strattotimeratebin: Transform patterns from Stratigraphic Height into Time (Binned)

Description

This function transforms a given binned stratigraphic pattern into the corresponding temporal pattern. The transformation is based on the age model derived from the given deposition rate. Essentially a wrapper of patterntransform(...,direction='height to time',depositionmodel='binned deposition rate',patternmode='binned') kept for backwards compatibility of the package. It is recommended to use patterntransform instead of this function.

Usage

strattotimeratebin(binborder, depoval, signalval, pos = NULL, hiatuslist = list(), 
  unit = "sediment per time")

Arguments

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]

signalval

Positive vector of length length(binborder)-1. Defines the stratigraphic pattern in the bins, i.e. signalval[i] is the value of the stratigraphic pattern between the stratigraphic heights binborder[i] and binborder[i+1]

pos

OPTIONAL. Vector of points in stratigrapic height that will be transformed into time, and where the temporal pattern will evaluated. Default setting is a vector spanning the interval of interest with evenly spaced points (no. is chosen by the code)

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 times

val

vector containign the values of the temporal pattern at the times given by the first entry of the list

The temporal pattern can be approximated by approxfun(output$age,output$val). Output of NA indicates that some values coincide with a hiatus or are located at places where the deposition rate/stratigraphic pattern are 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 and stratigraphic pattern
binborder=1:6 #bins in tratigraphic height
depoval=c(1,4,0.1,2,2)
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)))
#define stratigraphic rate
signalval=c(runif(5))
#plot stratigraphic pattern
plot(approx(binborder,c(signalval,tail(signalval,1)),method='constant', 
  xout=seq(min(binborder),max(binborder),length.out=100)),type='l',main='Deposition Rate',
  xlab='Stratigraphic Height', ylab='Stratigraphic Pattern',ylim=c(0,max(signalval)))
  
##transform stratigraphic pattern into temporal pattern
usedunit="sediment per time" #unit of deposition rate is sediment per time unit (default setting)
reslist=strattotimeratebin(binborder,depoval, signalval,unit=usedunit)
#plot results
plot(reslist$age,reslist$val,xlab='time',ylab='temporal pattern',
  main=paste('depoval interpreted as',usedunit))
usedunit="time per sediment" #use other input interpretation
reslist=strattotimeratebin(binborder,depoval, signalval,unit=usedunit)
#note how different the results look!!
plot(reslist$age,reslist$val,xlab='time',ylab='temporal pattern',
  main=paste('depoval interpreted as',usedunit))
  
##insert a hiatus
stratigraphicheight=3.5 #strat. height of the hiatus
duration=2 #duration of the hiatus
hiatuslist=list(c(stratigraphicheight,duration)) #required input format for hiatuses
#usedunit is back to default setting!
reslist=strattotimeratebin(binborder,depoval, signalval,hiatuslist=hiatuslist)
#the hiatus corresponds to the gap  in the middle of the temporal rate
plot(reslist$age,reslist$val,xlab='time',ylab='temporal pattern') 

# }