ubiquity 2.0.1
CRAN release: 2023-10-29
Notes
- Removed internal files that were no longer being used
- Added documentation for creating user defined observation functions when running parameter estimation
- Updated the reporting template to work with the development version of
onbrand - Changed terminal messaging to use
cli - Added termination criteria in estimation output
- Fixed wrapping issue in Fortran output where unwrappable strings resulted in infinite loop
- Added system-testing.txt example
- Added nlmxir output target
- Added template creation for NONMEM, Monolix, and nlmixr
- Fixed R command in compilation to use
R.home() - Fixed broken tests
- Updated CITATION to use bibentry
- Fixing error when building systems in windows
ubiquity 2.0.0
CRAN release: 2021-09-03
Notes
Lots of small updates to function documentation and the vignettes
Completely replaced the reporting functionality. Now using the
onbrandpackage for templated reporting. Note: This will break all reporting in version 1 of the R package. Old Word and PowerPoint templates will work, but you will need to create a yaml mapping file. This is detailed in the Reporting vignette.-
Reporting changes added the following functions
-
Reporting changes removed the following functions:
system_report_doc_add_content()system_report_doc_format_section()system_report_doc_set_ph()system_report_estimation()system_report_glp()system_report_init()system_report_nca()system_report_ph_content()system_report_save()system_report_set()system_report_slide_content()system_report_slide_section()system_report_slide_title()system_report_slide_two_col()system_report_view_layout()system_fetch_report()system_fetch_report_format()md_to_officer()md_to_oo()
Reporting changes updated vignettes, example scripts and function templates
ubiquity 1.0.4
CRAN release: 2021-04-18
Notes
- Renamed
system_report_fetchtosystem_fetch_report - Added reporting scripts to the unit tests
- Added import of officer functions starting with
body_end_ - Changed how table and figure captions were being numbered in Word reporting
- Created testthat scripts to run through workshop functions
New Features
- Added shaded region for observed AUC in NCA reporting
- Added cohort-specific output times option to the estimation workflow
- Updated references in the documentation and templates to point to r.ubiquity.tools
- Added checks in estimation routines to check for reasonable bounds for global optimizer and to notify users when estimates are near bounds
- Added
sessionInfo()to estimation Word reporting - Added
system_fetch_report_format - Integrated the markdown (md) header format option with flextable outputs
- Added default for
cfg$reporting$enabled(FALSE) - Added the ability to use markdown for the NCA summary tables generated with
system_nca_summary - Fixed the placeholder text, now the delimiters are
===on either side of the text - Added
system_set_optiongeneral group andoutput_directoryoption - For markdown in Word reporting, default font properties have been defined and the ability to specify them in the
org_functions.Rtemplate has been added. - Moved annotated layout generation of PowerPoint files in
system_report_view_layout()over to theannotate_base()command in officer - Added optional key fields for tables and figures in Word reporting
- Added the ability to pass PKNCA.options through to
system_nca_run - Added verbose option to the
system_viewcommand - Allowing pass through of dataset columns to summary NCA output
- Updated
system_report_ph_contentandsystem_report_doc_add_contentto allow for inclusion of flextable objects - Updated
system_viewto include nca results - Added the following functions:
-
system_fetch_nca- function to fetch NCA results -
system_fetch_nca_columns- function to fetch column descriptors of a specific analysis -
system_nca_parameters_meta- list of standard NCA parameters -
system_nca_summary- creates summary tables for NCA results
-
- Adding checks in
simulate_subjectsto ensure required columns are present - Added the ability to read xlsx data sets with
system_load_data
Bug Fixes
- CRAN erroring out because of tic() function. Removed tic() and toc() functions
- Fixed a bug where the dataset given to
system_run_ncadoes not have enough valid data to actually run NCA - Fixed “Coordinate system already present…” warning in
gg_axis - Fixed location of table generation in example script
analysis_nca_md.Rso that table styles would be picked up properly - Added scales package requirement
- Fixed missing rptname inputs to
system_report_ph_content - Fixed Bug in system view when there are cohort-specific parameters defined
- Fixed figure generation errors in the estimation workflow
- Fixed a bug in
system_report_save() - Removed aberrant gdata require calls in templates
- Fixed bug in
system_nca_runwhen DOSE is a factor - Fixed bug in
system_nca_runwhere back extrapolation was being done for doses that should have been skipped due to insufficient points. This was causing an error. - Removed coercion warnings: In tmpsumhalflife = NCA.resresult[NCA.resresultPPTESTCD == “half.life”, : Coercing LHS to a list
- Removed digits input from
system_nca_run(this is now handled withsystem_nca_summarybelow) - Fixed coercion warnings for covariates when building the system
- Using explicit declaration of officer functions and specifying those in importFrom this is to prevent namespace issues with readxl to allow the function readxl::read_xlsx
ubiquity 1.0.3
CRAN release: 2020-09-13
Notes
- Removed the gdata dependency
- Removed URL redirects from documentation to resolve CRAN submission warnings
Bug Fixes
- Converted
system_nca_run()from using $ to mostly using [[“”]] - Fixed NCA template
- Fixed bug in ShinyApp template where iiv tab was being displayed even when the system had no iiv elements