xpose.xtras

Extra Functionality for the 'xpose' Package

https://github.com/jprybylski/xpose.xtras

Repository

Extra Functionality for the 'xpose' Package

README.Rmd

---
output:
  rmarkdown::github_document:
    html_preview: FALSE
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

```{r setup, echo=FALSE, include = FALSE}
library(dplyr)
library(xpose)
library(xpose.xtras)
```
# xpose.xtras 


[![R-CMD-check](https://github.com/jprybylski/xpose.xtras/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jprybylski/xpose.xtras/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/jprybylski/xpose.xtras/graph/badge.svg)](https://app.codecov.io/gh/jprybylski/xpose.xtras)
[![CRAN status](https://www.r-pkg.org/badges/version/xpose.xtras)](https://CRAN.R-project.org/package=xpose.xtras)
[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/xpose.xtras?color=blue)](https://cran.r-project.org/package=xpose.xtras)


## Introduction

This package adds some extra functionality and plots to the [`xpose`](https://uupharmacometrics.github.io/xpose/) framework. This includes some plots that have been missing in translation from [`xpose4`](https://uupharmacometrics.github.io/xpose4/), but also some useful features that truly extend the capabilities of what can be done with `xpose`.

There are a few bugfixes here and functionality which could easily be suggested as pull requests to the parent package. Given the size and broad use of `xpose`, it appears even minor pull requests take some time to implement. As such, this package implements those features directly and if at any point in the future these are added (perhaps in a better state) to the parent package, they will be deprecated if this package is in active use. 

For those wondering, [`conflicted`](https://conflicted.r-lib.org/) is used to manage bugfix conflicts, so users should be comfortable loading packages in any order.

## Installation

The package can be installed from CRAN:

```{r install_cran, eval=FALSE}
install.packages("xpose.xtras")
```

The typical github installation will also work.

```{r install, eval=FALSE}
pak::pak("jprybylski/xpose.xtras")
```

The main github branch is reserved for CRAN release-ready versions. The dev branch is usually ahead if there is active development.

```{r installdev, eval=FALSE}
pak::pkg_install("jprybylski/xpose.xtras@dev")
```

## Preview

The grandparent package, `xpose4`, used to have a nice collection of figures and documentation that is referred to as a "bestiarium". The documentation site for this package serves as a complete bestiary, but see the uncommented examples below as a sort of menagerie. There is no assumption that these examples are self-explanatory, but hopefully users familiar with `xpose` will recognize the new (and *re*newed) tools made available by this package.

### EBEs versus covariates

```{r eta_vs, fig.width=unit(6,"in"), fig.height=unit(3,"in"), fig.align='center'}
described <- xpdb_x %>%
  set_var_labels(AGE="Age", MED1 = "Digoxin", .problem = 1) %>%
  set_var_units(AGE="yrs")  %>%
  set_var_levels(SEX=lvl_sex(), MED1 = lvl_bin())
eta_vs_contcov(described,etavar=ETA1, quiet=TRUE)
eta_vs_catcov(described,etavar=ETA1, quiet=TRUE)
```


### Shark plots

```{r shark, fig.width=unit(7,"in"), fig.height=unit(5,"in"), fig.align='center'}
pheno_set %>%
  focus_qapply(backfill_iofv) %>%
  dofv_vs_id(run6, run9, quiet = TRUE)
```


### Categorical DVs

```{r m3, fig.width=unit(7,"in"), fig.height=unit(5,"in"), fig.align='center'}
pkpd_m3 %>%
  set_var_types(catdv=BLQ,dvprobs=LIKE) %>%
  set_dv_probs(1, 1~LIKE, .dv_var = BLQ) %>%
  set_var_levels(1, BLQ = lvl_bin()) %>%
  catdv_vs_dvprobs(quiet=TRUE)
```

```{r m3_roc, fig.width=unit(7,"in"), fig.height=unit(5,"in"), fig.align='center'}
nlmixr2_m3 %>%
  set_var_types(catdv=CENS,dvprobs=BLQLIKE) %>%
  set_dv_probs(1, 1~BLQLIKE, .dv_var = CENS) %>%
  set_var_levels(1, CENS = lvl_bin()) %>%
  roc_plot(quiet = TRUE)
```

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