admtools: Getting Started

Niklas Hohmann

Introduction

This vignette is an introduction to the admtools package.

Loading the package

First, load the package using

library(admtools)

This makes all functions in the package available.

As example data we use outputs from CarboCAT Lite, a model of carbonate platform growth (Burgess 2013, 2023). This data is automatically loaded in the background by the package. To inspect it, you can load it into your workspace via

data("CarboCatLite_data")

Defining age-depth models

The standard constructor for age-depth models is tp_2_adm (“tiepoint to age-depth model”). It returns an adm (age-depth model) object. This object combines information of stratigraphic heights and times and erosive interval. It allows to transform data between the stratigraphic and the time domain, and indentify which data is destroyed due to hiatuses. We use the timing and stratigraphic positions of tie points to construct an age-depth model, and use the option to directly associate length and time units with it.

# see ?tp_2_adm for detailed documentation
my_adm = tp_2_adm(t = CarboCATLite_data$time_myr,
                  h = CarboCATLite_data$height_2_km_offshore_m,
                  L_unit = "m",
                  T_unit = "Myr")

You can use summary to get a quick overview of the properties of the age-depth model

summary(my_adm)
#> age-depth model 
#> Total duration: 2 Myr
#> Total thickness: 146.0621 m
#> Stratigraphic completeness: 32.65 % 
#> 10 hiatus(es)

Use the functions get_total_duration, get_total_thickness, get_completeness, and get_hiat_no extract that information directly from the age-depth model.

To get a visual representation, we plot it, and highlight hiatuses in red

# see ?plot.adm for plotting options for adm objects
plot(my_adm,
     col_hiat = "red",
     lwd_cons = 3)

The function is_destructive can be used to examine whether time points coincide with hiatuses:

is_destructive(adm = my_adm,
               t = c(0.1,0.5)) 
#> [1] FALSE  TRUE

Transforming data between time and stratigraphic domain

The functions get_height and get_time are the workhorses to transform data using age-depth models.

As example, say we want to know the time of deposition of the following stratigraphic positions:

h = c(30,120) # stratigraphic positions
get_time(adm = my_adm,
             h = h)
#> [1] 0.1380552 1.2704696

Conversely, to determine what parts of the section are deposited as a specific time, use

t = c(0.2,1.4)
get_height(adm = my_adm,
           t = t)
#> [1] 39.13951       NA

Here, the NA indicates that the time 1.4 coincides with erosion. If you want to know the stratigraphic position of the hiatus that coincides with that time, use the option destructive = FALSE:

t = c(0.2,1.4)
get_height(adm = my_adm,
           t = t,
           destructive = FALSE)
#> [1]  39.13951 126.27764

Further information

For information on estimating age-depth models from sedimentation rates, see

vignette("adm_from_sedrate")

For information on estimating age-depth models from tracer contents of rocks and sediments, see

vignette("adm_from_trace_cont")

References