MALAPP Age Depth Modeling and Pollen Diagrams
This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.
This document provides code used to build age depth models and pollen diagrams for sediment samples from the Malawi Ancient Lifeways and Peoples Project (MALAPP).
Load packages
library(rbacon)## Loading required package: IntCallibrary(rioja)## This is rioja 0.9-26AU8 age depth model
Bacon(core="AU8",d.min=0,d.max=146,accept.suggestions = TRUE,verbose=FALSE)## The run's files will be put in this folder: C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU8
## Reading C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU8/AU8_31.bacon
## Constant calibration curve.
## IntCal20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_intcal20.14C
## Marine20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_marine20.14C
## SHCal20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_shcal20.14C
## Added det: NA: 1794.0+-15742000.0 d=0 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69524: 1794.0+-32.0 d=11 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69523: 7759.0+-124.0 d=59 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69828: 9690.0+-51.0 d=74 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69522: 15742.0+-59.0 d=86 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: NA: 15742.0+-15742000000.0 d=146 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## BaconFixed: Bacon jumps model with fixed c's.
## K=31, H=0, dim=33, Seed=835158, Dc=5.000000, c(0)=0.000000, c(K)=155.000000
##
## twalk: 7260000 iterations to run, Thu Oct 20 11:44:13 2022
##
## twalk thinning: 1 out of every 165 accepted iterations will be saved in file C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU8/AU8_31.out
## twalk: Finished, 0.5% of moved pars per iteration (ratio 36801.030303/7260000). Output in file C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU8/AU8_31.out,
## Thu Oct 20 11:44:33 2022
##
## bacon: 177243 WarnBeyondLimits warnings:
## bacon: WARNING: calibration attempted beyond MinYr= -72.000000 or MaxYr= 1000000.000000
## bacon: burn in (initial iterations which will be removed): 33000
## Eso es to...eso es to...eso es to...eso es toooodo amigos!##
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|======================================================================| 100%# Note: Bacon requires user input to command line (typically "y" then enter).AU8 pollen depths and diagram
core<-rep("AU8",7)
pollenNo<-c("POL35","POL34","POL33","POL32","POL31","POL30","POL29")
depth<-c(11,45,59,74,86,110,146)
ageBP<-c()
ageMin<-c()
ageMax<-c()
for (i in depth){
ageBP<-append(ageBP,round(mean(Bacon.Age.d(i))))
ageMin<-append(ageMin,round(min(Bacon.Age.d(i))))
ageMax<-append(ageMax,round(max(Bacon.Age.d(i))))
}
AUG8data<-data.frame(core,pollenNo,depth,ageBP,ageMin,ageMax)
print(AUG8data)## core pollenNo depth ageBP ageMin ageMax
## 1 AU8 POL35 11 1654 1200 2290
## 2 AU8 POL34 45 6500 3816 9054
## 3 AU8 POL33 59 8578 7697 9798
## 4 AU8 POL32 74 10870 9325 11784
## 5 AU8 POL31 86 18931 17476 19571
## 6 AU8 POL30 110 23995 19866 33012
## 7 AU8 POL29 146 31277 22663 44397AU8 pollen diagram
AUG8pollen<-read.csv("Aug8Pollen.csv",stringsAsFactors = FALSE)
pollenData<-AUG8pollen[,6:ncol(AUG8pollen)]
cs<-colSums(pollenData)
pollenData2 <- pollenData[, which(cs > 5)]
#png("AU8pollen.png",width=6,height=3,units="in",res=600)
par(oma=c(4,4,3,4))
strat.plot(pollenData2,yvar=round(ageBP), y.tks=c(0,5000,10000,15000,20000,25000,30000,35000), y.rev=TRUE, plot.line=FALSE, plot.poly=TRUE, plot.bar=FALSE, col.poly="forestgreen", col.poly.line="white", lwd.poly=1, scale.percent=TRUE, xSpace=0.01, x.pc.lab=TRUE, x.pc.omit0=TRUE,cex.xlabel=0.4,cex.axis=0.5,cex.yaxis=0.5,ylabel = "Years BP",cex.ylabel=0.5,srt.xlabel=45,title="AU8",las=3,mgp=c(3,0.6,0))
#dev.off()AU7
AU7 age depth model
Bacon(core="AU7",d.min=0,d.max=77,accept.suggestions = TRUE,verbose=FALSE)## The run's files will be put in this folder: C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU7
## Reading C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU7/AU7_17.bacon
## Constant calibration curve.
## IntCal20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_intcal20.14C
## Marine20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_marine20.14C
## SHCal20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_shcal20.14C
## Added det: NA: 149.0+-2388000.0 d=0 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69829: 149.0+-29.0 d=15 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69526: 792.0+-27.0 d=32 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69527: 1233.0+-28.0 d=51 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69528: 927.0+-28.0 d=54 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69529: 2388.0+-37.0 d=77 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## BaconFixed: Bacon jumps model with fixed c's.
## K=17, H=0, dim=19, Seed=498469, Dc=5.000000, c(0)=0.000000, c(K)=85.000000
##
## twalk: 4180000 iterations to run, Thu Oct 20 11:44:43 2022
##
## twalk thinning: 1 out of every 95 accepted iterations will be saved in file C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU7/AU7_17.out
## twalk: Finished, 1.2% of moved pars per iteration (ratio 50876.894737/4180000). Output in file C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU7/AU7_17.out,
## Thu Oct 20 11:44:51 2022
##
## bacon: 179286 WarnBeyondLimits warnings:
## bacon: WARNING: calibration attempted beyond MinYr= -72.000000 or MaxYr= 1000000.000000
## bacon: burn in (initial iterations which will be removed): 19000
## Eso es to...eso es to...eso es to...eso es toooodo amigos!##
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|======================================================================| 100%# Note: Bacon requires user input to command line (typically "y" then enter).AU7 pollen depths
core<-rep("AU7",9)
pollenNo<-c("POL36","POL37","POL38","POL39","POL40","POL41","POL42","POL43","POL44")
depth<-c(6,15,26,32,42,51,54,66,77)
ageBP<-c()
ageMin<-c()
ageMax<-c()
for (i in depth){
ageBP<-append(ageBP,round(mean(Bacon.Age.d(i))))
ageMin<-append(ageMin,round(min(Bacon.Age.d(i))))
ageMax<-append(ageMax,round(max(Bacon.Age.d(i))))
}
AUG7data<-data.frame(core,pollenNo,depth,ageBP,ageMin,ageMax)
print(AUG7data)## core pollenNo depth ageBP ageMin ageMax
## 1 AU7 POL36 6 83 -64 372
## 2 AU7 POL37 15 207 -6 444
## 3 AU7 POL38 26 514 227 769
## 4 AU7 POL39 32 678 516 891
## 5 AU7 POL40 42 893 614 1230
## 6 AU7 POL41 51 1073 747 1338
## 7 AU7 POL42 54 1133 789 1552
## 8 AU7 POL43 66 1740 1088 2437
## 9 AU7 POL44 77 2355 1959 2740AU7 pollen diagram
AUG7pollen<-read.csv("Aug7Pollen.csv",stringsAsFactors = FALSE)
pollenData<-AUG7pollen[,6:ncol(AUG7pollen)]
cs<-colSums(pollenData)
pollenData2 <- pollenData[, which(cs > 5)]
#png("AU7pollen.png",width=6,height=3,units="in",res=600)
par(oma=c(4,4,3,4))
strat.plot(pollenData2,yvar=round(ageBP), y.tks=c(0,500,1000,1500,2000,2500), y.rev=TRUE, plot.line=FALSE, plot.poly=TRUE, plot.bar=FALSE, col.poly="forestgreen", col.poly.line="white", lwd.poly=1, scale.percent=TRUE, xSpace=0.01, x.pc.lab=TRUE, x.pc.omit0=TRUE,cex.xlabel=0.4,cex.axis=0.5,cex.yaxis=0.5,ylabel = "Years BP",cex.ylabel=0.5,srt.xlabel=45,title="AU7",las=3,mgp=c(3,0.6,0))
#dev.off()AU3
AU3 age depth model
Bacon(core="AU3",d.min=0,d.max=67,accept.suggestions = TRUE,verbose=FALSE)## The run's files will be put in this folder: C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU3
## Reading C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU3/AU3_15.bacon
## Constant calibration curve.
## IntCal20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_intcal20.14C
## Marine20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_marine20.14C
## SHCal20: Reading from file: C:\Users\bdav_\AppData\Local\R\win-library\4.2\IntCal\extdata/3Col_shcal20.14C
## Added det: NA: 49.0+-964000.0 d=0 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69826: 49.0+-29.0 d=14 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69825: 267.0+-29.0 d=19 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: Ua-69824: 964.0+-29.0 d=28 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## Added det: NA: 964.0+-964000000.0 d=67 ResCorr= 0.0+-0.0 a=3 b=4 cc=SHCal20
## BaconFixed: Bacon jumps model with fixed c's.
## K=15, H=0, dim=17, Seed=36335, Dc=5.000000, c(0)=0.000000, c(K)=75.000000
##
## twalk: 3740000 iterations to run, Thu Oct 20 11:45:00 2022
##
## twalk thinning: 1 out of every 85 accepted iterations will be saved in file C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU3/AU3_15.out
## twalk: Finished, 2.2% of moved pars per iteration (ratio 83925.588236/3740000). Output in file C:\Users\bdav_\Dropbox\Yale Paleo\AgeDepth\Cores/AU3/AU3_15.out,
## Thu Oct 20 11:45:06 2022
##
## bacon: 184809 WarnBeyondLimits warnings:
## bacon: WARNING: calibration attempted beyond MinYr= -96.000000 or MaxYr= 1000000.000000
## bacon: burn in (initial iterations which will be removed): 17000
## Eso es to...eso es to...eso es to...eso es toooodo amigos!##
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|======================================================================| 100%# Note: Bacon requires user input to command line (typically "y" then enter).AU3 pollen depths
core<-rep("AU3",9)
pollenNo<-c("POL11","POL10","POL9","POL8","POL12","POL13","POL16","POL14","POL15")
depth<-c(3,14,19,28,34,40,46,55,67)
ageBP<-c()
ageMin<-c()
ageMax<-c()
for (i in depth){
ageBP<-append(ageBP,round(mean(Bacon.Age.d(i))))
ageMin<-append(ageMin,round(min(Bacon.Age.d(i))))
ageMax<-append(ageMax,round(max(Bacon.Age.d(i))))
}
AUG3data<-data.frame(core,pollenNo,depth,ageBP,ageMin,ageMax)
print(AUG3data)## core pollenNo depth ageBP ageMin ageMax
## 1 AU3 POL11 3 15 -91 241
## 2 AU3 POL10 14 173 -54 393
## 3 AU3 POL9 19 295 -9 632
## 4 AU3 POL8 28 817 481 1058
## 5 AU3 POL12 34 1146 691 2660
## 6 AU3 POL13 40 1448 832 3339
## 7 AU3 POL16 46 1751 953 3708
## 8 AU3 POL14 55 2202 1127 5195
## 9 AU3 POL15 67 2805 1358 5817AU3 pollen diagram
AUG3pollen<-read.csv("Aug3Pollen.csv",stringsAsFactors = FALSE)
pollenData<-AUG3pollen[,6:ncol(AUG3pollen)]
pollenData[is.na(pollenData)] <- 0
cs<-colSums(pollenData)
pollenData2 <- pollenData[, which(cs > 5)]
#png("AU7pollen.png",width=6,height=3,units="in",res=600)
par(oma=c(4,4,3,4))
strat.plot(pollenData2,yvar=round(ageBP), y.tks=c(0,500,1000,1500,2000,2500), y.rev=TRUE, plot.line=FALSE, plot.poly=TRUE, plot.bar=FALSE, col.poly="forestgreen", col.poly.line="white", lwd.poly=1, scale.percent=TRUE, xSpace=0.01, x.pc.lab=TRUE, x.pc.omit0=TRUE,cex.xlabel=0.4,cex.axis=0.5,cex.yaxis=0.5,ylabel = "Years BP",cex.ylabel=0.5,srt.xlabel=45,title="AU3",las=3,mgp=c(3,0.6,0))
#dev.off()