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xpose

Graphical diagnostics for pharmacometric models

https://github.com/uupharmacometrics/xpose

Science Score: 36.0%

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
    1 of 13 committers (7.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.7%) to scientific vocabulary

Keywords

diagnostics ggplot2 nonmem pharmacometrics xpose

Keywords from Contributors

ropensci visualisation tidyverse libuv filesystem devtools rcpp r-packages c-plus-plus-20 c-plus-plus-17
Last synced: 6 months ago · JSON representation

Repository

Graphical diagnostics for pharmacometric models

Basic Info
Statistics
  • Stars: 63
  • Watchers: 14
  • Forks: 29
  • Open Issues: 42
  • Releases: 22
Topics
diagnostics ggplot2 nonmem pharmacometrics xpose
Created almost 10 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
library(xpose)

xpdb <- xpdb_ex_pk
xpdb$options$quiet <- TRUE

xpdb <- as.xpdb(xpdb)

knitr::opts_chunk$set(fig.path   = 'man/figures/', 
                      fig.dpi    = 96,
                      fig.align  = 'center')
```

# xpose 

[![R-CMD-check](https://github.com/UUPharmacometrics/xpose/workflows/R-CMD-check/badge.svg)](https://github.com/UUPharmacometrics/xpose/actions)
[![cran_version](https://www.r-pkg.org/badges/version/xpose)](https://CRAN.R-project.org/package=xpose)
[![Codecov test coverage](https://codecov.io/gh/UUPharmacometrics/xpose/branch/master/graph/badge.svg)](https://app.codecov.io/gh/UUPharmacometrics/xpose?branch=master)
[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/xpose)](https://CRAN.R-project.org/package=xpose)

## Overview
[xpose](https://UUPharmacometrics.github.io/xpose/) was designed as a [ggplot2](https://ggplot2.tidyverse.org/)-based alternative to [xpose4](https://uupharmacometrics.github.io/xpose4/). xpose aims to reduce the post processing burden and improve diagnostics commonly associated the development of non-linear mixed effect models.


## Installation
``` r
# Install the lastest release from the CRAN
install.packages('xpose')

# Or install the development version from GitHub
# install.packages('devtools')
devtools::install_github('UUPharmacometrics/xpose')
```


## Getting started

### Load xpose
``` r
library(xpose)
```

### Import run output
``` r
xpdb <- xpose_data(runno = '001')
```

### Glance at the data object
```{r, comment = ''}
xpdb
```

#### Model summary
```{r, comment = ''}
summary(xpdb, problem = 1)
```

### Generate diagnostics
#### Standard goodness-of-fit plots
```{r readme_example_figure_1, fig.width = 5, fig.height = 5.1, out.width = '50%', message=FALSE}
dv_vs_ipred(xpdb)
```

#### Individual plots
```{r readme_example_figure_2, fig.width = 7, out.width = '75%'}
ind_plots(xpdb, page = 1)
```

#### Visual predictive checks
```{r readme_example_figure_3, fig.width = 7, out.width = '75%', warning = FALSE}
xpdb %>% 
  vpc_data(stratify = 'SEX', opt = vpc_opt(n_bins = 7, lloq = 0.1)) %>% 
  vpc()
```

#### Distribution plots
```{r readme_example_figure_4, fig.width = 7, out.width = '75%'}
eta_distrib(xpdb, labeller = 'label_value')
```

#### Minimization diagnostics
```{r readme_example_figure_5, fig.width = 7, out.width = '75%'}
prm_vs_iteration(xpdb, labeller = 'label_value')
```


## Recommended reading
The [xpose website](https://UUPharmacometrics.github.io/xpose/) contains several useful articles to make full use of xpose

When working with xpose, a working knowledge of ggplot2 is recommended. Help for ggplot2 can be found in:

- The ggplot2 [documentation](https://ggplot2.tidyverse.org/reference/)
- The ggplot2 [mailing list](https://groups.google.com/forum/?fromgroups#!forum/ggplot2)
- Internet resources (stack overflow, etc.)


## Contribute
Please note that the xpose project is released with a [Contributor Code of Conduct](https://github.com/UUPharmacometrics/xpose/blob/master/.github/CODE_OF_CONDUCT.md) and [Contributing Guidelines](https://github.com/UUPharmacometrics/xpose/blob/master/.github/CONTRIBUTING.md). By contributing to this project, you agree to abide these.

Owner

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

GitHub Events

Total
  • Create event: 4
  • Release event: 3
  • Issues event: 9
  • Watch event: 11
  • Delete event: 1
  • Issue comment event: 15
  • Push event: 18
  • Pull request review event: 1
  • Pull request event: 3
  • Fork event: 1
Last Year
  • Create event: 4
  • Release event: 3
  • Issues event: 9
  • Watch event: 11
  • Delete event: 1
  • Issue comment event: 15
  • Push event: 18
  • Pull request review event: 1
  • Pull request event: 3
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,170
  • Total Committers: 13
  • Avg Commits per committer: 90.0
  • Development Distribution Score (DDS): 0.068
Past Year
  • Commits: 45
  • Committers: 4
  • Avg Commits per committer: 11.25
  • Development Distribution Score (DDS): 0.244
Top Committers
Name Email Commits
Benjamin g****c@g****m 1,090
Benjamin g****c 22
Sebastian Ueckert s****t@g****m 21
Benjamin Guiastrennec b****i@B****l 14
Anna Olofsson a****n@p****m 6
Viktor Rognås v****s@f****e 5
Hadley Wickham h****m@g****m 3
Ron Keizer r****n@i****m 2
Jim Hester j****r@g****m 2
Bill Denney w****y@h****m 2
Samuel Callisto c****5@u****u 1
Viktor Rognås v****s@f****e 1
Romain François r****n@p****t 1
Committer Domains (Top 20 + Academic)
purrple.cat: 1 farmbio.uu.se: 1 umn.edu: 1 humanpredictions.com: 1 insight-rx.com: 1 farmaci.uu.se: 1 pharmetheus.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 76
  • Total pull requests: 41
  • Average time to close issues: 5 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 42
  • Total pull request authors: 11
  • Average comments per issue: 2.36
  • Average comments per pull request: 1.0
  • Merged pull requests: 21
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 1
  • Average time to close issues: 14 days
  • Average time to close pull requests: about 2 months
  • Issue authors: 5
  • Pull request authors: 1
  • Average comments per issue: 0.6
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • billdenney (15)
  • mattfidler (5)
  • thomasp85 (3)
  • teunbrand (3)
  • adcascone (3)
  • AndreasCalvagone (3)
  • tonggne (2)
  • UNCcrawler (2)
  • sn248 (2)
  • NilsJohan (2)
  • guiastrennec (2)
  • ftuhin2828 (2)
  • sbihorel (2)
  • Kagedal (2)
  • jeslo328 (1)
Pull Request Authors
  • billdenney (16)
  • guiastrennec (9)
  • vrognas (5)
  • hadley (4)
  • sbihorel (2)
  • roninsightrx (1)
  • romainfrancois (1)
  • jimhester (1)
  • jpryby (1)
  • ronkeizer (1)
  • mattfidler (1)
Top Labels
Issue Labels
enhancement (17) feature request (12) question (10) bug (8) documentation (3) xpose.nlmixr (2) help wanted (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 967 last-month
  • Total docker downloads: 42,053
  • Total dependent packages: 6
  • Total dependent repositories: 6
  • Total versions: 21
  • Total maintainers: 1
cran.r-project.org: xpose

Diagnostics for Pharmacometric Models

  • Versions: 21
  • Dependent Packages: 6
  • Dependent Repositories: 6
  • Downloads: 967 Last month
  • Docker Downloads: 42,053
Rankings
Docker downloads count: 0.6%
Forks count: 2.6%
Stargazers count: 6.5%
Dependent packages count: 7.3%
Average: 7.6%
Dependent repos count: 11.9%
Downloads: 16.7%
Maintainers (1)
guiastrennec@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.3.0 depends
  • ggplot2 >= 3.1.0 depends
  • dplyr >= 0.8.0 imports
  • ggforce >= 0.2.0 imports
  • grDevices * imports
  • purrr >= 0.3.0 imports
  • readr >= 1.3.0 imports
  • rlang >= 0.3.0 imports
  • stats * imports
  • stringr >= 1.4.0 imports
  • tibble >= 2.1.0 imports
  • tidyr >= 0.8.0 imports
  • utils * imports
  • vpc >= 1.1.0 imports
  • gridExtra * suggests
  • here * suggests
  • knitr * suggests
  • mvtnorm * suggests
  • plotly * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • webshot * suggests
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  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
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