---
title: "Example Stratigraphic Architecture"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Example Stratigraphic Architecture}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

## Introduction

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

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

This vignette provides an overview over the example stratigraphic architecture provided with the `StratPal` package.

## Stratigraphic Context

The example data is taken from a synthetic carbonate platform simulated using CarboKitten.jl (Hidding et al. 2025). It emulates scenario A from Hohmann et al (2024), which was originally simulated in CarboCAT (Burgess 2013), and is characterized by a sinusoidal sea level curve and 2 long (\> 0.5 Myr) hiatuses over the 2 Myr duration of the run.

## Dataset structure

The structure of the dataset is explained on the help pages, which is available using

```{r, eval=FALSE}
?scenarioA
```

## Simulation settings

The full code to generate simulation data and visualizations is available [here](https://github.com/MindTheGap-ERC/StratPal_data_prep). The simulation was run over 2 Myr at steps of 1 kyr, with data extracted at 2, 4, 6, 8, 10, and 12 km from shore in the middle of the simulated platform. Three carbonate factories were used: euphotic, oligophotic, and aphotic:

```{r, echo=FALSE, fig.cap="Production profile of the three carbonate factories", out.width="70%"}
knitr::include_graphics("platform_production_curve.png")
```

The eustatic sea level curve is a combination of third and fifth order changes with an amplitude of 20 and 2 m and a period of 1 and 0.112 Myr:

```{r, echo=FALSE, out.width="70%"}
plot(x = scenarioA$t_myr, 
     y = scenarioA$sl_m,
     xlab = "Time [Myr]",
     ylab = "Sea level [m]",
     main = "Eustatic Sea Level",
     type = "l")
```

For users interested in more details, we recommend inspecting the simulation source code (written in Julia).

## Platform visualization

```{r, echo=FALSE, out.width='100%', fig.cap="Transect through the carbonate platform. Black lines separate systems tracts."}
knitr::include_graphics("platform_profile.png")
```

```{r, echo=FALSE, out.width='100%', fig.cap="Wheeler diagram of the platform, showing both dominant facies and seidimentation rate."}
knitr::include_graphics("platform_wheeler_diagram.png")
```

## References

-   Hidding, Johan, Jarochowska, Emilia, Hohmann, Niklas, Liu, Xianyi Burgess, Peter and Spreeuw, Hanno: "CarboKitten.jl – an open source toolkit for carbonate stratigraphic modeling." Preprint. <https://doi.org/10.5194/egusphere-2025-4561>
-   Burgess, Peter. 2013. "CarboCAT: A cellular automata model of heterogeneous carbonate strata." Computers & Geosciences. <https://doi.org/10.1016/j.cageo.2011.08.026>.
-   Hohmann, Niklas; Koelewijn, Joël R.; Burgess, Peter; Jarochowska, Emilia. 2024. "Identification of the mode of evolution in incomplete carbonate successions." BMC Ecology and Evolution 24, 113. <https://doi.org/10.1186/s12862-024-02287-2>.