knitr::opts_chunk$set(fig.width = 8,fig.height = 6) knitr::opts_knit$set(progress = FALSE,verbose = FALSE)
Here, we replicate the analysis of Boldt et al. (2015), performing age-uncertain calibration-in-time on a chlorophyll reflectance record from northern Alaska, using geoChronR.
The challenge of age-uncertain calibration-in-time is that age uncertainty affects both the calibration model (the relation between the proxy data and instrumental data) and the reconstruction (the timing of events in the reconstruction). geoChronR simplifies handling these issues.
Let's start by loading the packages we'll need.
library(lipdR) #to read and write LiPD files library(geoChronR) #of course library(readr) #to load in the instrumental data we need library(ggplot2) #for plotting
OK, we'll begin by loading in the Kurupa Lake record from Boldt et al., 2015. The system.file(...)
part of this pulls the example file from the package directory. You'd like just enter the path as a string for typical use.
K <- lipdR::readLipd("http://lipdverse.org/geoChronR-examples/Kurupa.Boldt.2015.lpd")
sp <- plotSummary(K,paleo.data.var = "RABD",summary.font.size = 6) print(sp)
K <- runBacon(K, lab.id.var = 'labID', age.14c.var = 'age14C', age.14c.uncertainty.var = 'age14CUncertainty', age.var = 'age', age.uncertainty.var = 'ageUncertainty', depth.var = 'depth', reservoir.age.14c.var = NULL, reservoir.age.14c.uncertainty.var = NULL, rejected.ages.var = NULL, bacon.acc.mean = 10, bacon.thick = 7, ask = FALSE, bacon.dir = "~/Cores", suggest = FALSE, close.connection = FALSE)
plotChron(K,age.var = "ageEnsemble",dist.scale = 0.2)
This is to get ensemble age estimates for each depth in the paleoData measurement table
K <- mapAgeEnsembleToPaleoData(K,age.var = "ageEnsemble")
kae <- selectData(K,"ageEnsemble") rabd <- selectData(K,"RABD")
kurupa.instrumental <- readr::read_csv("http://lipdverse.org/geoChronR-examples/KurupaInstrumental.csv")
kae$units
yep, we need to convert the units from BP to AD
kae <- convertBP2AD(kae)
kyear <- list() kyear$values <- kurupa.instrumental[,1] kyear$variableName <- "year" kyear$units <- "AD" kinst <- list() kinst$values <- kurupa.instrumental[,2] kinst$variableName <- "Temperature" kinst$units <- "deg (C)"
corout <- corEns(kae,rabd,kyear,kinst,bin.step=2,percentiles = c(.05,.5,.95 ))
Note that here we use the "Effective-N" significance option as we mimic the Boldt et al. (2015) paper.
plotCorEns(corout,significance.option = "eff-n")
Mixed results. But encouraging enough to move forward.
OK, you've convinced yourself that you want to use RABD to model temperature back through time. We can do this simply (perhaps naively) with regession, and lets do it with age uncertainty, both in the building of the model, and the reconstructing
regout <- regressEns(time.x = kae, values.x = rabd, time.y =kyear, values.y =kinst, bin.step=3, gaussianize = FALSE, recon.bin.vec = seq(-4010,2010,by=20))
regPlots <- plotRegressEns(regout,alp = 0.01,font.size = 8)
This result is consistent with that produced by Boldt et al., (2015), and was much simpler to produce with geoChronR.
In the next vignette learn about spectral analysis in geoChronR.
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