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Changelog

Source: NEWS.md

ospsuite.reportingengine 2.2.0

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)

ospsuite.reportingengine 2.1.244

New features

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

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 ticklabels (#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)

ospsuite.reportingengine 2.1

New features

  • Qualification workflows are now available ! (#2)
    • Qualification Workflows have their own vignette to help you start (#566)
    • A template qualification workflow R script is available on GitHub at system.file("extdata", "qualification-workflow-template.R", package = "ospsuite.reportingengine") and can also be downloaded from GitHub (#572)
    • Function adjustTitlePage can be used to personalize the report title page (#755)
    • Configuration plans can be re-loaded on 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 option timeOffset for time profile plots (#313) or through user defined PK parameters for PK parameter plots (#578).
  • User can define their own word report template to tune the styles of their report by providing a reference word document to the wordConversionTemplate of their Workflow object. A word reference template is available on GitHub (#756)
  • The function copyReport can be used to copy markdown/word reports (#814)

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 starting nonmem was replaced by dataset (#534)

ospsuite.reportingengine 1.2.0

New features

  • Descriptor of simulation sets is now available and can be defined in Excel template (#445) as well as using the function setSimulationDescriptor (#423).
  • Each task property settings is now an R6 object (#396). This allows users to have an easy and direct access to setting properties.
  • Possibility to read time and measurement units from nonmem columns (#414)

Minor improvements and bug fixes

  • Calculation of time profile residuals can use Linear or Logarithmic scale (#395).
  • Units for observed data is appropriately taken into account within dictionary (#414).
  • Settings for number format within reports are now available (#424). They can be updated in global settings using setDefaultNumericFormat or within specific tasks through their settings property.
  • The settings property for task plotTimeProfilesAndResiduals include
  • Application Ranges can be switched on/off from SimulationSet objects regarding simulations with multiple administrations (#419)
  • Population workflows: captions for tables (PK parameters) missing (#421)
  • Population workflows: units for tables (PK parameters) missing (#422)
  • Population/RatioComparison: box-Whisker Ratio plots (#425)

ospsuite.reportingengine 1.1.0

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.

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).