Nothing
R/calc.R
In rbacon: Age-Depth Modelling using Bayesian Statistics
Defines functions
stretch
squeeze
fromslump
toslump
agemodel.it
Bacon.rng
Bacon.hist
hiatus.slopes
Bacon.d.Age
Bacon.Age.d
Documented in
agemodel.it
Bacon.Age.d
Bacon.d.Age
Bacon.hist
squeeze
stretch
#' @name Bacon.Age.d
#' @title Output all ages for a single depth.
#' @description Output all MCMC-derived age estimates for a given depth.
#' @details Obtaining an age-depth model is often only a step towards a goal, e.g., plotting a core's
#' fossil series ('proxies') against calendar time. Bacon.Age.d can be used to list all MCMC-derived age estimates for a given (single) depth, for example to calculate mean ages for a depth. See also Bacon.d.Age which calculates the depths of a single age estimate.
#' @param d The depth of which Bacon age estimates are to be returned. Has to be a single depth.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param its The set of MCMC iterations to be used. Defaults to the entire MCMC output, \code{its=set$output}.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param na.rm Whether or not to remove NA values (ages within slumps)
#' @author Maarten Blaauw, J. Andres Christen
#' @return Outputs all MCMC-derived ages for a given depth.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' ages.d20 = Bacon.Age.d(20)
#' mean(ages.d20)
#' }
#' @export
Bacon.Age.d <- function(d, set=get('info'), its=set$output, BCAD=set$BCAD, na.rm=FALSE) {
if(length(d) > 1)
stop("Bacon.Age.d can handle one depth at a time only", call.=FALSE)
if(length(its) == 0)
stop("core's data not yet in memory. Please run agedepth first\n", call.=FALSE)
hiatus.depths <- set$hiatus.depths
if(length(set$slump) > 0) {
d <- toslump(d, set$slump, remove=na.rm)
if(!is.na(hiatus.depths[1]))
hiatus.depths <- set$slumphiatus
}
ages <- numeric(nrow(its)) # to sort R-base problem with c() and loops
if(!is.na(d))
if(d >= min(set$elbows)) { # we cannot calculate ages of depths above the top depth; was > d.min before Feb 2021
topages <- as.vector(its[,1]) # ages for the core top
maxd <- max(which(set$elbows <= d)) # find the relevant sections
accs <- as.matrix(its[,1+(1:maxd)]) # the accumulation rates xi for each relevant section
cumaccs <- cbind(0, t(apply(accs, 1, cumsum))) # cumulative accumulation
ages <- topages + (set$thick * cumaccs[,maxd]) + # topages + xi * dC + ...
((d-set$elbows[maxd]) * accs[,maxd]) # ... remaining bit of lowest section
# now using a uniform jump, not gamma
if(!is.na(hiatus.depths[1]))
for(i in 1:length(hiatus.depths)) {
above <- max(which(set$elbows < hiatus.depths[i]), 1)[1]
below <- above + 1
if(d > set$elbows[above] && d <= set$elbows[below]) { # adapt ages for sections with hiatus
if(d > hiatus.depths[i]) # April 2020, changed snippets below from [[i]]] to [,i]
ages <- set$elbow.below[,i] - (set$slope.below[,i] * (set$elbows[below] - d)) else
ages <- set$elbow.above[,i] + (set$slope.above[,i] * (d - set$elbows[above]))
}
}
} else
ages <- NA # Feb 2021
if(BCAD)
ages <- 1950 - ages
return(c(ages))
}
#' @name Bacon.d.Age
#' @title Output all depths for a single age.
#' @description Output all MCMC-derived depth estimates for a single given age.
#' @details Obtaining an age-depth model is often only a step towards a goal, e.g., plotting a core's
#' fossil series ('proxies') against calendar time. Bacon.d.Age can be used to list all MCMC-derived depths belonging to a given (single) age, for example to calculate mean depths belonging to a modelled depth.
#' This function was kindly written and provided by Timon Netzel (Bonn University). See also Bacon.Age.d, which calculates the ages for a single depth.
#' @param age The age estimate for which depths are to be returned. Has to be a single age.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param its The set of MCMC iterations to be used. Defaults to the entire MCMC output, \code{its=set$output}.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param na.rm Whether or not to remove NA values (ages within slumps)
#' @author Maarten Blaauw, J. Andres Christen
#' @return Outputs all MCMC-derived depths for a given age.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' ages.d20 = Bacon.Age.d(20)
#' mean(ages.d20)
#' }
#' @export
Bacon.d.Age <- function(age, set=get("info"), BCAD=set$BCAD, its=set$output, na.rm=FALSE ){
if(BCAD)
age <- 1950 - age # if the customer decides to enter the age in BCAD
if(length(age) > 1)
stop("Bacon.d.Age can handle one age at a time only", call. = FALSE)
if(length(its) == 0 )
stop("core's data not yet in memory. Please run agedepth first\n", call. = FALSE)
# create elbow ages
elbows <- set$elbows
topages <- as.vector(its[,1]) # ages for the core top
accs <- as.matrix(its[,1+(1:set$K)]) # the accumulation rates xi for each section
cumaccs <- set$thick * cbind(0, t(apply(accs, 1, cumsum))) # cumulative accumulation
elbow.ages <- topages + cumaccs
if ( age <= min(elbow.ages) || age > max(elbow.ages) )
message(" Warning, age outside the core's age range!\n")
# prepare slump
hiatus.depths <- set$hiatus.depths
if(length(set$slump) > 0) {
diff.slumps <- apply(set$slump,1,diff,na.rm=T) # vector containing the difference of each slump
if ( !is.na(hiatus.depths[1]) )
hiatus.depths <- set$slumphiatus
}
# prepare hiatus
hiatus.check <- rep(0,ncol(elbow.ages)) # vector containing the information for each elbow whether there is a hiatus (1) or no hiatus (0)
if ( !is.na(hiatus.depths[1]) ){
# if there is no slump
if ( length(set$slump) == 0 )
hiatus.depths <- set$hiatus.depths
# where are the hiatuses
for ( i in 1:length(hiatus.depths) ) {
hiatus.check[ min(which(elbows > hiatus.depths[i])) ] <- 1
}
}
# intersections which are below the last elbow
these.bottom <- which( elbow.ages[, ncol(elbow.ages)] < age )
# summary of the depths corresponding to the chosen age
depths <- rep(NA,nrow(its))
for ( i in 2:ncol(elbow.ages) ){
# consideration of hiatuses
if ( hiatus.check[i] == 1 ){
for ( j in 1:length(hiatus.depths) ) {
above <- max(which(elbows < hiatus.depths[j]), 1)[1]
below <- above + 1
# two age ranges for one hiatus (below/above) with the adapted slopes (could be included in the info list)
ages.above <- set$elbow.above[,j] + (set$slope.above[,j] * (hiatus.depths[j] - elbows[above]))
ages.below <- set$elbow.below[,j] - (set$slope.below[,j] * (elbows[below] - hiatus.depths[j]))
# intersections below and above
these.above <- (elbow.ages[, above] < age) * (ages.above > age)
these.below <- (ages.below < age) * (elbow.ages[, below] > age)
# find the depths which correspond to the intersections below and above the hiatus
if ( sum(these.above, na.rm=T) > 0 ){
# slopes above hiatus
accs.above <- (1/set$slope.above[,j])[which(these.above==1)]
# age difference with the last age range above the hiatus
age.diff.above <- age - elbow.ages[which(these.above==1), above]
# depths: last depth above hiatus depth + slopes * age difference
depths[which(these.above==1)] <- elbows[above] + accs.above * age.diff.above
}
if ( sum(these.below, na.rm=T) > 0 ){
# slopes below hiatus
accs.below <- (1/set$slope.below[,j])[which(these.below==1)]
# age difference with the lower hiatus age range
age.diff.below <- age - ages.below[which(these.below==1)]
# depths: hiatus depth + slopes * age difference
depths[which(these.below==1)] <- hiatus.depths[j] + accs.below * age.diff.below
}
}
} else {
# consideration of the cases without hiatuses
# find the correct intersections
these <- (elbow.ages[, i - 1] < age) * (elbow.ages[, i] > age)
# find the depths which correspond to these intersections
if ( sum(these, na.rm=T) > 0 ){
# which slopes
accs <- 1/set$output[which(these == 1), i]
# difference between the age and the elbow ages found
age.diff <- age - elbow.ages[which(these == 1), i - 1]
# depths: elbow depth + slopes * age difference
depths[which(these==1)] <- elbows[i-1] + accs * age.diff
}
# find these intersections which are below the last elbow
if( length(these.bottom) > 0 & i == ncol(elbow.ages) ){
# slopes below last elbow
accs.bottom <- 1/set$output[these.bottom, i]
# difference between the age and the last elbow ages found
age.diff.bottom <- age - elbow.ages[these.bottom, i ]
# depth: last elbow + slopes * age difference
depths[these.bottom] <- elbows[i-1] + accs.bottom * age.diff.bottom
}
}
}
# Query: remove NA entries if some entries are not NA (happens for some hiatuses).
# In these cases the depth vector does not have the same length for different age.
# In cases where the age entered is younger than min(elbow.ages), each entry in depth is NA and is returned as such.
if( !all(is.na(depths)) & na.rm ) depths <- depths[!is.na(depths)]
# consideration of slumps
if ( length(set$slump) > 0 ) {
for( j in 1:nrow(set$slump) ){
# which depths are below the slump
these.below.slump <- (depths >= set$slump[j,1])
below.slump <- sum(these.below.slump, na.rm = T)
if ( below.slump > 0 ){
# shift the found depths with the slump depths above
these.shift <- which(these.below.slump==1)
depths[these.shift] <- depths[these.shift] + diff.slumps[j]
}
}
}
# output
return(depths)
}
# First get ages and slopes of c's just above and below hiatus.
# then calculate slope.below and slope.above as extrapolations from the sections below resp. above (option 1, default), no adapting of slopes (option 0),
# or as w-weighted mix of prior and accrates, resp. prior only (option 2).
# then check if these slopes work (no reversals). Those with reversals revert to the original slopes.
# check approach for boundaries. check that elbows in correct order, then set slopes to either ages.below or ages.above???
hiatus.slopes <- function(set=get('info'), hiatus.option=1) {
elbows <- set$elbows
hiatus.depths <- set$hiatus.depths
if(length(set$slump) > 0)
hiatus.depths <- set$slumphiatus
its <- cbind(set$output)
w <- its[,ncol(its)]^(1/set$thick)
fillvals <- array(NA, dim=c(nrow(its), length(hiatus.depths))) # 17 Apr 2020
# set$slope.below <- numeric(nrow(its)) # 17 Apr 2020
# set$slope.above <- numeric(nrow(its)) # 17 Apr 2020
set$slope.below <- fillvals # 17 Apr 2020
set$slope.above <- fillvals # 17 Apr 2020
set$elbow.below <- fillvals # 17 Apr 2020
set$elbow.above <- fillvals # 17 Apr 2020
set$above <- numeric(1)
topages <- as.vector(its[,1]) # ages for the core top
accs <- as.matrix(its[,1+(1:set$K)]) # the accumulation rates xi for each section
cumaccs <- set$thick * cbind(0, t(apply(accs, 1, cumsum))) # cumulative accumulation
elbow.ages <- topages + cumaccs
for(i in 1:length(hiatus.depths)) {
above <- max(which(elbows < hiatus.depths[i]), 1) ### is this the correct one?
elbow.below <- elbow.ages[,above+1]
elbow.above <- elbow.ages[,above]
orig.slope <- accs[,above]
if(hiatus.option == 0) { # then do nothing
slope.below <- orig.slope
slope.above <- orig.slope
}
if(hiatus.option == 1) { # then extrapolate slopes above/below section w hiatus
slope.below <- its[,above+2]
slope.above <- its[,above]
}
if(hiatus.option == 2) { # then w-weighted for below, and prior-only for above
slope.below <- w*set$output[,above+2] + (1-w)*set$acc.mean[i+1]
slope.above <- rep(set$acc.mean[i], nrow(its))
}
# now calculate the ages at the hiatus/boundary, coming from below and from above
ages.above <- elbow.above + (slope.above * (hiatus.depths[i] - elbows[above]))
ages.below <- elbow.below - (slope.below * (elbows[above+1] - hiatus.depths[i]))
if(!is.na(set$boundary[1])) { # then set the boundary's elbow at ages.below for both sections
if(length(set$slumpboundary) > 0)
boundary <- set$slumpboundary else
boundary <- set$boundary
ages.boundary <- elbow.below - (slope.below * (elbows[above+1] - set$boundary[i]))
slope.above <- (ages.boundary - elbow.above) / (set$boundary[i] - elbows[above])
slope.below <- (ages.below - ages.boundary) / (elbows[above+1] - set$boundary[i])
}
# for sections with reversals, use the original slopes
reversed <- c(which(elbow.above > ages.above),
which(ages.above > ages.below),
which(ages.below > elbow.below),
which(slope.below < 0), which(slope.above < 0))
if(length(reversed) > 0) {
slope.above[reversed] <- orig.slope[reversed]
slope.below[reversed] <- orig.slope[reversed]
}
# store the updated information
# set$elbow.below[[i]] <- elbow.below # commented Apr 2020
# set$elbow.above[[i]] <- elbow.above
# set$slope.below[[i]] <- slope.below
# set$slope.above[[i]] <- slope.above
set$elbow.below[,i] <- elbow.below # new April 2020
set$elbow.above[,i] <- elbow.above # new
set$slope.below[,i] <- slope.below # new
set$slope.above[,i] <- slope.above # new
set$above <- above
}
return(set)
}
#' @name Bacon.hist
#' @title Calculate age distributions of depths.
#' @description Calculate the distribution of age estimates of single or multiple depths.
#' @details Age estimates of specific depths can also be plotted.
#' @param d The depth or depths for which a histogram and age ranges should be provided. If multiple depths are given, then just the age ranges, median and means (no graphs) are provided for each depth.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param age.lab The labels for the calendar axis (default \code{age.lab="cal BP"} or \code{"BC/AD"} if \code{BCAD=TRUE}).
#' @param age.lim Minimum and maximum calendar age ranges, calculated automatically by default (\code{age.lim=c()}).
#' @param hist.lab The y-axis is labelled \code{ylab="Frequency"} by default.
#' @param calc.range Calculate ranges? Takes time so can be left out
#' @param hist.lim Limits of the y-axis.
#' @param draw Draw a plot or not. Defaults to \code{draw=TRUE}, however no plots are made if more than one depth \code{d} is provided.
#' If \code{draw=FALSE}, then the age ranges, median and mean are given for each depth (as four columns).
#' @param prob Age ranges are given as quantiles, e.g., 2.5\% and 97.5\% for the default of 95\% confidence limits (\code{prob=0.95})).
#' @param hist.col Colour of the histogram. Default grey, \code{hist.col=grey(0.5)}.
#' @param hist.border Colour of the histogram's outline. Default dark grey, \code{hist.border=grey(0.2)}.
#' @param range.col Colour of confidence ranges. Defaults to \code{range.col="blue"}.
#' @param med.col Colour of the median. Defaults to \code{med.col="green"}.
#' @param mean.col Colour of the mean. Defaults to \code{mn.col="red"}.
#' @param verbose Provide feedback on what is happening (default \code{verbose=TRUE}).
#' @param save.info A variable called `info' with relevant information about the run (e.g., core name, priors, settings, ages, output) can be saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., \code{myvar <- Bacon()}, followed by supplying the variable \code{myvar} in any subsequent commands.
#' @author Maarten Blaauw, J. Andres Christen
#' @return A local variable called `hists', and a plot with the histogram and the age ranges, median and mean, or just the age ranges, medians and means if more than one depth \code{d} is given.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' Bacon.hist(20)
#' Bacon.hist(20:30)
#' }
#' @export
Bacon.hist <- function(d, set=get('info'), BCAD=set$BCAD, age.lab=c(), age.lim=c(), hist.lab="Frequency", calc.range=TRUE, hist.lim=c(), draw=TRUE, prob=set$prob, hist.col=grey(0.5), hist.border=grey(.2), range.col="blue", med.col="green", mean.col="red", verbose=TRUE, save.info=FALSE) {
outfile <- paste0(set$prefix, ".out")
if(length(set$output) == 0 || length(set$Tr) == 0) {
set <- Bacon.AnaOut(outfile, set, MCMC.resample=FALSE)
if(save.info)
assign_to_global("set", set) # should that be 'info'?
}
hist3 <- function(d, BCAD) {
hsts <- list(); maxhist <- 0; minhist <- 1
pb <- txtProgressBar(min=0, max=max(1,length(d)-1), style = 3)
for(i in 1:length(d)) {
if(length(d) > 1) {
if(length(d) < 500) # progress bar slows things down much if i is large
setTxtProgressBar(pb, i) else
if(i %% 10 == 0)
setTxtProgressBar(pb, i)
}
ages <- Bacon.Age.d(d[i], set, BCAD=BCAD)
if(length(ages[!is.na(ages)]) > 0) { # added !is.na(ages) 21 April 21
hst <- density(ages)
th0 <- min(hst$x)
th1 <- max(hst$x)
maxhist <- max(maxhist, hst$y)
minhist <- min(minhist, max(hst$y))
n <- length(hst$x)
counts <- hst$y
ds <- d[i]
hsts <- append(hsts, pairlist(list(d=ds, th0=th0, th1=th1, n=n, counts=counts, max=maxhist, min=minhist)))
} else hsts$d[[i]] <- d[i]
}
return(hsts)
}
hists <- hist3(d, BCAD)
assign_to_global("hists", hists)
rng <- array(NA, dim=c(length(d), 4)) # R > 4.0 does not like to fill c() using loops
if(calc.range) {
rng <- Bacon.rng(d, set, BCAD, prob)
for(i in 1:length(d))
hists$rng[[i]] <- rng[i,]
}
if(length(d)==1)
if(draw==TRUE) {
hst <- hists[[1]]
if(length(age.lab) == 0)
age.lab <- ifelse(BCAD, "BC/AD", "cal yr BP")
if(length(age.lim) == 0)
age.lim <- c(hst$th0, hst$th1)
if(BCAD)
age.lim <- rev(age.lim)
if(length(hist.lim) == 0)
hist.lim <- c(0, 1.1*hst$max)
pol <- cbind(c(hst$th0, seq(hst$th0, hst$th1, length=hst$n), hst$th1), c(0, hst$counts, 0))
plot(0, type="n", xlim=age.lim, ylim=hist.lim, xlab=age.lab, ylab=hist.lab, yaxs="i")
polygon(pol, col=hist.col, border=hist.border)
segments(rng[,1], 0, rng[,2], 0, col=range.col, lwd=3)
points(rng[,3], 0, col=med.col, pch=20)
points(rng[,4], 0, col=mean.col, pch=20)
if(verbose) {
message("mean (", mean.col, "): ", round(rng[4],1), " ", age.lab,
", median (", med.col, "): ", round(rng[3],1), " ", age.lab, "\n")
message(100*prob, "% range (", range.col, "): ", round(rng[1],1), " to ", round(rng[2],1), " ", age.lab, "\n")
}
}
invisible(rng) # should this become invisible(hists)?
}
# to calculate age ranges
Bacon.rng <- function(d, set=get('info'), BCAD=set$BCAD, prob=set$prob) {
outfile <- paste0(set$prefix, ".out")
if(length(set$output) == 0 || length(set$Tr) == 0) {
set <- Bacon.AnaOut(outfile, set, MCMC.resample=FALSE)
assign_to_global("set", set) # MB Jan 2024; can this go?
}
if(length(d) > 1)
pb <- txtProgressBar(min=0, max=max(1, length(d)-1), style=3)
rng <- array(NA, dim=c(length(d), 4))
for(i in 1:length(d)) {
ages <- Bacon.Age.d(d[i], set, BCAD=BCAD)
ages <- ages[!is.na(ages)]
if(length(ages) > 0) {
rng[i,1:3] <- quantile(ages, c(((1-prob)/2), 1-((1-prob)/2), .5), na.rm=TRUE)
rng[i,4] <- mean(ages)
}
if(length(d) > 1) {
if(length(d) < 500) # progress bar slows things down when i is large
setTxtProgressBar(pb, i) else
if(i %% 10 == 0)
setTxtProgressBar(pb, i)
}
# if(length(d) > 1)
# setTxtProgressBar(pb, i)
}
#if(length(d) > 1)
# close(pb)
return(rng)
}
#' @name agemodel.it
#' @title Extract one age-model iteration
#' @description For one MCMC iteration (it), extract the corresponding age-depth model.
#' @param it The MCMC iteration of which the age-model should be calculated.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param save.info If TRUE, a variable called `info' with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name.
#' @author Maarten Blaauw, J. Andres Christen
#' @return A variable with two columns - depth and the age-depth model of a single iteration.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' lines(agemodel.it(5), col="red")
#' }
#' @export
agemodel.it <- function(it, set=get('info'), BCAD=set$BCAD, save.info=FALSE) {
outfile <- paste0(set$prefix, ".out")
if(length(set$output) == 0 || length(set$Tr) == 0) {
set <- Bacon.AnaOut(outfile, set, MCMC.resample=FALSE)
if(save.info)
assign_to_global("info", set) # changed 'set' to 'info'
}
# does this function work in cores with slumps? also doesn't take into account hiatuses.
if(length(set$hiatus.depths) > 0)
age <- sort(c(set$d, set$hiatus.depths+.001, set$hiatus.depths))
age <- c()
for(i in 1:length(set$elbows))
age[i] <- Bacon.Age.d(set$elbows[i], set, BCAD=BCAD)[it]
cbind(set$elbows, age)
}
# calculate slumpfree depths
toslump <- function(d, slump, remove=FALSE) {
d <- sort(d)
slump <- matrix(sort(slump), ncol=2, byrow=TRUE)
slices <- c(0, slump[,2] - slump[,1])
dfree <- d
for(i in 1:nrow(slump)) {
inside <- which(d <= slump[i,2]) # find depths within slump, step 1
inside <- which(d[inside] >= slump[i,1]) # step 2
below <- which(d >= slump[i,2]) # adapt depths below slumps
if(length(below) > 0) # depths below slump
dfree[below] <- dfree[below] - slices[i+1]
if(length(inside) > 0) # depths within slump
if(min(d) < max(slump[i,]))
if(remove)
dfree[inside] <- NA else
dfree[inside] <- slump[i,1] - sum(slices[1:i])
}
return(dfree)
}
# calculate original depths. Needed?
fromslump <- function(d, slump) {
slump <- matrix(sort(slump), ncol=2, byrow=TRUE)
slices <- slump[,2] - slump[,1]
dorig <- d # original depths
for(i in 1:nrow(slump)) {
below <- which(d > min(slump[i,]))
if(length(below) > 0)
dorig[below] <- dorig[below] - slices[i]
}
return(dorig)
}
#' @name squeeze
#' @title Squeeze some depths of a core
#' @description Squeeze or compress depths below a boundary by a certain amount. Accompanies the stretch function; see the stretch function for code on running the accordion
#' @param d The depth(s) to be squeezed
#' @param boundary The depth below which depths should be squeezed
#' @param times The factor by which the depths should be squeezed
#' @author Maarten Blaauw
#' @return The squeezed depth(s)
#' @examples
#' squeeze(40,25,20)
#' @export
squeeze <- function(d, boundary, times) {
below <- which(d > boundary)
if(length(below) > 0)
d[below] <- boundary + (d[below]-boundary)/times
return(d)
}
#' @name stretch
#' @title Stretch some depths of a core
#' @description Stretch squeezed depths e.g., calculate the original depths of depths that were squeezed. Accompanies the squeeze function.
#' @param d The depth(s) to be stretched
#' @param boundary The depth below which depths should be stretched
#' @param times The factor by which the depths should be stretched
#' @author Maarten Blaauw
#' @return The stretched depth(s)
#' @examples
#' stretch(25.75,25,20)
#' \dontrun{
#' # To play the accordion, first squeeze an existing core.
#' # Let's squeeze the depths below 10 cm core depth 20 times:
#' Bacon("accordion", 1)
#' dets <- info$dets
#' dets[,4] <- squeeze(dets[,4], 10, 20)
#'
#' # make a new directory for the squeezed core, and place the dets file there:
#' dir.create("Bacon_runs/squeezed")
#' write.table(dets, "Bacon_runs/squeezed/squeezed.csv", row.names=FALSE, sep=",")
#'
#' # now run that squeezed core, adding a boundary (10cm) and adapting the acc.mean prior (20x):
#' Bacon("squeezed", 1, boundary=10, acc.mean=c(5, 20*5))
#' # finally, plot while stretching the depths onto the original scale:
#' agedepth(accordion=c(10,20))
#' }
#' @export
stretch <- function(d, boundary, times) {
below <- which(d > boundary)
if(length(below) > 0)
d[below] <- boundary + (d[below]-boundary)*times
return(d)
}
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Defines functions stretch squeeze fromslump toslump agemodel.it Bacon.rng Bacon.hist hiatus.slopes Bacon.d.Age Bacon.Age.d
Documented in agemodel.it Bacon.Age.d Bacon.d.Age Bacon.hist squeeze stretch
#' @name Bacon.Age.d
#' @title Output all ages for a single depth.
#' @description Output all MCMC-derived age estimates for a given depth.
#' @details Obtaining an age-depth model is often only a step towards a goal, e.g., plotting a core's
#' fossil series ('proxies') against calendar time. Bacon.Age.d can be used to list all MCMC-derived age estimates for a given (single) depth, for example to calculate mean ages for a depth. See also Bacon.d.Age which calculates the depths of a single age estimate.
#' @param d The depth of which Bacon age estimates are to be returned. Has to be a single depth.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param its The set of MCMC iterations to be used. Defaults to the entire MCMC output, \code{its=set$output}.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param na.rm Whether or not to remove NA values (ages within slumps)
#' @author Maarten Blaauw, J. Andres Christen
#' @return Outputs all MCMC-derived ages for a given depth.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' ages.d20 = Bacon.Age.d(20)
#' mean(ages.d20)
#' }
#' @export
Bacon.Age.d <- function(d, set=get('info'), its=set$output, BCAD=set$BCAD, na.rm=FALSE) {
if(length(d) > 1)
stop("Bacon.Age.d can handle one depth at a time only", call.=FALSE)
if(length(its) == 0)
stop("core's data not yet in memory. Please run agedepth first\n", call.=FALSE)
hiatus.depths <- set$hiatus.depths
if(length(set$slump) > 0) {
d <- toslump(d, set$slump, remove=na.rm)
if(!is.na(hiatus.depths[1]))
hiatus.depths <- set$slumphiatus
}
ages <- numeric(nrow(its)) # to sort R-base problem with c() and loops
if(!is.na(d))
if(d >= min(set$elbows)) { # we cannot calculate ages of depths above the top depth; was > d.min before Feb 2021
topages <- as.vector(its[,1]) # ages for the core top
maxd <- max(which(set$elbows <= d)) # find the relevant sections
accs <- as.matrix(its[,1+(1:maxd)]) # the accumulation rates xi for each relevant section
cumaccs <- cbind(0, t(apply(accs, 1, cumsum))) # cumulative accumulation
ages <- topages + (set$thick * cumaccs[,maxd]) + # topages + xi * dC + ...
((d-set$elbows[maxd]) * accs[,maxd]) # ... remaining bit of lowest section
# now using a uniform jump, not gamma
if(!is.na(hiatus.depths[1]))
for(i in 1:length(hiatus.depths)) {
above <- max(which(set$elbows < hiatus.depths[i]), 1)[1]
below <- above + 1
if(d > set$elbows[above] && d <= set$elbows[below]) { # adapt ages for sections with hiatus
if(d > hiatus.depths[i]) # April 2020, changed snippets below from [[i]]] to [,i]
ages <- set$elbow.below[,i] - (set$slope.below[,i] * (set$elbows[below] - d)) else
ages <- set$elbow.above[,i] + (set$slope.above[,i] * (d - set$elbows[above]))
}
}
} else
ages <- NA # Feb 2021
if(BCAD)
ages <- 1950 - ages
return(c(ages))
}
#' @name Bacon.d.Age
#' @title Output all depths for a single age.
#' @description Output all MCMC-derived depth estimates for a single given age.
#' @details Obtaining an age-depth model is often only a step towards a goal, e.g., plotting a core's
#' fossil series ('proxies') against calendar time. Bacon.d.Age can be used to list all MCMC-derived depths belonging to a given (single) age, for example to calculate mean depths belonging to a modelled depth.
#' This function was kindly written and provided by Timon Netzel (Bonn University). See also Bacon.Age.d, which calculates the ages for a single depth.
#' @param age The age estimate for which depths are to be returned. Has to be a single age.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param its The set of MCMC iterations to be used. Defaults to the entire MCMC output, \code{its=set$output}.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param na.rm Whether or not to remove NA values (ages within slumps)
#' @author Maarten Blaauw, J. Andres Christen
#' @return Outputs all MCMC-derived depths for a given age.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' ages.d20 = Bacon.Age.d(20)
#' mean(ages.d20)
#' }
#' @export
Bacon.d.Age <- function(age, set=get("info"), BCAD=set$BCAD, its=set$output, na.rm=FALSE ){
if(BCAD)
age <- 1950 - age # if the customer decides to enter the age in BCAD
if(length(age) > 1)
stop("Bacon.d.Age can handle one age at a time only", call. = FALSE)
if(length(its) == 0 )
stop("core's data not yet in memory. Please run agedepth first\n", call. = FALSE)
# create elbow ages
elbows <- set$elbows
topages <- as.vector(its[,1]) # ages for the core top
accs <- as.matrix(its[,1+(1:set$K)]) # the accumulation rates xi for each section
cumaccs <- set$thick * cbind(0, t(apply(accs, 1, cumsum))) # cumulative accumulation
elbow.ages <- topages + cumaccs
if ( age <= min(elbow.ages) || age > max(elbow.ages) )
message(" Warning, age outside the core's age range!\n")
# prepare slump
hiatus.depths <- set$hiatus.depths
if(length(set$slump) > 0) {
diff.slumps <- apply(set$slump,1,diff,na.rm=T) # vector containing the difference of each slump
if ( !is.na(hiatus.depths[1]) )
hiatus.depths <- set$slumphiatus
}
# prepare hiatus
hiatus.check <- rep(0,ncol(elbow.ages)) # vector containing the information for each elbow whether there is a hiatus (1) or no hiatus (0)
if ( !is.na(hiatus.depths[1]) ){
# if there is no slump
if ( length(set$slump) == 0 )
hiatus.depths <- set$hiatus.depths
# where are the hiatuses
for ( i in 1:length(hiatus.depths) ) {
hiatus.check[ min(which(elbows > hiatus.depths[i])) ] <- 1
}
}
# intersections which are below the last elbow
these.bottom <- which( elbow.ages[, ncol(elbow.ages)] < age )
# summary of the depths corresponding to the chosen age
depths <- rep(NA,nrow(its))
for ( i in 2:ncol(elbow.ages) ){
# consideration of hiatuses
if ( hiatus.check[i] == 1 ){
for ( j in 1:length(hiatus.depths) ) {
above <- max(which(elbows < hiatus.depths[j]), 1)[1]
below <- above + 1
# two age ranges for one hiatus (below/above) with the adapted slopes (could be included in the info list)
ages.above <- set$elbow.above[,j] + (set$slope.above[,j] * (hiatus.depths[j] - elbows[above]))
ages.below <- set$elbow.below[,j] - (set$slope.below[,j] * (elbows[below] - hiatus.depths[j]))
# intersections below and above
these.above <- (elbow.ages[, above] < age) * (ages.above > age)
these.below <- (ages.below < age) * (elbow.ages[, below] > age)
# find the depths which correspond to the intersections below and above the hiatus
if ( sum(these.above, na.rm=T) > 0 ){
# slopes above hiatus
accs.above <- (1/set$slope.above[,j])[which(these.above==1)]
# age difference with the last age range above the hiatus
age.diff.above <- age - elbow.ages[which(these.above==1), above]
# depths: last depth above hiatus depth + slopes * age difference
depths[which(these.above==1)] <- elbows[above] + accs.above * age.diff.above
}
if ( sum(these.below, na.rm=T) > 0 ){
# slopes below hiatus
accs.below <- (1/set$slope.below[,j])[which(these.below==1)]
# age difference with the lower hiatus age range
age.diff.below <- age - ages.below[which(these.below==1)]
# depths: hiatus depth + slopes * age difference
depths[which(these.below==1)] <- hiatus.depths[j] + accs.below * age.diff.below
}
}
} else {
# consideration of the cases without hiatuses
# find the correct intersections
these <- (elbow.ages[, i - 1] < age) * (elbow.ages[, i] > age)
# find the depths which correspond to these intersections
if ( sum(these, na.rm=T) > 0 ){
# which slopes
accs <- 1/set$output[which(these == 1), i]
# difference between the age and the elbow ages found
age.diff <- age - elbow.ages[which(these == 1), i - 1]
# depths: elbow depth + slopes * age difference
depths[which(these==1)] <- elbows[i-1] + accs * age.diff
}
# find these intersections which are below the last elbow
if( length(these.bottom) > 0 & i == ncol(elbow.ages) ){
# slopes below last elbow
accs.bottom <- 1/set$output[these.bottom, i]
# difference between the age and the last elbow ages found
age.diff.bottom <- age - elbow.ages[these.bottom, i ]
# depth: last elbow + slopes * age difference
depths[these.bottom] <- elbows[i-1] + accs.bottom * age.diff.bottom
}
}
}
# Query: remove NA entries if some entries are not NA (happens for some hiatuses).
# In these cases the depth vector does not have the same length for different age.
# In cases where the age entered is younger than min(elbow.ages), each entry in depth is NA and is returned as such.
if( !all(is.na(depths)) & na.rm ) depths <- depths[!is.na(depths)]
# consideration of slumps
if ( length(set$slump) > 0 ) {
for( j in 1:nrow(set$slump) ){
# which depths are below the slump
these.below.slump <- (depths >= set$slump[j,1])
below.slump <- sum(these.below.slump, na.rm = T)
if ( below.slump > 0 ){
# shift the found depths with the slump depths above
these.shift <- which(these.below.slump==1)
depths[these.shift] <- depths[these.shift] + diff.slumps[j]
}
}
}
# output
return(depths)
}
# First get ages and slopes of c's just above and below hiatus.
# then calculate slope.below and slope.above as extrapolations from the sections below resp. above (option 1, default), no adapting of slopes (option 0),
# or as w-weighted mix of prior and accrates, resp. prior only (option 2).
# then check if these slopes work (no reversals). Those with reversals revert to the original slopes.
# check approach for boundaries. check that elbows in correct order, then set slopes to either ages.below or ages.above???
hiatus.slopes <- function(set=get('info'), hiatus.option=1) {
elbows <- set$elbows
hiatus.depths <- set$hiatus.depths
if(length(set$slump) > 0)
hiatus.depths <- set$slumphiatus
its <- cbind(set$output)
w <- its[,ncol(its)]^(1/set$thick)
fillvals <- array(NA, dim=c(nrow(its), length(hiatus.depths))) # 17 Apr 2020
# set$slope.below <- numeric(nrow(its)) # 17 Apr 2020
# set$slope.above <- numeric(nrow(its)) # 17 Apr 2020
set$slope.below <- fillvals # 17 Apr 2020
set$slope.above <- fillvals # 17 Apr 2020
set$elbow.below <- fillvals # 17 Apr 2020
set$elbow.above <- fillvals # 17 Apr 2020
set$above <- numeric(1)
topages <- as.vector(its[,1]) # ages for the core top
accs <- as.matrix(its[,1+(1:set$K)]) # the accumulation rates xi for each section
cumaccs <- set$thick * cbind(0, t(apply(accs, 1, cumsum))) # cumulative accumulation
elbow.ages <- topages + cumaccs
for(i in 1:length(hiatus.depths)) {
above <- max(which(elbows < hiatus.depths[i]), 1) ### is this the correct one?
elbow.below <- elbow.ages[,above+1]
elbow.above <- elbow.ages[,above]
orig.slope <- accs[,above]
if(hiatus.option == 0) { # then do nothing
slope.below <- orig.slope
slope.above <- orig.slope
}
if(hiatus.option == 1) { # then extrapolate slopes above/below section w hiatus
slope.below <- its[,above+2]
slope.above <- its[,above]
}
if(hiatus.option == 2) { # then w-weighted for below, and prior-only for above
slope.below <- w*set$output[,above+2] + (1-w)*set$acc.mean[i+1]
slope.above <- rep(set$acc.mean[i], nrow(its))
}
# now calculate the ages at the hiatus/boundary, coming from below and from above
ages.above <- elbow.above + (slope.above * (hiatus.depths[i] - elbows[above]))
ages.below <- elbow.below - (slope.below * (elbows[above+1] - hiatus.depths[i]))
if(!is.na(set$boundary[1])) { # then set the boundary's elbow at ages.below for both sections
if(length(set$slumpboundary) > 0)
boundary <- set$slumpboundary else
boundary <- set$boundary
ages.boundary <- elbow.below - (slope.below * (elbows[above+1] - set$boundary[i]))
slope.above <- (ages.boundary - elbow.above) / (set$boundary[i] - elbows[above])
slope.below <- (ages.below - ages.boundary) / (elbows[above+1] - set$boundary[i])
}
# for sections with reversals, use the original slopes
reversed <- c(which(elbow.above > ages.above),
which(ages.above > ages.below),
which(ages.below > elbow.below),
which(slope.below < 0), which(slope.above < 0))
if(length(reversed) > 0) {
slope.above[reversed] <- orig.slope[reversed]
slope.below[reversed] <- orig.slope[reversed]
}
# store the updated information
# set$elbow.below[[i]] <- elbow.below # commented Apr 2020
# set$elbow.above[[i]] <- elbow.above
# set$slope.below[[i]] <- slope.below
# set$slope.above[[i]] <- slope.above
set$elbow.below[,i] <- elbow.below # new April 2020
set$elbow.above[,i] <- elbow.above # new
set$slope.below[,i] <- slope.below # new
set$slope.above[,i] <- slope.above # new
set$above <- above
}
return(set)
}
#' @name Bacon.hist
#' @title Calculate age distributions of depths.
#' @description Calculate the distribution of age estimates of single or multiple depths.
#' @details Age estimates of specific depths can also be plotted.
#' @param d The depth or depths for which a histogram and age ranges should be provided. If multiple depths are given, then just the age ranges, median and means (no graphs) are provided for each depth.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param age.lab The labels for the calendar axis (default \code{age.lab="cal BP"} or \code{"BC/AD"} if \code{BCAD=TRUE}).
#' @param age.lim Minimum and maximum calendar age ranges, calculated automatically by default (\code{age.lim=c()}).
#' @param hist.lab The y-axis is labelled \code{ylab="Frequency"} by default.
#' @param calc.range Calculate ranges? Takes time so can be left out
#' @param hist.lim Limits of the y-axis.
#' @param draw Draw a plot or not. Defaults to \code{draw=TRUE}, however no plots are made if more than one depth \code{d} is provided.
#' If \code{draw=FALSE}, then the age ranges, median and mean are given for each depth (as four columns).
#' @param prob Age ranges are given as quantiles, e.g., 2.5\% and 97.5\% for the default of 95\% confidence limits (\code{prob=0.95})).
#' @param hist.col Colour of the histogram. Default grey, \code{hist.col=grey(0.5)}.
#' @param hist.border Colour of the histogram's outline. Default dark grey, \code{hist.border=grey(0.2)}.
#' @param range.col Colour of confidence ranges. Defaults to \code{range.col="blue"}.
#' @param med.col Colour of the median. Defaults to \code{med.col="green"}.
#' @param mean.col Colour of the mean. Defaults to \code{mn.col="red"}.
#' @param verbose Provide feedback on what is happening (default \code{verbose=TRUE}).
#' @param save.info A variable called `info' with relevant information about the run (e.g., core name, priors, settings, ages, output) can be saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., \code{myvar <- Bacon()}, followed by supplying the variable \code{myvar} in any subsequent commands.
#' @author Maarten Blaauw, J. Andres Christen
#' @return A local variable called `hists', and a plot with the histogram and the age ranges, median and mean, or just the age ranges, medians and means if more than one depth \code{d} is given.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' Bacon.hist(20)
#' Bacon.hist(20:30)
#' }
#' @export
Bacon.hist <- function(d, set=get('info'), BCAD=set$BCAD, age.lab=c(), age.lim=c(), hist.lab="Frequency", calc.range=TRUE, hist.lim=c(), draw=TRUE, prob=set$prob, hist.col=grey(0.5), hist.border=grey(.2), range.col="blue", med.col="green", mean.col="red", verbose=TRUE, save.info=FALSE) {
outfile <- paste0(set$prefix, ".out")
if(length(set$output) == 0 || length(set$Tr) == 0) {
set <- Bacon.AnaOut(outfile, set, MCMC.resample=FALSE)
if(save.info)
assign_to_global("set", set) # should that be 'info'?
}
hist3 <- function(d, BCAD) {
hsts <- list(); maxhist <- 0; minhist <- 1
pb <- txtProgressBar(min=0, max=max(1,length(d)-1), style = 3)
for(i in 1:length(d)) {
if(length(d) > 1) {
if(length(d) < 500) # progress bar slows things down much if i is large
setTxtProgressBar(pb, i) else
if(i %% 10 == 0)
setTxtProgressBar(pb, i)
}
ages <- Bacon.Age.d(d[i], set, BCAD=BCAD)
if(length(ages[!is.na(ages)]) > 0) { # added !is.na(ages) 21 April 21
hst <- density(ages)
th0 <- min(hst$x)
th1 <- max(hst$x)
maxhist <- max(maxhist, hst$y)
minhist <- min(minhist, max(hst$y))
n <- length(hst$x)
counts <- hst$y
ds <- d[i]
hsts <- append(hsts, pairlist(list(d=ds, th0=th0, th1=th1, n=n, counts=counts, max=maxhist, min=minhist)))
} else hsts$d[[i]] <- d[i]
}
return(hsts)
}
hists <- hist3(d, BCAD)
assign_to_global("hists", hists)
rng <- array(NA, dim=c(length(d), 4)) # R > 4.0 does not like to fill c() using loops
if(calc.range) {
rng <- Bacon.rng(d, set, BCAD, prob)
for(i in 1:length(d))
hists$rng[[i]] <- rng[i,]
}
if(length(d)==1)
if(draw==TRUE) {
hst <- hists[[1]]
if(length(age.lab) == 0)
age.lab <- ifelse(BCAD, "BC/AD", "cal yr BP")
if(length(age.lim) == 0)
age.lim <- c(hst$th0, hst$th1)
if(BCAD)
age.lim <- rev(age.lim)
if(length(hist.lim) == 0)
hist.lim <- c(0, 1.1*hst$max)
pol <- cbind(c(hst$th0, seq(hst$th0, hst$th1, length=hst$n), hst$th1), c(0, hst$counts, 0))
plot(0, type="n", xlim=age.lim, ylim=hist.lim, xlab=age.lab, ylab=hist.lab, yaxs="i")
polygon(pol, col=hist.col, border=hist.border)
segments(rng[,1], 0, rng[,2], 0, col=range.col, lwd=3)
points(rng[,3], 0, col=med.col, pch=20)
points(rng[,4], 0, col=mean.col, pch=20)
if(verbose) {
message("mean (", mean.col, "): ", round(rng[4],1), " ", age.lab,
", median (", med.col, "): ", round(rng[3],1), " ", age.lab, "\n")
message(100*prob, "% range (", range.col, "): ", round(rng[1],1), " to ", round(rng[2],1), " ", age.lab, "\n")
}
}
invisible(rng) # should this become invisible(hists)?
}
# to calculate age ranges
Bacon.rng <- function(d, set=get('info'), BCAD=set$BCAD, prob=set$prob) {
outfile <- paste0(set$prefix, ".out")
if(length(set$output) == 0 || length(set$Tr) == 0) {
set <- Bacon.AnaOut(outfile, set, MCMC.resample=FALSE)
assign_to_global("set", set) # MB Jan 2024; can this go?
}
if(length(d) > 1)
pb <- txtProgressBar(min=0, max=max(1, length(d)-1), style=3)
rng <- array(NA, dim=c(length(d), 4))
for(i in 1:length(d)) {
ages <- Bacon.Age.d(d[i], set, BCAD=BCAD)
ages <- ages[!is.na(ages)]
if(length(ages) > 0) {
rng[i,1:3] <- quantile(ages, c(((1-prob)/2), 1-((1-prob)/2), .5), na.rm=TRUE)
rng[i,4] <- mean(ages)
}
if(length(d) > 1) {
if(length(d) < 500) # progress bar slows things down when i is large
setTxtProgressBar(pb, i) else
if(i %% 10 == 0)
setTxtProgressBar(pb, i)
}
# if(length(d) > 1)
# setTxtProgressBar(pb, i)
}
#if(length(d) > 1)
# close(pb)
return(rng)
}
#' @name agemodel.it
#' @title Extract one age-model iteration
#' @description For one MCMC iteration (it), extract the corresponding age-depth model.
#' @param it The MCMC iteration of which the age-model should be calculated.
#' @param set Detailed information of the current run, stored within this session's memory as variable info.
#' @param BCAD The calendar scale of graphs and age output-files is in \code{cal BP} by default, but can be changed to BC/AD using \code{BCAD=TRUE}.
#' @param save.info If TRUE, a variable called `info' with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name.
#' @author Maarten Blaauw, J. Andres Christen
#' @return A variable with two columns - depth and the age-depth model of a single iteration.
#' @examples
#' \dontrun{
#' Bacon(run=FALSE, coredir=tempfile())
#' agedepth(age.res=50, d.res=50, d.by=10)
#' lines(agemodel.it(5), col="red")
#' }
#' @export
agemodel.it <- function(it, set=get('info'), BCAD=set$BCAD, save.info=FALSE) {
outfile <- paste0(set$prefix, ".out")
if(length(set$output) == 0 || length(set$Tr) == 0) {
set <- Bacon.AnaOut(outfile, set, MCMC.resample=FALSE)
if(save.info)
assign_to_global("info", set) # changed 'set' to 'info'
}
# does this function work in cores with slumps? also doesn't take into account hiatuses.
if(length(set$hiatus.depths) > 0)
age <- sort(c(set$d, set$hiatus.depths+.001, set$hiatus.depths))
age <- c()
for(i in 1:length(set$elbows))
age[i] <- Bacon.Age.d(set$elbows[i], set, BCAD=BCAD)[it]
cbind(set$elbows, age)
}
# calculate slumpfree depths
toslump <- function(d, slump, remove=FALSE) {
d <- sort(d)
slump <- matrix(sort(slump), ncol=2, byrow=TRUE)
slices <- c(0, slump[,2] - slump[,1])
dfree <- d
for(i in 1:nrow(slump)) {
inside <- which(d <= slump[i,2]) # find depths within slump, step 1
inside <- which(d[inside] >= slump[i,1]) # step 2
below <- which(d >= slump[i,2]) # adapt depths below slumps
if(length(below) > 0) # depths below slump
dfree[below] <- dfree[below] - slices[i+1]
if(length(inside) > 0) # depths within slump
if(min(d) < max(slump[i,]))
if(remove)
dfree[inside] <- NA else
dfree[inside] <- slump[i,1] - sum(slices[1:i])
}
return(dfree)
}
# calculate original depths. Needed?
fromslump <- function(d, slump) {
slump <- matrix(sort(slump), ncol=2, byrow=TRUE)
slices <- slump[,2] - slump[,1]
dorig <- d # original depths
for(i in 1:nrow(slump)) {
below <- which(d > min(slump[i,]))
if(length(below) > 0)
dorig[below] <- dorig[below] - slices[i]
}
return(dorig)
}
#' @name squeeze
#' @title Squeeze some depths of a core
#' @description Squeeze or compress depths below a boundary by a certain amount. Accompanies the stretch function; see the stretch function for code on running the accordion
#' @param d The depth(s) to be squeezed
#' @param boundary The depth below which depths should be squeezed
#' @param times The factor by which the depths should be squeezed
#' @author Maarten Blaauw
#' @return The squeezed depth(s)
#' @examples
#' squeeze(40,25,20)
#' @export
squeeze <- function(d, boundary, times) {
below <- which(d > boundary)
if(length(below) > 0)
d[below] <- boundary + (d[below]-boundary)/times
return(d)
}
#' @name stretch
#' @title Stretch some depths of a core
#' @description Stretch squeezed depths e.g., calculate the original depths of depths that were squeezed. Accompanies the squeeze function.
#' @param d The depth(s) to be stretched
#' @param boundary The depth below which depths should be stretched
#' @param times The factor by which the depths should be stretched
#' @author Maarten Blaauw
#' @return The stretched depth(s)
#' @examples
#' stretch(25.75,25,20)
#' \dontrun{
#' # To play the accordion, first squeeze an existing core.
#' # Let's squeeze the depths below 10 cm core depth 20 times:
#' Bacon("accordion", 1)
#' dets <- info$dets
#' dets[,4] <- squeeze(dets[,4], 10, 20)
#'
#' # make a new directory for the squeezed core, and place the dets file there:
#' dir.create("Bacon_runs/squeezed")
#' write.table(dets, "Bacon_runs/squeezed/squeezed.csv", row.names=FALSE, sep=",")
#'
#' # now run that squeezed core, adding a boundary (10cm) and adapting the acc.mean prior (20x):
#' Bacon("squeezed", 1, boundary=10, acc.mean=c(5, 20*5))
#' # finally, plot while stretching the depths onto the original scale:
#' agedepth(accordion=c(10,20))
#' }
#' @export
stretch <- function(d, boundary, times) {
below <- which(d > boundary)
if(length(below) > 0)
d[below] <- boundary + (d[below]-boundary)*times
return(d)
}
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