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ubiquity 2.0.4 (development version)

Notes

  • Removed the NONMEM and Monolix outputs
  • Added translation of rxode2 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.

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