xpose4

Model building aid for population analysis using NONMEM

https://github.com/uupharmacometrics/xpose4

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (20.7%) to scientific vocabulary

Keywords

cran diagnostics nonmem pharmacometrics population-model xpose

Last synced: 6 months ago · JSON representation

Repository

Model building aid for population analysis using NONMEM

Basic Info

Host: GitHub
Owner: UUPharmacometrics
License: lgpl-3.0
Language: R
Default Branch: master
Homepage: http://uupharmacometrics.github.io/xpose4/
Size: 110 MB

Statistics

Stars: 37
Watchers: 4
Forks: 12
Open Issues: 21
Releases: 10

Topics

cran diagnostics nonmem pharmacometrics population-model xpose

Created almost 12 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License

README.Rmd

---
output:
  github_document:
    html_preview: false
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = 'man/figures/'#,
  #fig.dpi    = 96,
  #fig.height = 4, 
  #fig.width  = 4, 
  #out.width  = '50%', 
  #fig.align  = 'center'
)
```

# Xpose 4 


[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/xpose4)](https://CRAN.R-project.org/package=xpose4) 
[![codecov.io](https://codecov.io/github/UUPharmacometrics/xpose4/coverage.svg?branch=master)](https://app.codecov.io/github/UUPharmacometrics/xpose4?branch=master)
[![R-CMD-check](https://github.com/UUPharmacometrics/xpose4/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UUPharmacometrics/xpose4/actions/workflows/R-CMD-check.yaml)



by Andrew C. Hooker, Mats O. Karlsson and E. Niclas Jonsson

## Introduction

Xpose 4 is a collection of functions to be used as a model
building aid for nonlinear mixed-effects (population) analysis
using NONMEM. It facilitates data set checkout, exploration and
visualization, model diagnostics, candidate covariate identification
and model comparison.

## Installation

To install xpose you will need R (>= version 2.2.0).   
To install Xpose in R use one of the following methods:

* latest stable release -- From CRAN.  Write at the R command line:

    ```{r standard-installation, eval = FALSE}
    install.packages("xpose4")
    ```
     
* Latest development version -- from Github. Note that the command below installs the "master" 
(development) branch; if you want the release branch from Github add `ref="release"` to the
`install_github()` call. 

    ```{r gh-installation, eval = FALSE}
    # install.packages("devtools") # if you don't have devtools installed
    devtools::install_github("UUPharmacometrics/xpose4")
    ```

## Running Xpose 4

Start R and load xpose:
```{r}
library(xpose4)
```


To use the classic menu system, type at the R command prompt:
```{r classic-menu,eval=FALSE}
xpose4()
```

Each function is independently available from the command
line, once the Xpose library is loaded. 

First we create a set of files from a NONMEM run
```{r,eval=FALSE}
cur.files <- dir() # current files in temp directory

simprazExample() # write files from an example NONMEM run
new.files <- dir()[!(dir() %in% cur.files)]  # the new files created by simprazExample
```

Then we can import our files to Xpose

```{r,eval=FALSE}
xpdb <- xpose.data(1) 
```


```{r,echo=FALSE}
xpdb <- simpraz.xpdb
```


Display goodness-of-fit plots:

```{r readme_example_figure_1}
basic.gof(xpdb)
```

Clean up files that were created to show these examples:
```{r,eval=FALSE}
unlink(new.files)
```


More help is available in the online documentation, which can be found by
typing (for example) `?xpose4` at the R command line.  


## Don't Panic

Andrew Hooker (andrew.hooker at uu.se)
should be able to get you an answer if you run into trouble.  

The website  should also be of help.

If you are using the latest development version of the package the you can 
look at the development version of the website 
.

## Release Schedule

Bugfix releases will be released regularly, fixing any problems that are
found. 


## License

Xpose 4 is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Lesser General Public License for more details 
.


## Known Bugs

None at present, but there will certainly be a few. Report them at 
.

Owner

Name: Uppsala University, Pharmacometrics Research Group
Login: UUPharmacometrics
Kind: organization
Location: Uppsala, Sweden

Website: http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/?languageId=1
Repositories: 9
Profile: https://github.com/UUPharmacometrics

GitHub Events

Total

Create event: 1
Release event: 1
Issues event: 3
Watch event: 2
Issue comment event: 3
Push event: 5
Pull request event: 1

Last Year

Create event: 1
Release event: 1
Issues event: 3
Watch event: 2
Issue comment event: 3
Push event: 5
Pull request event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 230
Total Committers: 6
Avg Commits per committer: 38.333
Development Distribution Score (DDS): 0.048

Past Year

Commits: 2
Committers: 1
Avg Commits per committer: 2.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Andrew Hooker	a**r@g**m	219
ronkeizer	r**r@g**m	7
Viktor Rognås	v**s@f**e	1
Mike K Smith	M**h@P**m	1
Viktor Rognås	v**s@f**e	1
Rikard Nordgren	r**n@f**e	1

Committer Domains (Top 20 + Academic)

farmbio.uu.se: 2 farmaci.uu.se: 1 pfizer.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 21
Total pull requests: 8
Average time to close issues: 3 months
Average time to close pull requests: about 1 month
Total issue authors: 16
Total pull request authors: 6
Average comments per issue: 0.9
Average comments per pull request: 0.75
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 3
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

rikardn (4)
jeslo328 (2)
andrewhooker (2)
jianghuxiaodi (1)
MahmAbdelwahab (1)
blalovic (1)
rebeccaher (1)
YGAZ (1)
leovuong (1)
MikeKSmith (1)
sn248 (1)
SimonKoele (1)
adcascone (1)
JoanaXu (1)
billdenney (1)

Pull Request Authors

vrognas (3)
MikeKSmith (1)
leovuong (1)
rikardn (1)
ronkeizer (1)
andrewhooker (1)

Top Labels

Issue Labels

bug (2)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 538 last-month
Total docker downloads: 21,661

Total dependent packages: 1
Total dependent repositories: 6
Total versions: 13
Total maintainers: 1

cran.r-project.org: xpose4

Diagnostics for Nonlinear Mixed-Effect Models

Homepage: https://uupharmacometrics.github.io/xpose4/
Documentation: http://cran.r-project.org/web/packages/xpose4/xpose4.pdf
License: LGPL (≥ 3)
Latest release: 4.7.3
published almost 2 years ago

Versions: 13
Dependent Packages: 1
Dependent Repositories: 6
Downloads: 538 Last month
Docker Downloads: 21,661

Rankings

Docker downloads count: 0.6%

Forks count: 6.3%

Stargazers count: 9.5%

Average: 11.0%

Dependent repos count: 11.9%

Dependent packages count: 18.1%

Downloads: 19.4%

Maintainers (1)

andrew.hooker@farmaci.uu.se

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 2.2.0 depends
lattice * depends
Hmisc * imports
dplyr * imports
gam * imports
grid * imports
lazyeval * imports
methods * imports
readr * imports
splines * imports
survival * imports
tibble * imports
testthat * suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

xpose4

Science Score: 26.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: xpose4

Rankings

Maintainers (1)

Dependencies