NEWS.md

In john-harrold/ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

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ubiquity 2.0.4 (development version)

Notes

ubiquity 2.0.3

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

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

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

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

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

Bug Fixes

• Updated the components to fix issues encountered with R 4.0

john-harrold/ubiquity documentation built on March 13, 2024, 2:58 a.m.