Prepare input data to run the Stan model.
Creates / calculates all the required inputs as required by the data{} block of the MMRM Stan program.
prepare_stan_data(ddat, subjid, visit, outcome, group)A stan_data object. A named list as per data{} block of the related Stan file. In particular it returns:
N - The number of rows in the design matrix
P - The number of columns in the design matrix
G - The number of distinct covariance matrix groups (i.e. length(unique(group)))
n_visit - The number of unique outcome visits
n_pat - The total number of pattern groups (as defined by missingness patterns & covariance group)
pat_G - Index for which Sigma each pattern group should use
pat_n_pt - number of patients within each pattern group
pat_n_visit - number of non-missing visits in each pattern group
pat_sigma_index - rows/cols from Sigma to subset on for the pattern group (padded by 0's)
y - The outcome variable
Q - design matrix (after QR decomposition)
R - R matrix from the QR decomposition of the design matrix
A design matrix
Character vector containing the subjects IDs.
Vector containing the visits.
Numeric vector containing the outcome variable.
Vector containing the group variable.
The group argument determines which covariance matrix group the subject belongs to. If you
want all subjects to use a shared covariance matrix then set group to "1" for everyone.