Package "conc-QTc"

With our R package, formatting your dataset, running the conc-QTc analysis and generating a typical report takes only a few minutes. The method has been published in JPKPD: https://rdcu.be/elwuL.

Download the conc-QTc R package and check the step-by-step example.

Description of the package

The R scripts provide a set of functions to perform a standard conc-QTc analysis from data preparation to report generation. The main functions are:

• process_QTcData(): format an input dataset for analysis by averaging triplicates, extracting baseline values, calculating QTc, etc

• generateAllQTcProjects(): generate Monolix projects to run a conc-QTC analysis using the standard linear model as well as alternative non-linear models

• quarto_render(input = "../_mlxQTcTools/QTc_quarto_allModels.qmd"): generate a report (e.g as Word document) using a Quatro template. The report contains exploratory data analysis plots, assessment of key modeling hypotheses, and modeling results.

The code is open and can be adjusted to the users needs.

The .zip is organized in the following way:

• _mlxQTcTools: contains the scripts to run the analysis

  • mlxQTcTools.R: contains the functions process_QTcData() and generateAllQTcProjects(), as well as auxiliary functions.

  • mlxReportingTools.R: contains auxiliary functions to generate the Quarto report

  • QTc_quarto_allModels.qmd: Quarto template for the report

  • models: contains the structural models to create Monolix projects in case of ΔQTc and ΔΔQTc with no effect, linear, Emax, Hill, or Logarithmic effect, with or wihtout effect compartment to create a delay.

• Example_XXX: one folder per example dataset containing

  • XXX_QTc_analysis.R: R script calling three main functions process_QTcData(), generateAllQTcProjects() and quarto_render() to do the analysis and report

  • SCR002_clinicalData4drugs_originalFile.xlsx: input dataset

  • XXX_formated.csv: formatted dataset generated by process_QTcData()

  • mlx_runs: monolix runs generated by generateAllQTcProjects()

  • XXX_QTc_report_allModels.docx: report generated by quarto_render()