Biostatistics III in R

Installation for Biostatistics III in R

R will be used throughout the course. This section describes how to download and install the files required for the computing exercises (e.g., data files) as well as how to install packages for extending R. If you are working in a computer lab during a course it’s possible these files may have already been installed for you.

Download and installation of R packages is generally done within R. The packages can be installed from CRAN by

install.packages("biostat3")
install.packages(c("bshazard","rstpm2","Epi","dplyr"))

You can use the library function to check if an R package is installed (and load it).

library(biostat3)  # main package
## some additional packages
library(rstpm2)    # stpm2(), pstpm2()
library(bshazard)  # bshazard()
library(Epi)       # ccwc()
library(dplyr)     # mutate(), filter(), group_by(), summarise(), %>%

You can also read the data files directly from the web from within R. For example,

library(foreign)
colon <- read.dta("http://www.biostat3.net/download/colon.dta")