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)**