README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

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

# nlmixr2extra

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The goal of nlmixr2extra is to provide the tools to help with common pharmacometric tasks with nlmixr2 models like bootstrapping, covariate selection etc.

## Installation

You can install the development version of nlmixr2extra from [GitHub](https://github.com/) with:

``` r
# install.packages("remotes")
remotes::install_github("nlmixr2/nlmixr2data")
remotes::install_github("nlmixr2/lotri")
remotes::install_github("nlmixr2/rxode2")
remotes::install_github("nlmixr2/nlmixr2est")
remotes::install_github("nlmixr2/nlmixr2extra")
```

## Example of a `bootstrapFit()`

This is a basic example of bootstrapping provided by this package

```{r example}
library(nlmixr2est)
library(nlmixr2extra)
# basic example code
# The basic model consists of an ini block that has initial estimates
one.compartment <- function() {
  ini({
    tka <- 0.45; label("Absorption rate, Ka")
    tcl <- 1; label("Clearance, Cl")
    tv <- 3.45; label("Central volumne, V")
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7; label("Additive residual error")
  })
  # and a model block with the error specification and model specification
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl)
    v <- exp(tv + eta.v)
    d/dt(depot) = -ka * depot
    d/dt(center) = ka * depot - cl / v * center
    cp = center / v
    cp ~ add(add.sd)
  })
}

# The fit is performed by the function nlmixr/nlmixr2 specifying the model, data
# and estimate (in a real estimate, nBurn and nEm would be much higher.)
fit <- nlmixr2(one.compartment, theo_sd,  est="saem", saemControl(print=0, nBurn = 10, nEm = 20))

# In a real bootstrap, nboot would be much higher.
fit2 <- suppressMessages(bootstrapFit(fit, nboot = 5))
fit2
```