From e1d3e185bd7ff59ad95b036b429eb567c467042b Mon Sep 17 00:00:00 2001 From: Matthew Fidler Date: Sun, 15 Sep 2024 10:40:18 -0500 Subject: [PATCH] Update readme --- README.Rmd | 28 +++++++++++++++++++++------- README.md | 37 +++++++++++++++++++++++++------------ 2 files changed, 46 insertions(+), 19 deletions(-) diff --git a/README.Rmd b/README.Rmd index 6bfe4004..73a02bf6 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,7 +16,7 @@ knitr::opts_chunk$set( # babelmixr2 -[![R-CMD-check](https://github.com/nlmixr2/babelmixr2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/babelmixr2/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check](https://github.com/nlmixr2/babelmixr2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nlmixr2/babelmixr2/actions/workflows/R-CMD-check.yaml) [![CRAN version](http://www.r-pkg.org/badges/version/babelmixr2)](https://cran.r-project.org/package=babelmixr2) [![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/babelmixr2)](https://cran.r-project.org/package=babelmixr2) [![CRAN total downloads](https://cranlogs.r-pkg.org/badges/babelmixr2)](https://cran.r-project.org/package=babelmixr2) @@ -55,14 +55,19 @@ Babelmixr2 can help you by: - Running your nlmixr2 model in a commercial nonlinear mixed effects modeling tool like [`NONMEM`](https://nlmixr2.github.io/babelmixr2/articles/running-nonmem.html) or `Monolix` - + - Convert your [`NONMEM` model to a nlmixr2 model](https://nlmixr2.github.io/nonmem2rx/articles/convert-nlmixr2.html) (in conjunction with `nonmem2rx`) - + + - Convert you [`Monolix` model to a nlmixr2 + model](https://nlmixr2.github.io/nonmem2rx/articles/convert-nlmixr2.html) + (in conjunction with `monolix2rx`) + - Calculate scaling factors and automatically add initial conditions based on non-compartmental analysis (using `PKNCA`) + - Perform Optimal design using nlmixr2 as an interface to `PopED` ## Monolix Setup @@ -72,9 +77,10 @@ While not required, you can get/install the R 'lixoftConnectors' package in the 'lixoftConnectors' is available, R can run 'Monolix' directly instead of using a command line. -## Example +## PKNCA Example -After installed, if you use the standard interface, you can obtain new initial estimates with PKNCA: +After installed, if you use the standard interface, you can obtain new +initial estimates with PKNCA: ```r mod <- @@ -84,13 +90,21 @@ mod <- ) ``` -or, you can convert to Monolix with +## Monolix example + +With babelmixr2 loaded, you can use `nlmixr2` to convert a nlmixr2 +model to Monolix, run with monolix, and import back to nlmixr2 with +the following: ```r mod <- nlmixr(nlmixrFun, nlmmixrData, est="monolix") ``` -or, you can convert to NONMEM with +## NONMEM example + +With babelmixr2 loadid you can use `nlmixr2` to convert a nlmixr2 +model to NONMEM, run NONMEM and import back to nlmixr2 with the +following: ```r mod <- nlmixr(nlmixrFun, nlmmixrData, est="nonmem") diff --git a/README.md b/README.md index 93e7e8c8..d0d6bbe1 100644 --- a/README.md +++ b/README.md @@ -46,17 +46,23 @@ Otherwise you can always install from GitHub: Babelmixr2 can help you by: -- Running your nlmixr2 model in a commercial nonlinear mixed effects - modeling tool like - [`NONMEM`](https://nlmixr2.github.io/babelmixr2/articles/running-nonmem.html) - or `Monolix` + - Running your nlmixr2 model in a commercial nonlinear mixed effects + modeling tool like + [`NONMEM`](https://nlmixr2.github.io/babelmixr2/articles/running-nonmem.html) + or `Monolix` -- Convert your [`NONMEM` model to a nlmixr2 - model](https://nlmixr2.github.io/nonmem2rx/articles/convert-nlmixr2.html) - (in conjunction with `nonmem2rx`) + - Convert your [`NONMEM` model to a nlmixr2 + model](https://nlmixr2.github.io/nonmem2rx/articles/convert-nlmixr2.html) + (in conjunction with `nonmem2rx`) -- Calculate scaling factors and automatically add initial conditions - based on non-compartmental analysis (using `PKNCA`) + - Convert you [`Monolix` model to a nlmixr2 + model](https://nlmixr2.github.io/nonmem2rx/articles/convert-nlmixr2.html) + (in conjunction with `monolix2rx`) + + - Calculate scaling factors and automatically add initial conditions + based on non-compartmental analysis (using `PKNCA`) + + - Perform Optimal design using nlmixr2 as an interface to `PopED` ## Monolix Setup @@ -66,7 +72,7 @@ in the ‘Monolix’ installation, as described at the following url When ‘lixoftConnectors’ is available, R can run ‘Monolix’ directly instead of using a command line. -## Example +## PKNCA Example After installed, if you use the standard interface, you can obtain new initial estimates with PKNCA: @@ -79,13 +85,20 @@ mod <- ) ``` -or, you can convert to Monolix with +## Monolix example + +With babelmixr2 loaded, you can use `nlmixr2` to convert a nlmixr2 model +to Monolix, run with monolix, and import back to nlmixr2 with the +following: ``` r mod <- nlmixr(nlmixrFun, nlmmixrData, est="monolix") ``` -or, you can convert to NONMEM with +## NONMEM example + +With babelmixr2 loadid you can use `nlmixr2` to convert a nlmixr2 model +to NONMEM, run NONMEM and import back to nlmixr2 with the following: ``` r mod <- nlmixr(nlmixrFun, nlmmixrData, est="nonmem")