Scaling and Unfolding in R: smacof Version 2 A Practical Guide to the Numerical Implementation of Tensor Networks I: Contractions, Decompositions, and Gauge Freedom Rank-polyserial correlation. Quest for a "missing" coefficient of correlation Assessing and visualizing fragility of clinical results with binary outcomes in R using the fragility package backbone: An R package to extract network backbones Evaluation of spatial Bayesian Empirical Likelihood models in analysis of small area data Clinical artificial intelligence quality improvement: towards continual monitoring and updating of AI algorithms in healthcare The interplay between ranking and communities in networks Random assignment of subjects to groups in SAS Using formatted CLASS variables Python 3.11.0b2 is now available shadowr: Selenium plugin to manage multiple levels of shadow elements on web page Difference Between Standard Deviation and Standard Error Clopper-Pearson Exact Method Applications of Python | Top 10 uses of Python for The Real World 15 Fun & Easy Excel Project Ideas To Sharpen Your Skills 2022-01 Vectorised Pattern Fills in R Graphics April: “Top 40” New CRAN Packages R Packages Download Stats R-packages: AHSurv: Flexible Parametric Accelerated  Hazards Models misPRIME: Partial Replacement Imputation Estimation for Missing Covariates tracee: Easily Save Output and Trace it Back to Code backbone: Extracts the Backbone from Graphs
Jun 03, 202209:33
Episode 9: Boxes and Babies

Episode 9: Boxes and Babies

In this episode I thought outside the Box-Pierce; fuzzed, sweated, and flustered my way through basic stats; encountered functions and AI for babies; and chronicled the R-package ‘chronicler’. References: NeuralSens: Sensitivity Analysis of Neural Networks econet: An R Package for Parameter-Dependent Network Centrality Measures Modified Quantile Regression For Modeling the Low Birth Rate A Novel Correction for the Adjusted Box-Pierce Test Comments on identifying causal relationships in nonlinear dynamical systems via empirical mode decomposition Adaptive numerical simulations with Trixi.jl: A case study of Julia for scientific computing The balanced bootstrap in SAS Game-changer AI tool will save mothers and babies D. Mayo & D. Hand: “Statistical significance and its critics: practicing damaging science, or damaging scientific practice?” Fuzzy Clustering: Definition How to Find the P value: Process and Calculations The Difference Between an Odds Ratio and a Predicted Odds ‘Data analysis with tidyverse’ workshop Think like a programmeR: the workshop How to add labels at the end of each line in ggplot2? Subsetting with multiple conditions in R Hierarchical data visualization with Shiny and D3 chronicler: Add Logging to Functions R-packages: Rwclust: Random Walk Clustering on Weighted Graphs ScaleSpikeSlab: Scalable Spike-and-Slab webshot2: Take Screenshots of Web Pages mverse: Tidy Multiverse Analysis Made Simple chronicler: Adding Logging to Functions
May 27, 202210:09
Episode 8: Shortened Blankets

Episode 8: Shortened Blankets

In this episode, I got lost in among the statistical trees, flipped a Bernoulli trial coin, and wrapped myself up in package ‘ggblanket’. References: sensobol: An R Package to Compute Variance-Based Sensitivity Indices The R Package stagedtrees for Structural Learning of Stratified Staged Trees Wave Effects of the Fractional Shallow Water Equation and the Fractional Optical Fiber Equation Two Domains of Meandering Spiral Waves in a Modified Barkley Model Access for success: SAS Certification practice exams now offered for free How to unroll frequency data Sampling Methods: Different Types in Research Bernoulli Trials: Definition, Examples ANCOVA: Analysis of Covariance Measures of Model Fit for Linear Regression Models ggblanket: making beautiful ggplot2 visualisation simpler Self-documenting {ggplot}s thanks to the power of monads! Launch of R Screencasts How to draw heatmap in r: Quick and Easy way R packages: DemographicTable: Creating Demographic Table Linea:  Linear Regression Interface linelist : Tagging and Validating Epidemiological Data NovelDistns: Computes PDF, CDF, Quantile, Random Numbers and Measures of Inference for 3 General Families of  Distributions semtree: Recursive Partitioning for Structural Equation Models getwiki R: Wrapper for Wikipedia Data simer: Data Simulation for Life Science and Breeding ggblanket: Wrappers to Make Beautiful 'ggplot2' Visualization Simpler dimensionalAnalysis: Dimensional Analysis
May 18, 202208:05
Episode 7: Riding the Python Lightning

Episode 7: Riding the Python Lightning

In this episode, I dived into non-normal distributions, went from rags to ridges, rode the Python Language Summit lightning, and looked at the ‘GenericML’ package. References: Covsim: An R package for Simulating Non-Normal Data for Structural Equation Models Using Copulas Rags2ridges: A One-stop-L2-shop for Graphical Modeling of High-Dimensional Precision Matrices Transmissibility in Interactive Nanocomposite Diffusion: The Nonlinear Double-Diffusion Model Editorial: Modelling collective motion across scales The Application of the Functional Variable Method for Solving the Loaded Nonlinear Evaluation Equations The derivative of the determinant of a matrix Python 3.11.0b1 is now available The 2022 Python Language Summit: Upstreaming optimisations from Cinder The 2022 Python Language Summit: Performance Improvements by the Faster CPython team The 2022 Python Language Summit: Python in the browser The 2022 Python Language Summit: A per-interpreter GIL The 2022 Python Language Summit: Achieving immortality Fiducial Inference: Fisher’s Great Failure Beta Distribution: Uses, Parameters & Examples Geometric Distribution: Uses, Calculator & Formula Alignment cheatsheet 5 Key Data Visualization Principles Explained – Examples in R Three packages that port the tidyverse to Python How to embed a Shiny app into your blog posts R  packages: biogeom: Biological Geometries GenericML: Generic Machine Learning Inference PMA2:  Penalized Multivariate Analysis
May 13, 202208:36
Episode 6: Mixes and Metabolomics

Episode 6: Mixes and Metabolomics

In this episode, I dig into the first articles of a new Journal of Statistical Software volume, try not to mix up package ‘nvmix’ with ‘nmix’, scratch my head over Navier-Stokes equations, and take the random R-package section in a metabolomics direction. References: Journal of Statistical Software Volume 102 Convolutional Neural Networks for Very Low-Dimensional LPV Approximations of Incompressible Navier-Stokes Equations Simulate the null distribution for a hypothesis test Nmix package - Bayesian inference about univariate Gaussian mixtures with an unknown number of components What is Power in Statistics? Member Training: Introduction to SPSS Software Tutorial Announcing R/Medicine 2022! New Workshops Series Kick-off Little useless-useful R functions – Animating datasets March: “Top 40” New CRAN Packages An introduction to the metabolomicsR R   packages: arthistory:  Art History Textbook Data nls2:  Non-Linear Regression with Brute Force metabolomicsR:  Tools for Metabolomics Data conductor:  Create Tours in 'Shiny' Apps Using 'Shepherd.js'
May 06, 202209:26
Episode 5: Stretching the Limits and Vigorous Calisthenics

Episode 5: Stretching the Limits and Vigorous Calisthenics

In this episode, I stretch before vigorous calisthenics, give a thumbs up to O’Reilly coding books, get to the bottom of R vectorization, try not to panic during   debugging, and showcase the R-package ‘fauxnaif’. References: A NSFD Discretization of Two-Dimensional Singularly Perturbed Semilinear Convection-Diffusion Problems Misnomers regarding outliers and their usefulness in statistical modeling On Bartlett's sphericity test for correlation Two perspectives on numerical integration R 4.2.0 Released Parameter vs Statistic: Examples & Differences Spurious Correlation: Definition, Examples & Detecting Hey, check this out, it’s really cool: A Bayesian framework for interpreting findings from impact evaluations Top 10 Best R Books For Beginners How to create your own functions in R RObservations #30: Fixing R’s “messy string concatenation” with a special function Where for (loop) ARt Thou? RStudio Community Table Gallery Don’t Panic! a Scientific Approach to Debugging Production Failure R   packages: CircularSilhouette:   Fast Silhouette on Circular or Linear Data Clusters forplo:   Flexible Forest Plots pspatreg:   Spatial and Spatio-Temporal Semiparametric Regression Models with Spatial   Lags SLBDD:   Statistical Learning for Big Dependent Data cleaR:   Clean the R Console and Environment gameR:   Color Palettes Inspired by Video Games prettymapr:   Scale Bar, North Arrow, and Pretty Margins in R fauxnaif:   Convert Values to NA
Apr 29, 202207:37
Episode 4: Stealing Python’s Thunder and Rolling Your Rs

Episode 4: Stealing Python’s Thunder and Rolling Your Rs

In this episode, I jump into Julia packages, estimate how to pronounce the generalized Kibria-Lukman estimator, commiserate with Python, and showcase the R-package ‘rsconnect’. References: Generalized Kibria-Lukman Estimator: Method, Simulation, and Application Trending Julia Packages Use a heat map to visualize an ordinal response in longitudinal data The McNemar test in SAS Happy Birthday Neyman: What was Neyman opposing when he opposed the ‘Inferential’ Probabilists? Your weekend Phil Stat reading How to Interpret Adjusted R-Squared and Predicted R-Squared in Regression Analysis Three Principles of Experimental Designs MLDataR – Real-world Datasets for Machine Learning Applications Getting started with Python using R and reticulate Text Analysis of Job Descriptions for Data Scientists, Data Engineers, Machine Learning Engineers and Data Analysts R-packages: bookdown: Authoring Books and Technical Documents with R Markdown rconfig: Manage R Configuration at the Command Line BayesPPD:  Bayesian Power Prior Design spatialreg: Spatial Regression Analysis pagoda2: Single Cell Analysis and Differential Expression microeco: Microbial Community Ecology Data Analysis paletteknife: Create Colour Scales and Legend from Continuous or Categorical Vectors starter: Starter Kit for New Projects rsconnect: Deployment Interface for R Markdown Documents and Shiny Applications
Apr 22, 202206:22
Episode 3: Jackknifing, Leibniz, and Feeling the Python Breeze

Episode 3: Jackknifing, Leibniz, and Feeling the Python Breeze

In this episode, I play with jackknives, chuckle over Python, list upcoming R conferences, and showcase the R-package ‘RcppBDT’. References: Additive Noise-Induced System Evolution (ANISE) Face Recognition in Single Sample Per Person Fusing Multi-Scale Features Extraction and Virtual Sample Generation Methods An Epidemiological Compartmental Model With Automated Parameter Estimation and Forecasting of the Spread of COVID-19 With Analysis of Data From Germany and Brazil Accelerating Jackknife Resampling for the Canonical Polyadic Decomposition The last Python 3.11 alpha (3.11.0a7) is available New methods for solving differential equations in SAS Pascal matrices and inverses Enhancements to HTML Documentation Some discussion of “how to get confident with statistics”: Reading, practicing, and questioning Permutation vs Combination: Differences & Examples Chi-Square Goodness of Fit Test: Uses & Examples SPSS Syntax 101 The sftime Package To impute or not: the case of an RCT with baseline and follow-up measurements Why you should(n’t) care about Monads if you’re an R programmer Bayesian Estimation by using rjags Package Upcoming R conferences (2022) R-packages: clusterHD: Tools for Clustering High-Dimensional Data Allspice: RNA-Seq Profile Classifier cheatR: Catch Cheaters spooky: Time Feature Extrapolation Using Spectral Analysis and Jack-Knife Resampling taxonbridge: Create Custom Taxonomies Based on the NCBI Taxonomy and GBIF Backbone Taxonomy wrMisc: Analyze Experimental High-Throughput (Omics) Data findInFiles: Find Pattern in Files mclogit: Multinomial Logit Models, with or without Random Effects or Overdispersion aRtsy: Generative Art with 'ggplot2' glmm: Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation glmtoolbox: Set of Tools to Data Analysis using Genera RcppBDT: 'Rcpp' Bindings for the Boost Date_Time Library
Apr 15, 202208:38
Episode 2: Lies, Two-Truths and a Lie, and Statistical R-packages

Episode 2: Lies, Two-Truths and a Lie, and Statistical R-packages

In this episode, I drink from the firehose of CRAN packages, learn a use for ‘two truths and a lie’ in the statistics classroom, and showcase the R-package ‘pipeliner’. References: https://www.frontiersin.org/articles/10.3389/fams.2022.848898/abstract https://www.frontiersin.org/articles/10.3389/fams.2022.852314/full https://stat.ethz.ch/pipermail/r-announce/2022/000681.html https://cran.r-project.org/web/packages/available_packages_by_date.html https://www.spss-tutorials.com/open-excel-file-in-spss/ https://www.spss-tutorials.com/spss-missing-values-for-string-variables/ https://errorstatistics.com/2022/04/05/insevere-tests-of-severe-testing/ https://statmodeling.stat.columbia.edu/2022/04/04/two-truths-and-a-lie-as-a-class-participation-activity/ https://statmodeling.stat.columbia.edu/2022/04/05/confidence-intervals-compatability-intervals-uncertainty-intervals/ https://www.statisticshowto.com/research-methods-qualitative-research-and-quantitative-research/ https://statisticsbyjim.com/basics/cohort-study/ https://statisticsbyjim.com/hypothesis-testing/sampling-error/ https://www.r-bloggers.com/2022/04/paper-semi-markov-modeling-for-cancer-insurance/ https://www.r-bloggers.com/2022/04/teaching-data-science-in-the-cloud/ https://www.r-bloggers.com/2022/04/new-features-in-r-4-2-0/ https://www.r-bloggers.com/2022/04/bio7-3-4-released/ https://cran.r-project.org/web/packages/pipeliner/index.html https://cran.r-project.org/web/packages/pipeliner/vignettes/Introduction.html
Apr 08, 202207:17
Episode 1: Getting a Flat Distribution Under Us

Episode 1: Getting a Flat Distribution Under Us

In this episode, I brace myself for the R release of Vigorous Calisthenics, scratch my head at Lyapunov Exponents, survey the brewing battlefield in the AI/ML Wars, and showcase the R-package 'numform'. References: https://journal.r-project.org/archive/2021/RJ-2021-109/RJ-2021-109.pdf https://journal.r-project.org/archive/2021/RJ-2021-080/RJ-2021-080.pdf https://www.jstatsoft.org/article/view/v101i12 https://www.frontiersin.org/articles/10.3389/fams.2022.818799/full https://www.frontiersin.org/articles/10.3389/fams.2022.869999/full https://www.frontiersin.org/articles/10.3389/fams.2022.839669/full https://cran.r-project.org/index.html https://pythoninsider.blogspot.com/2022/03/python-3110a6-is-available.html https://blog.python.org/2022/03/python-3103-3911-3813-and-3713-are-now.html https://blog.python.org/2022/03/python-3104-and-3912-are-now-available.html https://julialang.org/blog/2022/02/10years/ https://www.statistics.com/data-literacy-the-chainsaw-case/ https://errorstatistics.com/2022/03/23/the-ai-ml-wars-explain-or-test-black-box-models/ https://statmodeling.stat.columbia.edu/2022/03/27/the-examples-you-see-in-the-textbooks-are-not-representative-of-the-sorts-of-problems-you-see-in-the-real-world/ https://statisticsbyjim.com/regression/interpret-coefficients-p-values-regression/ https://www.r-bloggers.com/2022/03/february-2022-top-40-new-cran-packages/ https://www.r-bloggers.com/2022/03/how-i-analyze-100-ggplots-at-once/ https://cran.r-project.org/web/packages/numform/numform.pdf
Apr 01, 202207:39
Statistics Weekly Trailer

Statistics Weekly Trailer

Trailer for the podcast Statistics Weekly.
Mar 30, 202201:03