strattotimeratecont: Transform Patterns from Stratigraphic Height into Time (Continuous)

Description

This function transforms a given continuous 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='piecewise linear deposition rate',patternmode='piecewise linear') kept for backwards compatibility of the package. It is recommended to use patterntransform instead of this function.

Usage

strattotimeratecont(xdep, ydep, xsig, ysig, pos = NULL,   hiatuslist = list(),
  unit = "sediment per time")

Arguments

xdep

Vector of strictly increasing real numbers

ydep

Vector of the same length of xdep, containing strictly positive real numbers. xdep and ydep define the deposition rate in the sense that depositionrate=approxfun(xdep,ydep). The units of te deposition rate are by default "sediment per time" and can be changed using the optional input unit

xsig

Vector of strictly increasing real numbers

ysig

Vector of the same length of xsig, containing positive real numbers. xsig and ysig define the stratigraphic pattern in the sense that stratigraphicrate=approxfun(xsig,ysig).

pos

OPTIONAL. Vector of points in stratigrapic height that will be transformed into time, and determine where the temporal pattern is 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 deposition rate.

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 then 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
xdep=seq(0,12,length.out=100)
ydep=splinefunH(x=c(0,2,4,6,8,10,12),y=c(1,5,6,1,0.5,1,6),m=c(0,1.5,-0.5,-0.5,0,0.5,0))(xdep)
usedunit="sediment per time" #unit of deposition rate is sediment per time unit (default setting)
#Plot deposition rate
plot(xdep,ydep,type='l',main='Deposition Rate',xlab='Stratigraphic Height',
  ylab=usedunit)
#define a pattern
xsig= seq(from=min(xdep),to=max(xdep),length.out=100)
ysig=splinefunH(x=c(0,4,12),y=c(0.5,2,0.5),m=c(0,0,0))(xsig) #function values of the signal
plot(xsig,ysig,type='l',main='Stratigraphic Pattern',
  xlab='Stratigraphic Height',ylab='Intensity')
  
##transform stratigraphic pattern into temporal pattern
usedunit="sediment per time" #unit of deposition rate is sediment per time unit (default setting)
reslist=strattotimeratecont(xdep,ydep,xsig,ysig,unit=usedunit)
#plot temporal pattern (transformed stratigrapic pattern)
plot(reslist$age,reslist$val,type='l',xlab='Time',ylab='Intensity',
  main=paste('deposition rate interpreted as',usedunit))
#now using same input, but different interpretation of units
usedunit="time per sediment" #now interpret the deposition rate in different units
reslist=strattotimeratecont(xdep,ydep,xsig,ysig,unit=usedunit)
#plot temporal pattern (transformed stratigrapic pattern)
plot(reslist$age,reslist$val,type='l',xlab='Time',ylab='Intensity temporal pattern',
  main=paste('deposition rate interpreted as',usedunit))
#note how different the results look!!

#Insert hiatus
stratigraphicheight=5 #strat. height of the hiatus
duration=4 #duration of the hiatus
hiatuslist=list(c(stratigraphicheight,duration)) #required input format for hiatuses
reslist=strattotimeratecont(xdep,ydep,xsig,ysig,hiatuslist=hiatuslist) #unit is back to default
plot(reslist$age,reslist$val,xlab='Time',ylab='Intensity',main='Temporal Pattern')
#hiatus is approx between 2 and 5
# }