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
system_report_fetch
to system_fetch_report
body_end_
sessionInfo()
to estimation Word reportingsystem_fetch_report_format
cfg$reporting$enabled
(FALSE)system_nca_summary
===
on either side of the textsystem_set_option
general group and output_directory
optionorg_functions.R
template has been added.system_report_view_layout()
over to the annotate_base()
command in officersystem_nca_run
system_view
commandsystem_report_ph_content
and system_report_doc_add_content
to allow for inclusion of flextable objectssystem_view
to include nca resultssystem_fetch_nca
- function to fetch NCA resultssystem_fetch_nca_columns
- function to fetch column descriptors of a specific analysissystem_nca_parameters_meta
- list of standard NCA parameterssystem_nca_summary
- creates summary tables for NCA resultssimulate_subjects
to ensure required columns are presentsystem_load_data
system_run_nca
does not have enough valid data to actually run NCAgg_axis
analysis_nca_md.R
so that table styles would be picked up properlysystem_report_ph_content
system_report_save()
system_nca_run
when DOSE is a factorsystem_nca_run
where back extrapolation was being done for doses that should have been skipped due to insufficient points. This was causing an error.system_nca_run
(this is now handled with system_nca_summary
below)system_nca_run()
from using $ to mostly using [[""]]