Changes in version 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 Changes in version 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 to variance models in cohort definitions. - Fixed issue where initial conditions were not being passed to nlmixr2 output. Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 1.0.2 (2020-07-05) Bug Fixes - Updated the components to fix issues encountered with R 4.0