This document provides a brief introduction into the structure of the R package DAIME with an overview of the available functions and some explantions regarding their options.

Introduction

Changing deposition rates determine how much time it takes to deposit a given thickness of sediment. This determines how diluted or condensed the information contained in this sediment is, and accordingly alters our perception of time and speed when working with the rock record.

The DAIME package allows to

  1. model how changing deposition rates alter the expression of temporal patterns in sections

  2. account for the effects of changing deposition rates in data derived from the rock record

Available Functions

The 2.0 version of the package contains the following core functions:

  1. pointtransform to transform the location of individual points from time into stratigraphic height and vice versa. This can also be used to create age models from deposition rates and transform isotope ratios between time and height

  2. patterntransform to transform patterns from time into stratigraphic height and vice versa. A pattern can be any grain-based input into the sediment (e.g. fossil occurrences, some geochemical proxies) and rates derived from it (e.g. rate of morphological change or first/last fossil occurrences, both derived from fossil occurrences)

It further contains the following supplementary function:

  1. patterntodepositionmodel to construct a deposition model based on the sedimentary condensation/dilution of a known pattern

In addition to that, the following functions are available for backwards compatibility:

Nomenclature

Deposition models

Deposition models are central to the DAIME package and describe how sediment input into the system changes through time. There are three ways to hand a deposition model over to the functions pointtransform and patterntransform: as age model, as piecewise linear deposition rate, and as binned deposition rate. This is determined by the depositionmodel option in pointtransform and patterntransform.

The function patterntodepositionmodel can be used to create a deposition model based on the dilution/condensation of a known pattern which can then be handed over to pointtransform or patterntransform.

Age models

Age models assign a stratigraphic height to an age and vice versa. They are described via two vectors I will here call agemodelage and agemodelheight. The entry agemodelage[i] is the age of the sediment at the stratigraphic height agemodelheight[i] and vice versa.


par(mar=c(4,4,1,0),mgp=c(2.1,0.4,0))
agemodelage=seq(0,3,length.out = 100)
agemodelheight=splinefunH(x=c(0,1,3),y=c(0,0.8,2),m=c(0.2,2,0.3))(agemodelage)
plot(agemodelage,agemodelheight,type='l',xlab='Time/Age \n ( agemodelage )',ylab='Stratigraphic Height \n ( agemodelheight )',main='Age Model',lwd=4)

plot of chunk fig1

When the functions are used with direction in the setting height to time, agemodelheight corresponds to xdep and agemodelage corresponds to ydep. In this case, both agemodelage and agemodelheight need to be strictly increasing. Hiatuses can be inserted into the age model using the hiatuslist option.

When direction is set to time to height, agemodelage corresponds to xdepand agemodelheight corresponds to ydep. Here, agemodelheight can also be decreasing or stagnating. This will be interpreted as erosion or periods of nondeposition, and accordingly incoorporated into the transformation.

Deposition Rates

Deposition rates describe the sediment input into a system through time. They can be handed over either as piecewise linear deposition rate by setting depositionmodel to piecewise linear deposition rate or as binned deposition rate by setting depositionmodel to binned deposition rate.

For piecewise linear deposition rates, the deposition rate is given by depositionrate=approxfun(xdep,ydep). Accordingly xdep and ydep need to be of the same size.

For binned deposition rates, the values of the deposition rate between xdep[i] and xdep[i+1] is given by ydep[i]. Accordingly ydep is one entry shorter than xdep

When direction is set to height to time, deposition rates need to be strictly positive, since negative deposition rates (=erosion) would not be visible in the section. In this case, hiatuses can be inserted using the hiatuslist option. When direction is set to time to height, deposition rates can also be negative, which is interpreted as erosion and accordingly incorporated into the transformation.

In the case of the transformation from height to time, the additional option unitis available. This is since deposition rates in the section can be described in two ways:

  1. Either they give a description of the deposition rates with which the heights in the section were deposited

  2. Or they describe how much time is “contained” in sediment.

Setting unit to sediment per time and the functions will interpret the deposition rate described by xdep and ydep in the first way. Setting is to time per sediment will lead to the functions interpreting the deposition rates in the second way.

NOTE: The default setting is unit='sediment per time'. For the effects of this options see the examples given in the help pages of pointtransform and patterntransform.

Isotope Ratios

Isotope ratios need to be treated differently than patterns, because they are based on the ratio of two inputs into the sediment. Since numerator and denominator are condensed and diluted equally, ratios are not affected by sedimentary condensation/dilution. What changes is the location of the points where those ratios were measured. Equally spaced points in stratigraphic height will generate very irregular spaces between the points when deposition rates in the section vary drastically.

For these reasons, only the locations where isotope ratios were measured need to be transformed using pointtransform. The isotope ratios remain unchanged. For an example, see the help page of pointtransform.

Examples

For examples please refer to the help pages of the corresponding functions