Advances and further comparison of software tools for Fisher Information Matrix-based design evaluation in pharmacometrics

This repository contains the code and data used for design evaluation in the publication:

“Advances and further comparison of software tools for Fisher Information Matrix-based design evaluation in pharmacometrics”

Each folder contains the material required to reproduce the corresponding example.

• /source.R: Contains shared functions and utilities used across examples

/01: Warfarin PK Model

• /NONMEM: NONMEM model files and outputs for block-diagonal FIM evaluation

• /NONMEM_fullFIM: NONMEM model files and outputs for full FIM evaluation

• /results: Aggregated results and exported tables

• 01_Mlx.R: Design evaluation using MlxDesignEval

• 01_runAll.R: Script to run all evaluations

• 01_NONMEM.R: Design evaluation using NONMEM

• 01_PFIM.R: Design evaluation using PFIM

• 01_PopED.R: Design evaluation using PopED

• 01_Pumas.jl: Design evaluation using Pumas (Julia)

• 01_resultsAll.R: Aggregation and comparison of results across tools

/02: PK/PD in HCV

• /NONMEM: NONMEM model files and outputs for block-diagonal FIM evaluation

• /NONMEM_fullFIM: NONMEM model files and outputs for full FIM evaluation

• /results: Aggregated results and exported tables

• 02_Mlx.R: Design evaluation using MlxDesignEval

• 02_runAll.R: Script to run all evaluations

• 02_NONMEM.R: Design evaluation using NONMEM

• 02_PFIM.R: Design evaluation using PFIM

• 02_PopED.R: Design evaluation using PopED

• HCV_ode.dll: comppiled ode model used in PopED

• 02_Pumas.jl: Design evaluation using Pumas (Julia)

• 02_resultsAll.R: Aggregation and comparison of results across tools

/03: PK model with covariates

• /data_covariates: Input datasets including covariate information
• /NONMEM_Combined1: NONMEM model files and outputs for Combined1 design (block-diagonal FIM)
• /NONMEM_Combined1_fullFIM: NONMEM model files and outputs for Combined1 design (full FIM)
• /NONMEM_Combined2: NONMEM model files and outputs for Combined2 design (block-diagonal FIM)
• /NONMEM_Combined2_fullFIM: NONMEM model files and outputs for Combined2 design (full FIM)
• /results: Aggregated results and exported tables
• 03_Combined1_Mlx.R: Design evaluation using MlxDesignEval for Combined1
• 03_Combined1_NONMEM.R: Design evaluation using NONMEM for Combined1
• 03_Combined1_PFIM.R: Design evaluation using PFIM for Combined1
• 03_Combined1_PopED.R: Design evaluation using PopED for Combined1
• 03_Combined1_resultsAll.R: Aggregation and comparison of results for Combined1
• 03_Combined2_Mlx.R: Design evaluation using MlxDesignEval for Combined2
• 03_Combined2_NONMEM.R: Design evaluation using NONMEM for Combined2
• 03_Combined2_PopED.R: Design evaluation using PopED for Combined2
• 03_Combined2_resultsAll.R: Aggregation and comparison of results for Combined2
• 03_runAll.R: Script to run all evaluations for Combined1 and Combined2
• 03_Combined1_Pumas.jl: Design evaluation using Pumas (Julia) for Combined1
• 03_Combined2_Pumas.jl: Design evaluation using Pumas (Julia) for Combined2

/04: PK model with crossover study

• /NONMEM: NONMEM model files and outputs for block-diagonal FIM evaluation

• /NONMEM_fullFIM: NONMEM model files and outputs for full FIM evaluation

• /results: Aggregated results and exported tables

• 04_Mlx.R: Design evaluation using MlxDesignEval

• 04_NONMEM.R: Design evaluation using NONMEM

• 04_PopED.R: Design evaluation using PopED

• 04_resultsAll.R: Aggregates and compares results across tools

• 04_runAll.R: Script to run all evaluations

• 04_Pumas.jl: Design evaluation using Pumas (Julia)