In this practical, a number of R packages are used. If any of them are not installed you may be able to follow the practical but will not be able to run all of the code. The packages used (with versions that were used to generate the solutions) are:
mice (version: 3.6.0)nlme (version: 3.1.140)JointAI (version: 0.6.0)splines (version: 3.6.1)ggplot2 (version: 3.2.1)In this practical we will work with data from a trial on primary biliary cirrhosis (PBC) of the liver.
To get the pbclong data, load the file pbclong.RData. You can download it here. To load this dataset, you can use the command file.choose() which opens the explorer and allows you to navigate to the location of the downloaded file on your computer. If you know the path to the file, you can also use load("<path>/<pbclong.RData").
The variables contained in the dataset pbclong are:
id
|
patient identifier |
day
|
continuously measured day of follow-up time (the time variable) |
sex
|
patients’ sex (f: female, m: male) |
trt
|
treatment group (0: D-penicillmain, 1: placebo) |
age
|
patients’ age at intake |
ascites
|
presence of ascites at baseline (0:no, 1:yes) |
hepato
|
presence of hepatomegaly or enlarged liver |
bili
|
serum bilirubin level at baseline |
copper
|
urine copper (ug/day) |
albumin
|
serum albumin level at follow-up (time-varying) |
The variables have the following distributions and proportions of missing values: