strattotimepointbin: Transform Points and Isotope Ratios from Stratigraphic Height into Time (Binned)

Description

This function takes a binned deposition rate and reconstructs at what time a given stratigraphic height was deposited. Essentially a wrapper of pointtransform(...,direction='height to time',depositionmodel='binned deposition rate') kept for backwards compatibility of the package. It is recommended to use pointtransform instead of this function.

Usage

strattotimepointbin(x, binborder, depoval, hiatuslist = list(),
  unit = "sediment per time")

Arguments

Vector containing the stratigraphic heights whose time of deposition are to be determined

binborder

Vector of strictly increasing numerical values. Defines the borders of the bins in stratigraphic height

depoval

Strictly positive vector of length length(binborder)-1. Defines the deposition rate in the bins, i.e. depoval[i] is the deposition rate between the stratigraphic heights binborder[i] and binborder[i+1]

hiatuslist

OPTIONAL, default is an empty list. A list of hiatuses to insert. Every entry in the list corresponds to a hiatus, which is given as a vector of length two. The first entry of the vector is the stratigraphic height of the hiatus, the second entry is the duration of the hiatus.

unit

OPTIONAL, default is "sediment per time". Either "sediment per time" or "time per sediment". Determines the unit that is assumed for the input given by depoval.

Value

Returns a list containing

age

vector containing ages of deposition of the stratigraphic heights given by the input x

height

vector containing the heights that were deposited at the times given by age. Essentially a duplicate of the input x

Output of NA in age indicates that some values coincide with a hiatus or are located at places where the deposition rate is undefined.

References

Hohmann, Niklas. 2018. Quantifying the Effects of Changing Deposition Rates and Hiatii on the Stratigraphic Distribution of Fossils. <doi:10.13140/RG.2.2.23372.51841>

Examples

Run this code

# NOT RUN {
##define deposition rate
binborder=1:6 #bins in tratigraphic height
depoval=c(1,4,5,2,2)
usedunit="sediment per time" #unit of deposition rate is sediment per time unit (default setting)
#Plot deposition rate
plot(approx(binborder,c(depoval,tail(depoval,1)),method='constant',xout=seq(min(binborder),
  max(binborder),length.out=100)),type='l',main='Deposition Rate',xlab='Stratigraphic Height',
  ylab=usedunit,ylim=c(0,max(depoval)))
  
##at what time was the point with tratigraphic height 3.5 deposited?
strattotimepointbin(3.5,binborder,depoval) 

##create an age model
stratheight=seq(min(binborder),max(binborder),length.out=100)
reslist=strattotimepointbin(stratheight,binborder,depoval,unit=usedunit)
#plot age model
usedunit="sediment per time"
plot(reslist$age,reslist$height,xlab='Time',ylab='Stratigraphic Height',
  main=paste('Age model with unit',usedunit))
#create age model but with other units for sedimentn input
usedunit='time per sediment'
reslist=strattotimepointbin(stratheight,binborder,depoval,unit=usedunit)
#plot age model (note the difference this setting makes)
plot(reslist$age,reslist$height,xlab='Time',ylab='Stratigraphic Height',
  main=paste('Age model with unit',usedunit))

##create age model with a hiatus
stratigraphicheight=5 #strat. height of the hiatus
duration=2 #duration of the hiatus
hiatuslist=list(c(stratigraphicheight,duration)) #required input format for hiatuses
reslist=strattotimepointbin(stratheight,binborder,depoval,hiatuslist=hiatuslist)
#!using default setting for units again!
plot(reslist$age,reslist$height,xlab='Time',ylab='stratigraphic height') 

##Transform isotope ratios
depoval=c(1,4,0.1,2,2) 
#create fake oxygen isotope curves
samplelocation=sort(runif(20,min=min(binborder),max=max(binborder))) #where the samples are taken
isotoperatio=sin(samplelocation)*rnorm(length(samplelocation)) #isotope ratios of the samples
plot(samplelocation,isotoperatio,type='l',xlab='Stratigraphic Height',ylab='Isotope Ratio')
#transform only (!) sample locations, NOT values
reslist=strattotimepointbin(samplelocation,binborder,depoval)
#Isotope ratios in time 
plot(reslist$age,isotoperatio,type='l',xlab='Time',ylab='Isotope Ratio')

# }