Programing language and software

The software used in the course is the statistical language R and the IDE (Integrated Development Environment) used is RStudio. A basic prior knowledge of both is assumed. Basic introductions to R and RStudio are presented in the Appendix C and B for those students lacking basic expertise on them.

The required packages for the course are:

# Install packages
install.packages(c("survival", "condSURV", "JM", "dplyr", "survminer", "ggplot2"))
devtools::install_github("noramvillanueva/clustcurv")

The codes in the notes may assume that the packages have been loaded, so it is better to do it now:

# Load packages
library(survival)
library(condSURV)
library(JM)
library(dplyr)
library(survminer)
library(clustcurv)
library(ggplot2)

Links: survival(Therneau 2015), condSURV(Meira-Machado and Sestelo 2016a; Meira-Machado and Sestelo 2016b), JM(Rizopoulos 2010), dplyr(Wickham et al. 2017), survminer(Kassambara and Kosinski 2017), ggplot2(Wickham 2009), and clustcurv.

References

Therneau, Terry M. 2015. A Package for Survival Analysis in S. https://CRAN.R-project.org/package=survival.

Meira-Machado, Luis, and Marta Sestelo. 2016a. “condSURV: Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data.” R package version 2.0.1.

Meira-Machado, Luis, and Marta Sestelo. 2016b. “condSURV: An R Package for the Estimation of the Conditional Survival Function for Ordered Multivariate Failure Time Data.” The R Journal 8 (2): 460–73. http://journal.r-project.org/archive/2016-2/meiramachado-sestelo.pdf.

Rizopoulos, Dimitris. 2010. “JM: An R Package for the Joint Modelling of Longitudinal and Time-to-Event Data.” Journal of Statistical Software 35 (9): 1–33. http://www.jstatsoft.org/v35/i09/.

Wickham, Hadley, Romain Francois, Lionel Henry, and Kirill Müller. 2017. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.

Kassambara, Alboukadel, and Marcin Kosinski. 2017. Survminer: Drawing Survival Curves Using ’Ggplot2’. https://CRAN.R-project.org/package=survminer.

Wickham, Hadley. 2009. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. http://ggplot2.org.