# ubiquity 2.0.0

[//]: ## Notes
[//]: ## New Features
[//]: ## Bug Fixes

## 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

