Structure and classes of the admtools package

Niklas Hohmann

library(admtools)
#> Loading required package: ape

Introduction

This vignette provides an overview of the larger scale structure of the admtools package and the classes used therein.

S3 Classes

S3 class adm

Description

The S3 class adm represents age depth models. Structurally, they are lists with five fields:

• t : numeric vector, time points

• h : numeric vectors, heights

• destr: logical vector, is the interval destructive

• T_unit : NULL or a string, time unit

• L_unit : NULL or a string, length unit

h[i] is the height at time t[i]. h and t must be of same length and have at least 2 elements, t must be strictly increasing and h must be nondecreasing. length(destr) must be identical to length(t) - 1. destr[i] == TRUE indicates that the time interval from t[i] to t[i+1] is destructive and no information is preserved. Whether tie points are considered destructive is determined by the function is_destructive. Geologically, destr[i] == TRUE should imply h[i] == h[i+1] , as no sediment is accumulated during hiatuses.

Construction

The following functions construct adm objects:

• tp_to_adm for construction from tie points
• sac_to_adm for construction from sediment accumulation curves sac
• split_multiadm for extraction from multiple age-depth models multiadm

Logic

The following functions examine the logic of adm objects:

• is_adm to check for validity of an adm object

Representation

The following functions yield a representation of adm objects:

• plot.adm for plotting
• print.adm for printing to the console
• summary.adm to provide a quick summary of an object

Modification

The following functions modify adm objects:

• set_L_unit and set_T_unit to change units

Extracting information

The following functions extract information from adm objects:

• condensation and condensation_fun to extract condensation
• get_L_unit and get_T_unit to extract data
• get_completeness and get_incompleteness
• get_height
• get_time
• get_hiat_duration
• get_hiat_list
• get_hiat_no
• get_hiat_pos
• get_total_duration
• get_total_thickness
• is_destructive
• sed_rate_l and sed_rate_l_fun to extract sedimentation rate in height domain
• sed_rate_t and sed_rate_t_fun to extract sedimentation rate in time domain

Transformation into other S3 classes

The following functions transform adm objects into other S3 classes:

• merge_adm_to_multiadm into multiamd
• add_adm_to_multiadm to add adm to multiadm

S3 class sac

Description

The S3 class sac represents sediment accumulation curves. Structurally, they are lists with four fields:

• t : numeric vector, time points
• h : numeric vectors, heights
• T_unit : NULL or a string, time unit
• L_unit : NULL or a string, length unit

h[i] is the height at time t[i]. h and t must be of same length and have at least 2 elements, t must be increasing.

Construction

The following functions construct sac objects:

Standard constructor is tp_to_sac (tie point to sediment accumulation curve)

Logic

The following functions inspect the logic of sac objects:

• is_sac to check validity of sac object

Representation

The following functions yield a representation of sac objects:

• plot.sac for plotting
• print.sac for printing to the console

Modification

The following functions modify sac objects:

• set_L_unit and set_T_unit to change units

Extracting information

The following functions extract information from sac objects:

• get_L_unit and get_T_unit to extract units

Transformation into other S3 classes

The following functions transform sac objects into other S3 classes:

• sac_to_adm to transform sac into the S3 class adm

S3 class multiadm

Description

The S3 class multiadm represents multiple age depth models.. Structurally, they are lists with the following elements:

• no_of_entries: Positive integer, number of age depth models contained
• t list of length no_of_entries. Each element contains a numeric vector
• h: list of length no_of_entries. Each element contain a numeric vector
• destr: list of length no_of_entries. Each element contain a logic
• T_unit : NULL or a string, time unit
• L_unit : NULL or a string, length unit

h[[i]][j] is the height of the i-th age-depth model at time t[[i]][j]. For each i, the quintuple h[[i]], t[[i]], destr[[i]], T_unit and L_unit specify an adm object with the constraints as specified in the section S3 class adm (e.g., on monotonicity, length, etc.). T_unit and L_unit are shared among all age-depth models in an multiamd object.

Construction

The following functions construct multiadm objects:

• merge_adm_to_multiadm to contruct multiadm from adm objects
• sedrate_to_multiadm construct multiadm from info on sedimentation rates, see vignette("adm_from_sedrate")
• strat_cont_to_multiadm construct multiadm from tracer information, see vignette("adm_from_trace_cont")

Logic

The following functions inspect the logic of multiadm objects:

• is_multiadm to check for validity of multiadm object

Representation

The following functions yield a representation multiadm objects:

• plot.multiadm for plotting
• print.multiadm for printing to console
• summary.multiadm for providing summary statistics

Modification

The following functions modify multiadm objects:

• merge_multiadm to combine multiple multiadm objects
• set_L_unit and set_T_unit to change units

Extracting information

The following functions extract information from multiadm objects:

• condensation to extract condensation
• get_completeness and get_incompleteness
• get_height
• get_hiat_duration
• get_hiat_list
• get_hiat_no
• get_hiat_pos
• get_L_unit and get_T_unit to extract data
• get_time
• get_total_duration
• get_total_thickness
• is_destructive
• sed_rate_l
• sed_rate_t

Transformation into other S3 classes

The following functions transform multiadm objects into other S3 classes:

• split_multiadm to split multiadm into list of adm objects

Methods implemented for external S3 classes

S3 class list

admtools implements the following methods for list:

• strat_to_time: Transform strat-val pairs into time domain
• time_to_strat: Transform time-val pairs into strat domain

S3 class phylo

admtools implements the following methods for phylo:

• strat_to_time: Transform stratigraphic tree into time domain
• time_to_strat: Transform time tree into strat domain

Plotting

The following functions are used for plotting:

• plot.adm plotting for S3 class adm

• plot.multiadm plotting for S3 class multiadm

• plot.sac plotting for S3 class sac

• T_axis_lab to annotate time axis

• L_axis_lab to annotate length/depth axis

• plot_sed_rate_l to plot sedimentation rate in length/depth domain

• plot_sed_rate_t to plot sedimentation rate in time domain

• plot_condensation

• plot_erosive_intervals to highlight erosive intervals, called after plot.adm

Internals

The following functions are used internally and not exposed to users. They can be accessed via admtools:::function_name.

• plot_destr_parts

• plot_acc_parts

• make_adm_canvas