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ubiquity 2.0.2 (development version)
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
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