Setup

Authors

Affiliations

Hannah Rosenthal

Albert Einstein College of Medicine

Vagish Hemmige

Montefiore Medical Center/ Albert Einstein College of Medicine

The code in this script imports libraries, initializes constants, and performs other such preparatory work for the main analysis.

Source code

The full R script is available at:

• R/setup.R

Libraries

The analysis relies on a set of open-source R packages for data management, cohort construction, visualization, and statistical modeling. These libraries were selected based on their stability, community support, and suitability for large-scale longitudinal health data.

# Libraries necessary for the analysis

#File import libraries
library(haven)
library(readr)
library(readxl)

#File export libraries
library(writexl)

#Data management libraries
library(tidyverse)
library(labelled)
library(dplyr)
library(tidyr)
library(janitor)
library(purrr)
library(lubridate)
library(conflicted)

#Core library for the SRTR
library(sRtr)

#Flowchart libraries
library(strobe)
library(flowchart)

#Statistical modeling libraries
library(MatchIt)
library(survival)
library(MASS)
library(sandwich)
library(lmtest)


#Table libraries
library(gtsummary)
library(gt)

#Plotting libraries
library(ggplot2)
library(survminer)


#Use the conflicted package to ensure that the select and filter functions are not superseded
conflict_prefer("select", "dplyr")
conflict_prefer("filter", "dplyr")
conflict_prefer("lag", "dplyr")

The table below lists the required packages along with links to their primary documentation.

Required R Packages
Libraries used for data processing, visualization, and statistical modeling
Category	R package	Documentation
File import	haven	CRAN – haven
File import	readr	CRAN – readr
File import	readxl	CRAN – readxl
File export	writexl	CRAN – writexl
Data management	tidyverse	tidyverse.org
Data management	labelled	CRAN – labelled
Data management	dplyr	CRAN – dplyr
Data management	tidyr	CRAN – tidyr
Data management	janitor	CRAN – janitor
Data management	purrr	CRAN – purrr
Data management	lubridate	lubridate.tidyverse.org
Data management	conflicted	CRAN – conflicted
SRTR-specific	sRtr	GitHub – sRtr
Flowcharting	strobe	GitHub – strobe
Flowcharting	flowchart	CRAN – flowchart
Statistical modeling	MatchIt	CRAN – MatchIt
Statistical modeling	survival	CRAN – survival
Statistical modeling	MASS	CRAN – MASS
Statistical modeling	sandwich	CRAN – sandwich
Statistical modeling	lmtest	CRAN – lmtest
Tables	gtsummary	gtsummary documentation
Tables	gt	gt documentation
Plotting	ggplot2	ggplot2.tidyverse.org
Plotting	survminer	CRAN – survminer

Other portions of the analysis

• About: methods, assumptions, and disclosures