Chapter 1 Introduction

1.1 Thanks

Various people have helped in the process of putting together these materials (either knowingly, or unknowingly). Big thanks go to:

• Alexandra Chouldechova
• Allison Horst
• Andrew Heiss
• Ben Baumer
• Benoit Monin
• Bodo Winter
• David Lagnado
• Ewart Thomas
• Henrik Singmann
• Julian Jara-Ettinger
• Justin Gardner
• Kevin Smith
• Lisa DeBruine
• Maarten Speekenbrink
• Matthew Kay
• Matthew Salganik
• Michael Franke
• Mika Braginsky
• Mike Frank
• Mine Çetinkaya-Rundel
• Nick C. Huntington-Klein
• Nilam Ram
• Patrick Mair
• Paul-Christian Bürkner
• Peter Cushner Mohanty
• Richard McElreath
• Russ Poldrack
• Stephen Dewitt
• Solomon Kurz
• Tom Hardwicke
• Tristan Mahr

Special thanks go to my teaching teams:

• 2024:
  • Ari Beller
  • Beth Rispoli
  • Satchel Grant
  • Shawn Schwartz
• 2023:
  • Nilam Ram (instructor)
  • Ari Beller
  • Yoonji Lee
  • Satchel Grant
  • Josh Wilson
• 2022:
  • Ari Beller
  • Sarah Wu
  • Chengxu Zhuang
• 2021:
  • Andrew Nam
  • Catherine Thomas
  • Jon Walters
  • Dan Yamins
• 2020:
  • Tyler Bonnen
  • Andrew Nam
  • Jinxiao Zhang
• 2019:
  • Andrew Lampinen
  • Mona Rosenke
  • Shao-Fang (Pam) Wang

1.2 List of R packages used in this book

# RMarkdown
library("knitr")            # markdown things
library("bookdown")         # markdown things
library("kableExtra")       # for nicely formatted tables

# Datasets
library("gapminder")        # data available from Gapminder.org
library("NHANES")           # data set
library("datarium")         # data set
library("titanic")          # titanic dataset

# Data manipulation
library("arrangements")     # fast generators and iterators for permutations, combinations and partitions
library("magrittr")         # for wrangling
library("tidyverse")        # everything else

# Visualization
library("patchwork")        # making figure panels
library("ggpol")            # for making fancy boxplots
library("ggridges")         # for making joyplots
library("gganimate")        # for making animations
library("GGally")           # for pairs plot
library("ggrepel")          # for labels in ggplots
library("corrr")            # for calculating correlations between many variables
library("corrplot")         # for plotting correlations
library("DiagrammeR")       # for drawing diagrams
library("DiagrammeRsvg")    # for visualizing diagrams
library("ggeffects")        # for visualizing effects
library("bayesplot")        # for visualization of Bayesian model fits
library("skimr")            # for quick data visualizations
library("visdat")           # for quick data visualizations
library("rsvg")             # for visualization
library("see")              # for visualizing data

# Modeling
library("afex")             # also for running ANOVAs
library("lme4")             # mixed effects models
library("emmeans")          # comparing estimated marginal means
library("broom.mixed")      # getting tidy mixed model summaries
library("janitor")          # cleaning variable names
library("car")              # for running ANOVAs
library("rstanarm")         # for Bayesian models
library("greta")            # Bayesian models
library("tidybayes")        # tidying up results from Bayesian models
library("boot")             # bootstrapping
library("modelr")           # cross-validation and bootstrapping
library("mediation")        # for mediation and moderation analysis
library("multilevel")       # Sobel test
library("extraDistr")       # additional probability distributions
library("effects")          # for showing effects in linear, generalized linear, and other models
library("brms")             # Bayesian regression
library("parameters")       # For extracting parameters

# Misc
library("tictoc")           # timing things
library("MASS")             # various useful functions (e.g. bootstrapped confidence intervals)
library("lsr")              # for computing effect size measures
library("extrafont")        # additional fonts
library("pwr")              # for power calculations
library("arrangements")     # fast generators and iterators for permutations, combinations and partitions
library("stargazer")        # for regression tables
library("sjPlot")           # for regression tables
library("xtable")           # for tables
library("DT")               # for tables
library("papaja")           # for reporting results
library("statsExpressions") # for extracting stats results APA style

1.3 Session info

## R version 4.3.2 (2023-10-31)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.1.2
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/Los_Angeles
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.33     R6_2.5.1          bookdown_0.37     fastmap_1.1.1    
##  [5] xfun_0.41         cachem_1.0.8      knitr_1.45        htmltools_0.5.7  
##  [9] rmarkdown_2.25    lifecycle_1.0.4   cli_3.6.2         sass_0.4.8       
## [13] jquerylib_0.1.4   compiler_4.3.2    rstudioapi_0.15.0 tools_4.3.2      
## [17] evaluate_0.23     bslib_0.6.1       yaml_2.3.8        jsonlite_1.8.8   
## [21] rlang_1.1.2