NEWS

ubiquity 2.1.1

Notes

Fixed depreciated min and max options in GA::ga() to use lower and upper
Added support for optimization packages: ppso, parallelPSO, and FME

ubiquity 2.1.0 (2025-01-07)

Notes

Removed the NONMEM and Monolix outputs
Added translation of nlmixr2 output into NONMEM and Monolix outputs
Added simulation option dynamic set to TRUE by default and when set to FALSE it will fix ODEs to 0 and allow for in vitro analysis.
Applying <OE:?> to variance models in cohort definitions.
Fixed issue where initial conditions were not being passed to nlmixr2 output.

ubiquity 2.0.3 (2024-03-08)

Notes

Fixed IIV comments breaking nlmixr2 output
Fixed bug where spaces were breaking compilation of C output
Fixed bug in CRAN where flextable/officer update broke saved values in vignettes

ubiquity 2.0.1 (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 (2021-09-03)

Notes

Lots of small updates to function documentation and the vignettes
Completely replaced the reporting functionality. Now using the onbrand package 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
- system_rpt_add_slide()
- system_rpt_add_doc_content()
- system_rpt_read_template()
- system_rpt_save_report()
- system_rpt_template_details()
- system_fetch_rpt_officer_object()
- system_fetch_rpt_onbrand_object()
- system_set_rpt_officer_object()
- system_set_rpt_onbrand_object()
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 (2021-04-18)

Notes

Renamed system_report_fetch to system_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_option general group and output_directory option
For markdown in Word reporting, default font properties have been defined and the ability to specify them in the org_functions.R template has been added.
Moved annotated layout generation of PowerPoint files in system_report_view_layout() over to the annotate_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_view command
Allowing pass through of dataset columns to summary NCA output
Updated system_report_ph_content and system_report_doc_add_content to allow for inclusion of flextable objects
Updated system_view to 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_subjects to 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_nca does 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.R so 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_run when DOSE is a factor
Fixed bug in system_nca_run where 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 tmpsum$halflife = NCA.res$result[NCA.res$result$PPTESTCD == "half.life", : Coercing LHS to a list
Removed digits input from system_nca_run (this is now handled with system_nca_summary below)
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 (2020-09-13)

Notes

Removed the gdata dependency
Removed URL redirects from documentation to resolve CRAN submission warnings

New Features

Added the option in simulate subjects to specify secondary parameters to be saved

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

ubiquity 1.0.2 (2020-07-05)

Bug Fixes

Updated the components to fix issues encountered with R 4.0