prepare_stan_data function

Prepare input data to run the Stan model

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)

Arguments

• ddat: A design matrix
• subjid: Character vector containing the subjects IDs.
• visit: Vector containing the visits.
• outcome: Numeric vector containing the outcome variable.
• group: Vector containing the group variable.

Returns

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

Details

• 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.