Estimate state occupation probabilities to be illustrated by a bar plot in msmhist

Estimate state occupation probabilities to be illustrated by a bar plot in msmhist

Usage

msmhist_bardata(
  data,
  state,
  time,
  subject,
  nbins,
  absorbing = NULL,
  censtimes = NULL
)

data: Data frame giving the observed data.
state: Character string naming the observed state variable in the data. This variable must either be an integer in 1,2,...,K, where K is the number of states, or a factor with these integers as level labels.
time: Character string naming the observation time variable in the data
subject: Character string naming the individual ID variable in the data
nbins: Number of time intervals to bin the state observations into. The underlying distribution of states illustrated by the plot will be assumed constant within each interval.
absorbing: Indices of any absorbing states. Individuals are assumed to stay in their absorbing state, and contribute one observation to each bin after their absorption time. By default, no states are assumed to be absorbing.
censtimes: Vector of maximum intended follow-up times for the people in the data who entered absorbing states. This supposes that had the person not entered the absorbing state, they would not have been observed after this time.

Data frame with one row per bin and state, and columns:

binid: Integer ID for bin
binlabel: Character label for bin, with time interval
state: State
binstart, binend: Start and end time of the bin (numeric)
props: estimates of state $s$ occupancy proportions $p(s)$ for each bin
cumpstart, cumpend: Cumulative sum of props over the set of states, where cumpstart starts at 0, and cumpend ends at
1. Intended for creating stacked bar plots with geom_rect or similar.