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Releases: Open-Systems-Pharmacology/OSPSuite.ReportingEngine

Version 2.1.244

11 Mar 14:37
@Yuri05 Yuri05
v2.1.244
f2e8c0f
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Version 2.1.244 Latest
Latest

Download and installation

S. the Installation section below.

Documentation

New features and improvements

New features

Qualification workflows

  • Qualification Time Profiles handle dual axis plots (#934, #985)

MeanModel- and Population-Workflows

  • Population workflows can use Monte Carlo sampling to handle ratio comparison (#536) as documented in the article PK Parameters in Population Workflows.
  • Output objects can now include color and fill properties that will be displayed in the corresponding plots (#418, #883)
  • dataSelection is now available at both SimulationSet and Output levels (#881)
  • Excel template is up-to-date with the new features (#882) and documented in the article Excel Template
  • Mean and Population workflows can display a title/cover page at the beginning of the report (#854) as documented in article Add a title page to your workflow report

Minor improvements and bug fixes

  • In qualification workflows, logging now includes information regarding the configuration plan location (#930)
  • By default, plot dimensions are now quadratic (#877)
  • Statistics in population workflow time profiles now use geometric mean and sd as default and can be easily updated with enum helper StatisticsTypes and function setDefaultTimeProfileStatistics() (#862)
  • Goodness of fit plots and captions were improved (#418, #863, #865, #867, #871, #874, #875, #878, #884, #886, #887, #888)
  • Displayed qualification plots now includes following updates:
    • better scaled watermark (#849)
    • margin added to prevent truncated tick labels (#951)
    • gof and time profile use correct colors (#952)
    • residual label match calculation method (#953)
    • legend does not shrink the plot size (#861)
  • Creation of word reports now includes following updates:
    • page breaks at appropriate places (#971)
    • figure/table numbering (#967) are now fixed
    • default reference word document has been updated (#748, #749, #750 and #754)
    • tags for subscript (wrapped by <sub>...</sub>) and superscript (wrapped by <sup>...</sup>) are converted to word (#968)
    • equations wrapped by $$...$$ and written in LaTeX format are converted to word
    • bookmarks are now created from markdown anchors (#923)
  • Qualification time profiles use base unit if unit is not defined by user (#867, #991)

Installation

1. Prerequisites

The OSPSuite.ReportingEngine package is compatible with version 3.6.x AND version 4.x.x of R. One of its indirect dependency, rClr needs to be installed specifically for the targeted R version. Please follow the installation instructions below:

OSPSuite.ReportingEngine requires following packages to be installed:

[OPTIONAL] Install Pandoc (required for generation of reports in MS-Word format):

2. Package installation

Finally, install the OSPSuite.ReportingEngine package:

Assets 4

Version 2.0.191

29 Jul 15:55
@Yuri05 Yuri05
v2.0.191
f50345c
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Version 2.0.191

Download and installation

S. the Installation section below.

Documentation

New features and improvements

New features in the Reporting Engine

  • Qualification workflows are now available
    • Get started: https://www.open-systems-pharmacology.org/OSPSuite.ReportingEngine/articles/qualification-workflow.html
    • A template R script for qualification workflows is available at system.file("extdata", "qualification-workflow-template.R", package = "ospsuite.reportingengine"). Copy this file into your workflow folder, rename to "workflow.R" and follow the instructions in the file.
    • Function adjustTitlePage can be used to personalize the report title page (#755)
    • Configuration plans can be reloaded by the QualificationWorkflow objects to update the report display (#567)
    • DDI subunits option is available (#642)
  • With ospsuite version >=10, simulations can be run in parallel (#526)
  • Workflows account for time offset in simulation sets using the option timeOffset for time profile plots (#313) or through user defined PK parameters for PK parameter plots (#578).
  • The function copyReport can be used to copy markdown/word reports (#814)
  • User can define their own word report template to tune the styles of their (MS-Word) report by setting the wordConversionTemplate property of a Workflow object. The default word template is available at system.file("extdata", "reference.docx", package = "ospsuite.reportingengine"). Copy this file to another location and make required modifications.
Adjusting the word template (Instructions copied from the Pandoc documentation, https://pandoc.org/MANUAL.html)
Open reference.docx in Word, modify the styles as you wish, and save the file. For best results, do not make changes to this file other than modifying the styles used by pandoc:

Paragraph styles:

  • Normal
  • Body Text
  • First Paragraph
  • Compact
  • Title
  • Subtitle
  • Author
  • Date
  • Abstract
  • Bibliography
  • Heading 1
  • Heading 2
  • Heading 3
  • Heading 4
  • Heading 5
  • Heading 6
  • Heading 7
  • Heading 8
  • Heading 9
  • Block Text
  • Footnote Text
  • Definition Term
  • Definition
  • Caption
  • Table Caption
  • Image Caption
  • Figure
  • Captioned Figure
  • TOC Heading

Character styles:

  • Default Paragraph Font
  • Body Text Char
  • Verbatim Char
  • Footnote Reference
  • Hyperlink
  • Section Number

Table style:

  • Table

Minor improvements and bug fixes

  • With tlf version 1.2.0, plots in log scale are better displayed (#603)
  • Too long legend captions are now displayed on multiple lines (#568, #602)
  • Output objects are now cloneable (#542)
  • In population workflows, option for adding reference observed data in time profile plots was created (#540).
  • Confusing observed data terminology improved (nonmem was replaced by dataset) (#534)

New features and improvements in the TLF Library

New features

  • New helper functions and parameters to facilitate usage of plot functions (#301):

    • Function getLinesFromFoldDistance translates fold distance values into lines argument for dataMapping objects.
    • Functions plotDDIRatio, plotPKRatio, plotObsVsPred, plotResVsPred and plotResVsTime include optional parameters such as foldDistance, deltaGuest or smoother.

  • New helper enumerated lists:

    • TagPosition (tag position in a plot grid) (#293)
    • HorizontalJustification (horizontal justifications for plot annotation text) (#293)
    • VerticalJustification (vertical justifications for plot annotation text) (#293)
    • PlotAnnotationTextSize (default text sizes for plot annotations) (#293)
    • TickLabelTransforms (predefined tick labeling) (#304)

Minor improvements and bug fixes

  • PlotGridConfiguration class adds new fields to control the position of the individual plot tags and aesthetic properties of the tag text. (#293)

Installation

Option 1 - install from scratch

The OSPSuite.ReportingEngine package is compatible with version 3.6.x AND version 4.x.x of R. One of its indirect dependencies, rClr needs to be installed specifically for the targeted R version. Please follow the installation instructions below:

OSPSuite.ReportingEngine requires following packages to be installed:

[OPTIONAL] Install Pandoc (required for generation of reports in MS-Word format):

Option 2 - use docker images

Assets 5

Version 1.2

20 May 12:36
@Yuri05 Yuri05
v1.2.40
3aa8fc2
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Version 1.2

New features: s. here

Installation

Assets 9

Version 1.1

12 Dec 16:32
@Yuri05 Yuri05
v1.1.12
411223d
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Version 1.1

New features

  • createWorkflowFromExcelInput writes a commented workflow script ready to run based on Excel input file (#25).
    An Excel input file template is available at system.file("extdata", "WorkflowInput.xlsx", package = "ospsuite.reportingengine")
excelFile <- system.file("extdata", "WorkflowInput.xlsx", package = "ospsuite.reportingengine")
workflowFile <- createWorkflowFromExcelInput(excelFile)

  • setWorkflowParameterDisplayPathsFromFile overwrites display path names for simulation parameters in workflow plotDemography and plotPKParameters tasks (#399).
    The input needs to be a csv file with parameter and displayPath in its header.

  • New functions (#391)

    • addXParametersForDemogrpahyPlot
    • addXParametersForPkParametersPlot
    • addYParametersForDemogrpahyPlot
    • addYParametersForPkParametersPlot

Minor improvements and bug fixes

  • Default settings in workflow plotDemography and plotPKParameters tasks improved the binning (#383).
  • bins and stairstep are now included in settings options of workflow plotDemography and plotPKParameters tasks (#383).
  • Reference population (#394) and reference observed data (#316) are plotted in the time profiles of a population workflow
Assets 10

Version 1.0

18 Sep 12:50
@msevestre msevestre
v1.0.73
974b5fe
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Version 1.0 
Fix #318 legend in demography and pk parameter vpcs

* Fix #318 legend in demography and pk parameter vpcs

* Remove word "Population" from legend title
Assets 5