---
title: "Documentation of defined S3 classes"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Documentation of defined S3 classes}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

This vignette documents the S3 classes defined by the `StratPal` package.  
For documentation of functionality, see the help page of individual functions (available via `?functionname`), for working examples see the vignettes (available via `browseVignettes("StratPal")`).

## S3 class `pre_paleoTS`

Represents trait values of individual specimens of a lineage sampled along time or stratigraphic position. For the motivation of this class, see the vignette on usage with the `paleoTS` package via `vignette("paleoTS_functionality")`.

### Structure

`pre-paleoTS` is a list with two elements:

* the first element is  named `t` or `h`: a numeric vector, corresponding to sampling heights or times

* the second element is named `vals`: a list with the same number of elements as the vector `h`/`t`. Each element of the list contains the trait values of specimens sampled at that time/height.

### Construction

`pre_paleoTS` is constructed by functions to simulate trait evolution on a specimen level/in pre-paleoTS format. These functions have suffix `_sl` for "specimen level". This is

* `stasis_sl`

* `strict_stasis_sl`

* `random_walk_sl`

* `ornstein_uhlenbeck_sl`

### Modification

`pre_paleoTS` can be modified using

* `apply_niche`

* `apply_taphonomy`

* `time_to_strat`

* `strat_to_time`

### Transformation into other S3 classes

`pre_paleoTS` can be transformed into `paleoTS` format using `reduce_to_paleoTS`

### Plotting

No standalone plotting procedure is implemented for `pre_paleoTS`. For plotting, first use `reduce_to_paleoTS` and plot the results via `plot` after loading the `paleoTS` package.

## S3 class `char_mat`

Describes a character matrix associated with positional information (time/height) for application of taphonomic and stratigraphic effects.

### Structure

List with two elements:

- `mat`: The matrix, with taxon names as column names
- `pos`: named vector containing positional information (time or height) for the taxa

### Construction

`char_mat` is constructed using `as_char_mat`.

### Modification

Modified by `apply_taphonomy`. For logical reasons, `apply_niche.char_mat` throws an error.

### Transformation into other S3 classes

None

### Plotting

None