mapbayr 0.9.0

New features

Data Helpers

• New adm_rows() and obs_rows() replace and improve adm_lines() and obs_lines(), respectively. See ?data_helpers for a comprehensive documentation (#175).
• In adm_rows(), obs_rows(), and add_covariates(), the first argument x:
  • can be missing, which enables the creation of a new dataset from scratch.
  • accepts a data.frame, which enables the modification of a pre-existing dataset (#155). For example:

    adm_rows(amt = 100, cmt = 1) %>% 
      obs_rows(time = 24, cmt = 2, DV = 0.123)

  • still accepts an 'mrgsolve' model, which enables the modification of a dataset stored in the model arguments.
• In adm_rows() and obs_rows(), new argument .datehour in order to compute time as function of date and hours provided as character. The value passed to .datehour is parsed with parse_datehour() into a date-time value ("POSIXct"). For example:

  obs_rows(.datehour = c("2023/02/01 12:00", "2023/02/01 12:34"), DV = c(0.123, 0.456), cmt = 1)

• Data helpers now always rearrange data to fulfill the NM-TRAN compatibility and readability: filling missing covariate values with the last observation carried forward rule, relocation of NM-TRAN variables in the first positions etc...

Below Limit of Quantification

• Data below the limit of quantification can now be handled with the so-called "M3 method" which consists in computing the likelihood of being below the limit of quantification. This is achieved when the variables LLOQ (lower limit of quantification, e.g. 0.22 mg/L) and BLQ (below limit of quantification, e.g. 1 or 0) are in the data (@pchelle, #182).
• This can be achieved by:
  • adding the variables LLOQ and BLQ to the data by yourself.
  • adding the variable LLOQ to the data by yourself: BLQ will automatically be inferred from LLOQ and DV.
  • using mapbayest(lloq = ) to automatically add the LLOQ and BLQ variables in the data.
• In mapbayest(), new argument lloq in order to add a variable LLOQ to the data. For example: mapbayest(model, data, lloq = 0.22).

Estimation features

• In mapbayest(), new argument select_eta in order to select the numbers of the ETAs to estimate. Default are ETAs related to an OMEGA not equal to zero. Non-selected ETAs will not be estimated and returned equal to zero. This can be useful in order to ignore the estimation of ETAs not of interest, e.g. in case of inter-occasion variability or non-identifiability. For example: mapbayest(model, data, select_eta = c(1,3)) (#170).

• In mapbayest(), new argument lambda in order to modify the weight of the priors in the Bayesian estimation. This could be useful in order to flatten the priors with the objective to favor observed data instead of a priori information. For example: mapbayest(model, data, lambda = 0.1) to decrease the weight of priors of a ten-fold (#174).

Minor changes and bug fixes

• Export adm_rows.data.frame(), adm_rows.missing(), adm_rows.mrgmod(), obs_rows.data.frame(), obs_rows.missing(), obs_rows.mrgmod(), and add_covariates.data.frame(), as new methods for data helpers.
• Export parse_datehour(), used to parse arguments passed to .datehour in adm_rows() and obs_rows().
• Export filter.mrgmod(), a method, wrapper around dplyr::filter() for dataset stored in mrgsolve model object ('mrgmod').
• Deprecate adm_lines() and obs_lines(). Stop exporting adm_lines.mrgmod() and obs_lines.mrgmod().
• Stop exporting see_data(). Was deprecated since 0.4. Use get_data() instead.
• Suggests lubridate.
• In the final estimation object, new arg.optim$select_eta element, arg.ofv.fix$omega_inv now has the dimensions of the number of ETAs selected.
• OMEGA values equal to zero are allowed in the model and will be ignored during the estimations steps thanks to the new select_eta argument. This condition is not tested anymore with check_mapbayr_model().
• print.mapbayests(), now only shows the estimated ETAs.
• In hist(), new argument select_eta in order to select the ETAs to plot. Default are ETAs estimated with mapbayest() (#167).
• eta() properly sorts vectors of length superior to 9 (#159).
• use_posterior() works if covariates had not been defined in data (#160).
• In hist(), get_phi() and plot_phi(), ETAs are now properly re-ordered if they are more than 9 (#165).
• Classification of absolute difference equal to zero now works (#166).
• Observations at time = 0 are now allowed (#168).
• Fix deprecations related to tidyverse packages (#171).
• Depends on ggplot2 >= 3.4.0.
• add_covariates() accepts empty arguments.
• In mapbayest(), new argument ... in order to fix compatibility issues, not used yet.