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Releases: Open-Systems-Pharmacology/OSPSuite.ReportingEngine

Version 2.2.367

09 Sep 13:27
@Yuri05 Yuri05
v2.2.367
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Version 2.2.367 Pre-release
Pre-release

Download and installation

S. the Installation section below.

Documentation

New features and improvements

New features

Note

Users can now check out Reporting Engine Test Reports and access a bunch of template workflows including their R code, models, data and corresponding reports.

  • Demography task received significant updates:
    • The article for demography has been updated with more comprehensive examples using more representative virtual populations and illustrating the effects of population workflows and settings (#1095, #1102)
    • Categorical parameters, such as Gender, are now accounted for demography range plots and displayed as boxplots (#1088)
    • Demography plots can now display observed data (#535)
  • Mass Balance task received significant updates:
  • Qualification DDI plots received the following improvements
    • Delta symbol (δ) from Guest et al. formula is indicated in table caption (#1069)
    • Guest criterion (δ) can be tuned through the configuration plan (#789)
    • DDI plot format is quadratic by default (#1051)
  • Formatting to word reports can translate additional html tags (#382)
  • Goodness of Fit task leverages groupID from Output objects to group multiple outputs in same time profile and residual plots (#1188).
    groupID is also leveraged in the plots of residuals across the simulations (#1251).

Minor improvements and bug fixes

  • Monte Carlo sampling in ratio comparison workflows is now centralized, performed in the PK parameter calculation step and significantly faster (#536, #1086).
  • Wording for ratio comparison workflow figures and tables has been updated (#1087)
  • Number of bins in demography and PK parameter range plots is consistent with input (#1128)
  • Link/bookmark targets in word reports are better placed (#1084)
  • Qualification time profiles work when no observed data is contained (#1082)
  • Qualification PKRatio uses ml/min/kg as default clearance - CL - unit (#1242)
  • Static images in qualification reports are better handled (#955, #1071)
  • Figure captions are displayed below the figure in the reports (#1053)
  • Word report is updated if it already existed (#1055)
  • LLOQ line is better displayed in the legend of time profile plots (#478)

Full Changelog: v2.1.244...v2.2.367

Installation

1. Prerequisites

  • Install required packages from CRAN and from GitHub as described here.
  • [OPTIONAL] Install Pandoc and SVG-Converter (required only for generation of reports in MS-Word format) as described here

2. Package installation

Finally, install the OSPSuite.ReportingEngine package:

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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:

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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

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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

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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
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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
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