_common.R

knitr::opts_chunk$set(
  warning   = FALSE
  ,message   = FALSE
  ,collapse  = TRUE
  ,cache     = TRUE
# ,out.width = "70%"
# ,fig.align = 'center'
# ,fig.width = 6
# ,fig.asp   = 0.618 # 1 / phi
# ,fig.show  = "hold"
)

list.of.packages <- c("ggplot2", "Rcpp", "rstanarm", "lme4", "mice", "VIM", "pander", "kableExtra",
                      "corrplot", "psych", "ggfortify", "GPArotation", "sjPlot", "gridExtra", "knitr", 
                      "ggmap", "spdep", "housingData", "Hmisc", "waffle", "ROCR", "caret", "ggjoy", 
                      "ggdist", "glmmTMB", "ggpubr", 
                      "stargazer", "missForest", "forestplot", "emo", "tidyr", "factoextra", 
                      "performance", "broom", "dotwhisker", "survey", "marginaleffects", "gtsummary", 
                      "sjPlot", "mice", "palmerpenguins")

## devtools::install_github("hadley/emo")

# issues with MKMisk requiring 'limma' which is in bioconductor
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages>0)){install.packages(new.packages)}

library(ggplot2)
library(gridExtra)
library(dplyr)
library(pander)
library(knitr)
library(kableExtra)
library(sjPlot)
library(broom)
library(ggpubr)
library(gtsummary)

options(knitr.kable.NA = '', knitr.table.format = "html")
theme_set(theme_bw())

# loading data sets used in multiple chapters

depress <- read.delim("data/depress_081217.txt")
names(depress) <- tolower(names(depress))

pen <- palmerpenguins::penguins

load("data/addhealth_clean.Rdata")
addhealth$smoke <- ifelse(addhealth$eversmoke_c=="Smoker", 1, 0)

fev <- read.delim("data/Lung_081217.txt", sep="\t", header=TRUE)