Software
Packages
All the exercise are solved using R (ver. 3.4.2) has been used provided with packages: survival (Therneau (2017)) for the survival data analyses (reference package), survminer (Kassambara and Kosinski (2017)) for advance survival plot using ggplot2 (Wickham and Chang (2016)) package, cmprsk (Gray (2014)) for competing risk, rms (Harrell, Jr. (2017)) for additional features on regression modeling strategies (survival ones included).
With regards to the data management, the collection of package tidyverse (Wickham (2017)) is loaded, which includes: dplyr (Wickham et al. (2017)) for data manipulation, purrr (Henry and Wickham (2017)) for functional programming, readr (R-readr) for data import, tidyr (R-tidyr) for funtions to tidy the data, tibble (R-tibble) to take advantage of the tible data frame class and ggplot2 as a interface for the Gramar of Grahics.
The present book was written in RMarkdown (R-rmarkdown), compiled using knitr (Xie (2017b)) and rendered as an HTML book by bookdown (Xie (2017a)).
System Information
All the code is compiled on a system with the following overall characteristics and loaded packages.
devtools::session_info()## setting value
## version R version 3.4.2 (2017-09-28)
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate English_United States.1252
## tz Europe/Berlin
## date 2017-10-05
##
## package * version date source
## acepack 1.4.1 2016-10-29 CRAN (R 3.4.1)
## assertthat 0.2.0 2017-04-11 CRAN (R 3.4.1)
## backports 1.1.0 2017-05-22 CRAN (R 3.4.0)
## base * 3.4.2 2017-09-28 local
## base64enc 0.1-3 2015-07-28 CRAN (R 3.4.0)
## bindr 0.1 2016-11-13 CRAN (R 3.4.1)
## bindrcpp * 0.2 2017-06-17 CRAN (R 3.4.1)
## bookdown 0.5 2017-08-20 CRAN (R 3.4.1)
## broom 0.4.2 2017-02-13 CRAN (R 3.4.0)
## cellranger 1.1.0 2016-07-27 CRAN (R 3.4.1)
## checkmate 1.8.3 2017-07-03 CRAN (R 3.4.1)
## cluster 2.0.6 2017-03-16 CRAN (R 3.4.1)
## cmprsk * 2.2-7 2014-06-17 CRAN (R 3.4.1)
## codetools 0.2-15 2016-10-05 CRAN (R 3.4.0)
## colorspace 1.3-2 2016-12-14 CRAN (R 3.4.1)
## compiler 3.4.2 2017-09-28 local
## data.table 1.10.4 2017-02-01 CRAN (R 3.4.0)
## datasets * 3.4.2 2017-09-28 local
## devtools 1.13.3 2017-08-02 CRAN (R 3.4.1)
## digest 0.6.12 2017-01-27 CRAN (R 3.4.1)
## dplyr * 0.7.3 2017-09-09 CRAN (R 3.4.1)
## evaluate 0.10.1 2017-06-24 CRAN (R 3.4.1)
## forcats 0.2.0 2017-01-23 CRAN (R 3.4.1)
## foreign 0.8-69 2017-06-21 CRAN (R 3.4.0)
## Formula * 1.2-2 2017-07-10 CRAN (R 3.4.1)
## ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.4.1)
## ggpubr * 0.1.5 2017-08-22 CRAN (R 3.4.1)
## glue 1.1.1 2017-06-21 CRAN (R 3.4.1)
## graphics * 3.4.2 2017-09-28 local
## grDevices * 3.4.2 2017-09-28 local
## grid 3.4.2 2017-09-28 local
## gridExtra 2.3 2017-09-09 CRAN (R 3.4.1)
## gtable 0.2.0 2016-02-26 CRAN (R 3.4.1)
## haven 1.1.0 2017-07-09 CRAN (R 3.4.1)
## Hmisc * 4.0-3 2017-05-02 CRAN (R 3.4.1)
## hms 0.3 2016-11-22 CRAN (R 3.4.1)
## htmlTable 1.9 2017-01-26 CRAN (R 3.4.1)
## htmltools 0.3.6 2017-04-28 CRAN (R 3.4.1)
## htmlwidgets 0.9 2017-07-10 CRAN (R 3.4.1)
## httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
## jsonlite 1.5 2017-06-01 CRAN (R 3.4.1)
## km.ci 0.5-2 2009-08-30 CRAN (R 3.4.1)
## KMsurv 0.1-5 2012-12-03 CRAN (R 3.4.0)
## knitr 1.17 2017-08-10 CRAN (R 3.4.1)
## labeling 0.3 2014-08-23 CRAN (R 3.4.0)
## lattice * 0.20-35 2017-03-25 CRAN (R 3.4.1)
## latticeExtra 0.6-28 2016-02-09 CRAN (R 3.4.1)
## lazyeval 0.2.0 2016-06-12 CRAN (R 3.4.1)
## lubridate 1.6.0 2016-09-13 CRAN (R 3.4.1)
## magrittr * 1.5 2014-11-22 CRAN (R 3.4.1)
## MASS 7.3-47 2017-04-21 CRAN (R 3.4.1)
## Matrix 1.2-11 2017-08-16 CRAN (R 3.4.1)
## MatrixModels 0.4-1 2015-08-22 CRAN (R 3.4.1)
## memoise 1.1.0 2017-04-21 CRAN (R 3.4.1)
## methods * 3.4.2 2017-09-28 local
## mnormt 1.5-5 2016-10-15 CRAN (R 3.4.0)
## modelr 0.1.1 2017-07-24 CRAN (R 3.4.1)
## multcomp 1.4-7 2017-09-07 CRAN (R 3.4.1)
## munsell 0.4.3 2016-02-13 CRAN (R 3.4.1)
## mvtnorm 1.0-6 2017-03-02 CRAN (R 3.4.0)
## nlme 3.1-131 2017-02-06 CRAN (R 3.4.1)
## nnet 7.3-12 2016-02-02 CRAN (R 3.4.1)
## parallel 3.4.2 2017-09-28 local
## pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.1)
## plyr 1.8.4 2016-06-08 CRAN (R 3.4.1)
## polspline 1.1.12 2015-07-14 CRAN (R 3.4.0)
## psych 1.7.8 2017-09-09 CRAN (R 3.4.1)
## purrr * 0.2.3 2017-08-02 CRAN (R 3.4.1)
## quantreg 5.33 2017-04-18 CRAN (R 3.4.1)
## R6 2.2.2 2017-06-17 CRAN (R 3.4.1)
## RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.4.0)
## Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.1)
## readr * 1.1.1 2017-05-16 CRAN (R 3.4.1)
## readxl 1.0.0 2017-04-18 CRAN (R 3.4.1)
## reshape2 1.4.2 2016-10-22 CRAN (R 3.4.1)
## rlang 0.1.2 2017-08-09 CRAN (R 3.4.1)
## rmarkdown 1.6 2017-06-15 CRAN (R 3.4.1)
## rms * 5.1-1 2017-05-03 CRAN (R 3.4.1)
## rpart 4.1-11 2017-04-21 CRAN (R 3.4.1)
## rprojroot 1.2 2017-01-16 CRAN (R 3.4.1)
## rstudioapi 0.7 2017-09-07 CRAN (R 3.4.1)
## rvest 0.3.2 2016-06-17 CRAN (R 3.4.1)
## sandwich 2.4-0 2017-07-26 CRAN (R 3.4.1)
## scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
## SparseM * 1.77 2017-04-23 CRAN (R 3.4.0)
## splines 3.4.2 2017-09-28 local
## stats * 3.4.2 2017-09-28 local
## stringi 1.1.5 2017-04-07 CRAN (R 3.4.0)
## stringr 1.2.0 2017-02-18 CRAN (R 3.4.1)
## survival * 2.41-3 2017-04-04 CRAN (R 3.4.1)
## survminer * 0.4.0 2017-06-07 CRAN (R 3.4.1)
## survMisc 0.5.4 2016-11-23 CRAN (R 3.4.1)
## TH.data 1.0-8 2017-01-23 CRAN (R 3.4.1)
## tibble * 1.3.4 2017-08-22 CRAN (R 3.4.1)
## tidyr * 0.7.1 2017-09-01 CRAN (R 3.4.1)
## tidyverse * 1.1.1 2017-01-27 CRAN (R 3.4.1)
## tools 3.4.2 2017-09-28 local
## utils * 3.4.2 2017-09-28 local
## withr 2.0.0 2017-07-28 CRAN (R 3.4.1)
## xml2 1.1.1 2017-01-24 CRAN (R 3.4.1)
## xtable 1.8-2 2016-02-05 CRAN (R 3.4.1)
## yaml 2.1.14 2016-11-12 CRAN (R 3.4.1)
## zoo 1.8-0 2017-04-12 CRAN (R 3.4.1)References
Therneau, Terry M. 2017. Survival: Survival Analysis. https://CRAN.R-project.org/package=survival.
Kassambara, Alboukadel, and Marcin Kosinski. 2017. Survminer: Drawing Survival Curves Using ’Ggplot2’. https://CRAN.R-project.org/package=survminer.
Wickham, Hadley, and Winston Chang. 2016. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. https://CRAN.R-project.org/package=ggplot2.
Gray, Bob. 2014. Cmprsk: Subdistribution Analysis of Competing Risks. https://CRAN.R-project.org/package=cmprsk.
Harrell, Jr., Frank E. 2017. Rms: Regression Modeling Strategies. https://CRAN.R-project.org/package=rms.
Wickham, Hadley. 2017. Tidyverse: Easily Install and Load ’Tidyverse’ Packages. https://CRAN.R-project.org/package=tidyverse.
Wickham, Hadley, Romain Francois, Lionel Henry, and Kirill Müller. 2017. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.
Henry, Lionel, and Hadley Wickham. 2017. Purrr: Functional Programming Tools. https://CRAN.R-project.org/package=purrr.
Xie, Yihui. 2017b. Knitr: A General-Purpose Package for Dynamic Report Generation in R. https://CRAN.R-project.org/package=knitr.
Xie, Yihui. 2017a. Bookdown: Authoring Books and Technical Documents with R Markdown. https://CRAN.R-project.org/package=bookdown.