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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE,
comment = "#>",
fig.path = 'man/figures/',
fig.align = 'center',
out.width = '80%',
dev = 'png',
dev.args = list(type = 'cairo'))
```
[](https://cran.r-project.org/package=popkinr)
# popkinr
PopkinR is an R package aiming at facilitating the development of non-linear mixed effects models with NONMEM.
It contains interactive web-applications based on `shiny` for:
* Post-processing of NONMEM runs results (`PMXploit`)
* Launch of NONMEM runs and editing control files (`PMXecute`)
* Exploration of NONMEM-like datasets (`PMXplore`)
*Reference: [PopkinR: a suite of Shiny applications focused on the pharmacometrics workflow](https://www.page-meeting.org/pdf_assets/7336-PAGE%20Poster%20PopkinR%20-%20Final%20version.pdf) presented at PAGE 2018*
## Installation
``` r
# Install the latest version from GitHub
# install.packages('devtools')
# Install pmxploit package first
devtools::install_github('pnolain/pmxploit')
# Install PopkinR
devtools::install_github('pnolain/popkinr')
```
## Getting started with the applications
```{r, eval = FALSE}
library(popkinr)
# PMXploit
nonmem_toolbox()
# PMXploit with VPC feature
nonmem_toolbox(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")
# PMXecute
nonmem_monitor(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe",
nonmem_parafile = "/path/to/nonmem/runfiles/mpilinux8.pnm")
# PMXecute (with PsN execute)
nonmem_monitor(nonmem_exe = "/usr/local/bin/execute",
nonmem_call = "{nonmem_exe} {control_file} -nodes={n_nodes}",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")
# PMXplore
dataset_exploration()
```
### PMXploit `popkinr::nonmem_toolbox` <img id="logo" src="pkgdown/pmxploit.svg" alt="pmxploit" width="125px" align="right" />
Together with the [**pmxploit**](https://github.com/pnolain/pmxploit) package, brings interactivity to NONMEM runs post-processing analysis.
Dynamically generates corresponding R-code to most of the plots and tables provided by the application so it can be embedded in any R script.
```{r, eval = FALSE}
library(popkinr)
# PMXploit
nonmem_toolbox()
# PMXploit with VPC feature
nonmem_toolbox(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")
```
### PMXecute `popkinr::nonmem_monitor` <img id="logo" src="pkgdown/pmxecute.svg" alt="pmxecute" width="125px" align="right" />
Application for launching and monitoring NONMEM runs on a local setup.
Provides control file generation functionalities for models with $PRIOR and for $SIMULATION.
```{r, eval = FALSE}
library(popkinr)
# PMXecute
nonmem_monitor(nonmem_exe = "/path/to/nonmem/run/nmfe74",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe",
nonmem_parafile = "/path/to/nonmem/runfiles/mpilinux8.pnm")
# PMXecute (with PsN execute)
nonmem_monitor(nonmem_exe = "/usr/local/bin/execute",
nonmem_call = "{nonmem_exe} {control_file} -nodes={n_nodes}",
nmcheck_exe = "/path/to/nonmem/tr/NMTRAN.exe")
```
*Gif preview...*
### PMXplore `popkinr::dataset_exploration` <img id="logo" src="pkgdown/pmxplore.svg" alt="pmxplore" width="125px" align="right" />
Application for exploratory data analysis of NONMEM-like datasets.
Provides interactive visualizations and summaries of dependent variables, dosing regimens and covariates (distributions, longitudinal evolution) and dataset manipulation functionalities.
```{r, eval = FALSE}
library(popkinr)
# PMXplore
dataset_exploration()
```
*Gif preview...*