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MMVmalaria 1.4.0

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@joness-w joness-w released this 31 Jul 14:32
1.4.0
f78c288

MMVmalaria 1.4.0 updates to depend on IQRtools 2025.05

Documentation

Dependencies

  • IQRtools (>= 2025.05 from >= 2024.09 )
  • MMVbase (>=1.2.1 from ==1.2.0)
  • Imports added: survival

Build.sh

Build.sh script added to build the R package

.gitignore

Updated to be more functional and in line with MMVbase, but allowing .Rdata files

Functions

All

  • Extensive documentation pass to ensure all arguments are well captured by Roxygen2 standards

Confusion Matrix functions used to evaluate true/false positives/negatives added to MMVmalaria

  • ConfusionMatrix() added to 09-KeyParameters.R
  • SummarizeConfusionMatrix() added to 09-KeyParameters.R
    MMVbase:: prefixed to all functions exported from MMVbase that were previously in MMVmalaria
    predictDose_Generic
  • Adjusted to import and declare IQRtools:: for IQRmodel()

03-DataPreparation.R

  • import_SCIDpkpdDataCombo_TAD : Argument PDrangeDoseTimeRange removed as unused
  • load_AfricanPediatricMalariaPopulation2to5 REMOVED

19-IQRaux.R

  • verifyArg() Removed, now in IQRtools
  • createSimIQRmodelSpec() Removed, now in IQRtools
  • split_eventTable() Removed, now in IQRtools
  • getDefaultEventTable() Removed, now in IQRtools
  • addTminToEventTable() Removed, now in IQRtools
  • sim_IQRmodel_consistent() Removed, now in IQRtools as sim_IQRmodel_strict()

98-OldFunctions.R

  • REMOVED

Vignettes

PredictHumanDoses.Rmd

  • IQRtools::IQRmodel(modelFile) explicitly called in vignette (previously IQRmodel(modelFile))
  • Calls to MalariaPopulation.Rdata adjusted
  • Definition of WT0 from WEIGHT_kg added

Tests

test-predictHumanDose.R

  • Calls to MalariaPopulation.Rdata adjusted

Examples

findMinMMV_ex

  • Adjusted findMinMMV to MMVbase::find_MinMMV to reflect function being moved to MMVbase and renamed
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