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Introduction to the StratPal package

Source: vignettes/StratPal.Rmd
StratPal.Rmd

Overview

Welcome to the StratPal package. This vignette provides an overview of the structure of the package and preliminaries needed to efficiently use it. We go through installation, dependencies, provide an overview of the available example data, piping, and working with age-depth models.

If you want to skip the introduction, you can also get started right away.

Throughout the vignettes there are several tasks that you can solve. They are not required for understanding the functionality of the package. Their aim is to explore the available models and data and develop an intuition for stratigraphic paleobiology.

Installation

CRAN

To install the StratPal package from CRAN, run

install.packages("StratPal")

in the R console.

GitHub

To install the StratPal package from GitHub, first install the remotes package by running

install.packages("remotes")

in the R console. Then, run

remotes::install_github(repo = "MindTheGap-ERC/StratPal",
                        build_vignettes = TRUE,
                        ref = "HEAD",
                        dependencies = TRUE)

to install the latest stable version of the package and all its dependencies.

Dependencies

The StratPal heavily relies on the age-depth modeling tools provided by the admtools package, which is automatically installed when you install StratPal.

To use its functionality, you need to run

before running any of the examples. Specifically, this is needed for plotting of age-depth models and trait evolution. Below we provide a brief overview of the functionality of the admtools package we need. If you want more information, you can browse through the package vignettes using

browseVignettes(package = "admtools")

or by visiting the package website at https://mindthegap-erc.github.io/admtools/.

Example data

StratPal comes with synthetic example data, which contains model parameters and outputs of a carbonate platform simulated using CarboCAT Lite (Burgess (2013), Burgess (2023)). The data is stored in the variable scenarioA, which is automatically available when the package is loaded. The structure of the data is described under ?scenarioA.

The data is taken from scenario A in Hohmann et al. (2023), the modeling procedure is described in detail in Hohmann et al. 2024, see therein for a chronostratigraphic diagram and a transect through the carbonate platform.

The data contains information on the eustatic sea level curve used for the model run, elapsed model time, as well information on accumulated sediment thickness, water depth, and bed thicknesses and facies at locations 2, 4, 6, 8, 10, and 12 km from shore in the simulated carbonate platform.

As an example, here is the eustatic sea level curve used for the model run:

plot(x = scenarioA$t_myr,
     y = scenarioA$sl_m,
     type = "l",
     xlab = "Time [Myr]",
     ylab = "Eustatic sea level [m]",
     main = "Sea level curve used as model input")

Plot of a sinusoidal sea level curve.

Piping

In the vignettes of the StratPal package, we use the base R pipe operator |>. While this is not required to run the package, it simplifies the code and makes the underlying logic of a modeling pipeline clearer.

This functionality is available from R version 4.2 on.

Motivation and usage

Consider the following code for simulating and plotting a random walk using the random_walk function:

set.seed(42)             # set seed for computational reproducibility
t = seq(0, 1, by = 0.01) # times where we evaluate the random walk
l = random_walk(t)       # simulate the random walk
plot(l, type = "l")      # line plot of the results

plot of a random walk

This code does the job, but it has some flaws: We introduced a lot of intermediate variables, which makes it hard to trace the logic of what we are trying to achieve: plotting a random walk. Using the pipe operator |> we can clarify the logic and simplify the code:

set.seed(42)            # set seed for computational reproducibility
seq(0, 1, by = 0.01) |> # define times of simulation  
  random_walk() |>      # simulate random walk
  plot(type = "l")      # plot

plot of a random walk, identical to the one above

You see that the code does the same thing: it plots a random walk, but it does so in one step without intermediate variables by chaining together the commands using the pipe |>. This becomes a powerful tool once we combine more and more components into longer modeling pipelines. It also makes the code readable, as you can simply read it from left to right, without having to track any intermediate steps.

Semantically, you can read the |> as “take the data on the left of |> and use it as the first argument in the function to the right of |>.

Advanced usage

You can also use |> to pass arguments that are not in the first place. For this, simply replace the argument with a underscore _:

# calculate deciles of normal distribution
seq(0, 1, by = 0.1) |>
  quantile(x = runif(100), p = _) # pass left hand side to the p argument
#>         0%        10%        20%        30%        40%        50%        60% 
#> 0.01754832 0.08499473 0.15879393 0.25042315 0.33077722 0.41258062 0.48894916 
#>        70%        80%        90%       100% 
#> 0.55111005 0.76271437 0.88512802 0.99655268

Age-depth models

The StratPal package use of age-depth modeling functionality from the admtools package. Here we go through some basics of dealing with age-depth models. For more details on available functionality you can browse through the package vignettes using

browseVignettes(package = "admtools")

or visit the package website at https://mindthegap-erc.github.io/admtools/.

To get started, first load the package using

The StratPal package comes with some example data for age-depth models stored in the scenarioA variable, see the section on example data or ?scenarioA for details.

Defining age-depth models

Let’s start with defining the age-depth model 2 km from shore in scenario A. This can be done with tp_to_adm (tie points to age-depth model):

t = scenarioA$t_myr       # extract time tie points
h = scenarioA$h_m[,"2km"] # get height tie points 2 km offshore in scenario A

# define age-depth model
# h[i] is the stratigraphic position at time t[i]
adm = tp_to_adm(t = t,          # tie points in time
                h = h,          # tie points at height
                T_unit = "Myr", # add time unit 
                L_unit = "m")   # add length unit

The nice thing about constructing age-depth models this way is that there is plenty of functionality available to extract data from age-depth models, plot them, or transform data using them.

Plotting

Now you can plot the age-depth model using the basic plot command:

# plot age-depth model, see ?plot.adm for details
plot(adm,
     lwd_acc = 2,   # plot thicker lines for intervals with sediment accumulation (lwd = line width)
     lty_destr = 0) # don't plot destructive intervals/gaps (lty = line type)
T_axis_lab()        # add time axis label
L_axis_lab()        # add length axis label
title("Age-depth model 2 km from shore")

plot of an age-depth model, showing how the time and depth domain are connected

Extracting information

There is a lot of functionality available to extract information from an age-depth model:

get_total_duration(adm) # time interval covered by adm
#> [1] 1.999
get_total_thickness(adm) # sediment accumulated 
#> [1] 145.9416
get_completeness(adm) # stratigraphic completeness
#> [1] 0.3261631
summary(adm) # some summary statistics
#> age-depth model 
#> Total duration: 1.999 Myr
#> Total thickness: 145.9416 m
#> Stratigraphic completeness: 32.61631 % 
#> 10 hiatus(es)

We can now use the pipe operator to do some first analysis of the age-depth model


# plot histogram of hiatus durations
adm |>    
  get_hiat_duration() |>
  hist( xlab = paste("Hiatus duration", "[", get_T_unit(adm),"]"))

histogram of hiatus durations 2 km offshore in scenario A

You can see that there are a 8 shorter hiatuses (below 100 kyr) and 2 long hiatuses with a duration of more than 500 kyr. To get a detailed list with information on hiatuses you can use get_hiat_list.

Transforming data

Given a stratigraphic position, an age-depth model can tell us how old that positions is. Conversely, if we know the timing of an event, an age-depth model can tell us at what stratigraphic position that event will occur. This can be used to transform all types of data from the time domain to the stratigraphic domain and vice versa.

In admtools, the transformation of data is done by the functions time_to_strat (for transforming temporal data into stratigraphic data) and strat_to_time (for transforming stratigraphic data into temporal data). Details on how this is done and what types of data can be transformed can be found in the vignette of the admtools package, for applications to stratigraphic paleobiology see the vignettes linked below under “Getting started”.

Getting started

With the preliminaries out of the way, you can go to

vignette("phenotypic_evolution")

for details on how to model stratigraphic paleobiology of phenotypic evolution, or explore the vignette online under mindthegap-erc.github.io/StratPal/articles/phenotypic_evolution.

Go to

vignette("event_data")

for details on how to model stratigraphic paleobiology of event data such as individual fossils and first/last occurrences of taxa, or explore the vignette online under mindthegap-erc.github.io/StratPal/articles/event_data.

If you want to explore how to link the StratPal package with the paleoTS package go to

vignette("paleoTS_funcionality")

See also

vignette("advanced_functionality")

for details on how to expand on the modeling pipelines described here, or explore the vignette online under mindthegap-erc.github.io/StratPal/articles/advanced_functionality.

For details on the defined data structures, see

vignette("StratPal_docs")

References