mapbayr 0.6.0

This version of mapbayr introduces several features that aim to express uncertainty around the point estimate. Please note that the results of these functions were not validated vs a gold-standard software such as NONMEM. This is why they are referred as "experimental features" in the following subsections. They are exported with the objective to ease their future validation, and to provide a very rough idea of the estimation uncertainty.

Breaking changes

• Remove data slot in estimation object. Use get_data() instead. #64
• The $model@args$data is now always NULL in the estimation object. It was carried out if the data was initially passed with data_set() or built with adm_lines()/obs_lines(). #64
• The time grid used to plot the results is now adapted as function of data, and not fixed (refactor of augment). Also use recsort=3 to deal with steady-state administrations. #85
• Argument passed to plot() are now directly passed to augment().
• Depends on mrgsolve >= 1.0.0 to use the newly exported collapse_omega() function. (thanks @kylebaron)

Experimental features

• Compute and use a normal approximation of conditional distribution. The function called in mapbayest(hessian = ) is used to compute the hessian with stats::optimHess() by default. The variance-covariance matrix is returned in a covariance slot in the estimation object, and can be accessed with get_cov().
• Simulate with uncertainty. use_posterior(update_omega = TRUE) update the OMEGA matrix with the covariance matrix, in order to simulate with uncertainty and derive confidence intervals.
• Plot confidence interval. plot(ci = TRUE) displays approximate confidence intervals on predicted concentrations. Parameter uncertainty is approximated with the covariance matrix. Confidence interval computation relies on the delta approximation (ci_method = "delta"), but can also be computed thanks to simulations (see augment() documentation).

New exports

• get_cov(): function to get the covariance matrix of estimation. #43
• get_phi(), read_nmphi(), merge_phi() and plot_phi(): functions to compare the estimations vs NONMEM. #55
• est001: an example mapbayests estimation object. #94

use_posterior()

• add update_omega, update_cov, and update_eta arguments to control what to update.
• .zero_re default behavior now depends on update_ arguments values.
• no longer warns if time-varying covariates are used. The first value will be used by default.
• now works on multiple individuals: a list of mrgsolve models will be returned if multiple individuals found.

Miscellaneous

• Print a message indicating a difficulty when there is a reset during optimization, instead of a warning indicating an error. #96
• mapbayest(verbose = ) now mutes the message that indicates a reset during optimization. #96
• Remove the attributes of opt.value inherited from optimx. #95
• Detect non-numeric column(s). Stop and inform the user if any. #86 #88 (thanks @jkamp91)
• get_data() can now return a list of individual data sets with output = "list". #64
• Check for undesirable zero in OMEGA/SIGMA matrices instead of crashing. #44
• Remove stats from dependencies.
• Add Kyle Baron as contributor.
• Update README since article publication.
• Update documentation.