R Packages used in these notes

Here, we’ll load in some packages used in these notes. The list of R Packages we will use in 432 is more extensive, and is available on our course website.

library(here)
library(janitor) 
library(magrittr)
library(conflicted)

library(tableone) 

library(broom) 
library(haven)
library(janitor)
library(patchwork)
library(Hmisc)
library(rms)

library(MASS)
library(visdat) 
library(naniar) 
library(caret)
library(simputation)
library(car)
library(mice)
library(leaps)
library(lars)
library(Epi)
library(pROC)
library(ROCR)
library(VGAM)
library(ggridges)
library(pander)
library(arm)
library(survival)
library(survminer)
library(kableExtra)

## and of course, we conclude with...

library(tidymodels)
library(tidyverse) 

Dealing with Conflicts

I’m loading a lot of packages here, and sometimes individual functions are in conflict. R’s default conflict resolution system gives precedence to the most recently loaded package. This can make it hard to detect conflicts, particularly when introduced by an update to an existing package.

Using the code below helps the entire book run properly. You may or may not need to look into the conflicted package for your work.

conflict_prefer("filter", "dplyr")

[conflicted] Will prefer dplyr::filter over any other package

conflict_prefer("select", "dplyr")

[conflicted] Will prefer dplyr::select over any other package

conflict_prefer("Predict", "rms")

[conflicted] Will prefer rms::Predict over any other package

conflict_prefer("impute_median", "simputation")

[conflicted] Will prefer simputation::impute_median over any other package

conflict_prefer("summarize", "dplyr")

[conflicted] Will prefer dplyr::summarize over any other package

specify_decimal <- function(x, k) format(round(x, k), nsmall=k)

General Theme for ggplot work

theme_set(theme_bw())

Data used in these notes

All data sets used in these notes are available on our Data and Code website.

Dr. Love is in the process of moving all of the data loads below to their individual chapters.

prost <- read_csv("data/prost.csv") 
pollution <- read_csv("data/pollution.csv") 

bonding <- read_csv("data/bonding.csv") 
cortisol <- read_csv("data/cortisol.csv") 
emphysema <- read_csv("data/emphysema.csv") 
resect <- read_csv("data/resect.csv") 
colscr <- read_csv("data/screening.csv") 
colscr2 <- read_csv("data/screening2.csv") 
authorship <- read_csv("data/authorship.csv") 
hem <- read_csv("data/hem.csv") 
leukem <- read_csv("data/leukem.csv")