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:

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("transformr")       # for gganmiate
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
library("rstanarm")         # For Bayesian modeling with Stan

# 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
library("devtools")         # for installing packages from GitHub
library("sf")               # package needed for the transformr package

1.3 Install all packages needed for this book

install.packages(c("knitr", "bookdown", "kableExtra", "gapminder", "NHANES", "datarium", "titanic", "arrangements", "magrittr", "tidyverse", "patchwork", "ggpol", "ggridges", "gganimate", "GGally", "ggrepel", "corrr", "corrplot", "DiagrammeR", "DiagrammeRsvg", "ggeffects", "bayesplot", "skimr", "visdat", "rsvg", "see", "afex", "lme4", "emmeans", "broom.mixed", "janitor", "car", "rstanarm", "greta", "tidybayes", "boot", "modelr", "mediation", "multilevel", "extraDistr", "effects", "brms", "parameters", "tictoc", "MASS", "lsr", "extrafont", "pwr", "arrangements", "stargazer", "sjPlot", "xtable", "DT", "papaja", "statsExpressions", "devtools", "sf", "rstanarm"))

devtools::install_github("thomasp85/transformr")

1.4 Session info

## R version 4.4.1 (2024-06-14)
## Platform: aarch64-apple-darwin20
## Running under: macOS Sonoma 14.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## 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_0.6.36     R6_2.5.1          bookdown_0.40     fastmap_1.2.0    
##  [5] xfun_0.45         cachem_1.1.0      knitr_1.48        htmltools_0.5.8.1
##  [9] rmarkdown_2.27    lifecycle_1.0.4   cli_3.6.3         sass_0.4.9       
## [13] jquerylib_0.1.4   compiler_4.4.1    tools_4.4.1       evaluate_0.24.0  
## [17] bslib_0.7.0       yaml_2.3.9        rlang_1.1.4       jsonlite_1.8.8