---
title: "Integration with the FossilSim and paleotree packages"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Integration with the FossilSim and paleotree packages}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(StratPal)
```

This vignette describes how to integrate the `StratPal` package with the `FossilSim` and the `paleotree` packages.

## Integration with the `FossilSim` package

As is, the `StratPal` package handles `fossils` objects as constructed by the `FossilSim` package. These objects represent fossils sampled along a tree (phylogeny). They can be transformed using the functions `apply_taphonomy` and `apply_niche`. This will remove fossil occurrences according to preservation potential and change on taphonomic conditions (or niche definition and change in gradient). Note that this corresponds to an nonparametric expansion of the variable recovery model as implemented in `FossilSim`.

For examples see the documentation of the functions `apply_niche` and `apply_taphonomy`.

## Integration with `paleotree`

To combine the `StratPal` package with the `paleotree` package, please convert the `paleotree` format into the `FossilSim` format as described in the `paleotree` vignette of the `FossilSim` vignette:

```{r eval=FALSE}
vignette("paleotree", package = "FossilSim")
```

After conversion you can proceed as described in the section *Integration with the `FossilSim` package*

## References

*  Barido-Sottani J, Pett W, O'Reilly JE, Warnock RCM. Fossilsim: An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery. Methods Ecol Evol. 2019; 10: 835–840. <https://doi.org/10.1111/2041-210X.13170>
*  Bapst, D.W. (2012), paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution, 3: 803-807. <https://doi.org/10.1111/j.2041-210X.2012.00223.x>
*  Warnock R, Barido-Sottani J, Pett W, Joseph O, Stolz U (2024). _FossilSim: Simulation and Plots for Fossil and Taxonomy Data_. R package version 2.4.1,
  <https://CRAN.R-project.org/package=FossilSim>