Temporal density of 14C dating

Posted on February 14, 2019February 14, 2019 by Olivier | Posted in Code & Data, R

In this tutorial I illustrate the methods that have been used to reconstruct the curve of the temporal density of archeological dating around the Folly peat bog in Blarquez et al. (2018).

The approach is inspired by ‘clam’ package age-depth modeling (Blaauw, 2010). For each archeological dating, we will randomly pick one age according to its calibrated probability density (i.e., ages with a higher probability are more likely to be selected). We will then use a kernel density function to assess the temporal density of archeological dating. We will repeat this procedure 1000 times to assess the 95% confidence interval (CI) around the median trend in archeological sites dating during the Holocene.

In the original paper the archeological 14C dates came from the CARD database for sites that were located within a 200 km radius of Folly peat bog (Martindale et al., 2016), and wer completed with an additional set of 7 dates from an archeological site in Gatineau, which had yet to be included in the database (Archeotec, 2014). In this example we will simply simulate some 14C dating:

# rm(list=ls())
library(Bchron)
library(ggplot2)

## Generate a random list of 14C dating --------------------------------------------------
set.seed(12)
age_14C=round(runif(100, 40, 500))*10
age_sd=round(runif(100, 2, 7))*10

We then calibrate each date in the database using the IntCal13 calibration curve (Reimer et al., 2013):

## Calibrate these dates using Bchron ---------------------------------------------------

age=BchronCalibrate(ages=age_14C,
ageSds=age_sd,
calCurves=rep('intcal13',length(age_14C)))

Here we define a custom function that will be used to sample an age within each dates distribution. This sampling is done according to the probability density distribution of each age. This procedure is somewhat equivalent with clam and bacon sampling procedure.

## Sample one age with probability (equivalent to clam and ?bacon) -----------------------
## Use lapply to sample inside a list of ages

foo=function(x){
y=sample(x$ageGrid,1,prob=x$densities)
return(y)
}
# Test a single iteration
ragelist=lapply(age,foo)
dates=as.vector(unlist(ragelist));dates

Now we will run this sampling 1000 times and for each iteration we will reconstruct the density of calibrated ages using kernel density estimation with a bandwidth of 150 years. We will subsequently calculate the median density of ages and 95% confidence intervals.

n=length(age_14C) #number of events
age_=seq(100, 6000, 10); # adapt to your time frame

## Bootstrap --------------------------------------------------
nbboot=1000
fmat=matrix(nrow=length(age_),ncol=nbboot)

for(i in 1:nbboot){
ragelist=lapply(age,foo)
dates=as.vector(unlist(ragelist))
fmat[,i]=c(density(dates,
bw=150,kernel="gaussian",from=100,
to=6000, n=length(age_))$y*n)
cat(i," ")
}

alpha=0.05
CI=apply(fmat, 1, quantile, probs=c(alpha/2,0.5,1-(alpha/2)) )

Plot the temporal trends in the density of archeological dating (along with max intercepts for each date sensu Telford et al. (2004), for display purpose only):

## Plot --------------------------------------------------------
bar=function(x){
z=x$ageGrid[which.max(x$densities)]
return(z)
}
magelist=lapply(age,bar)
mdates=as.vector(unlist(magelist));
df2=data.frame(x=mdates,y =0)

df=data.frame(age=age_, t(CI))
ggplot()+
geom_ribbon(data=df,aes(x=age,ymax=X97.5.,ymin=X2.5.),fill="grey")+
geom_line(data=df,aes(x=age_,y=X50.))+
geom_point(data=df2,aes(x,y),pch="|",size=3)+
scale_x_reverse()+
ylab("Dating density")+xlab("Age cal. BP")+
theme_bw()

## --------------------------------------------------------------

Archéotec, 2014. Travaux de réaménagement de la rue Jacques-Cartier, ville de Gatineau Site BiFw-172,

Blaauw, M., 2010. Methods and code for “classical” age-modelling of radiocarbon sequences. Quaternary Geochronology, 5(5), pp.512–518. Available at: http://dx.doi.org/10.1016/j.quageo.2010.01.002.

Blarquez, O. et al., 2018. Late Holocene influence of societies on the fire regime in southern Québec temperate forests. Quaternary Science Reviews, 180, pp.63–74. Available at: http://linkinghub.elsevier.com/retrieve/pii/S0277379117307060 [Accessed December 15, 2017].

Martindale, A. et al., 2016. Canadian Archaeological Radiocarbon Database (CARD 2.1), accessed 15 September 2017. , 2004.

Reimer, P.J. et al., 2013. IntCal13 and Marine13 Radiocarbon Age Calibration Curves 0–50,000 Years cal BP. Radiocarbon, 55(04), pp.1869–1887. Available at: https://www.cambridge.org/core/product/identifier/S0033822200048864/type/journal_article.

Telford, R.J., Heegaard, E. & Birks, H.J.B., 2004. The intercept is a poor estimate of a calibrated radiocarbon age. The Holocene, 14(2), pp.296–298. Available at: http://journals.sagepub.com/doi/10.1191/0959683604hl707fa.

GCD 4.0.2 and paleofire 1.2.2

Posted on May 3, 2018August 2, 2018 by Olivier | Posted in Code & Data, R

We are please to announce that the GCD and paleofire R packages have been updated to their 4.0.2 and 1.2.2 versions, respectively. GCD major update from 3.X.X to 4.X.X version number is associated to extensive changes in the way data is added into the package. GCD 4.X.X is now mirroring the online GCD SQL database on a monthly basis or whenever a significant number of new charcoal sites are added to the database.

Three new fields in the paleofiresites table (see ?paleofiresites for details) enable to perform analyses with specific database versions or enable to select sites according to the date at which they have been added into the database. See the quick example below for explanations:

par(mfrow=c(2,2))
plot( pfSiteSel(num_version < 400 ) ) # All sites in GCD version before 4.0.0
plot( pfSiteSel(gcd_version == "GCD1" ) ) # All sites in GCDv1
plot( pfSiteSel(update_date < "2016-01-01" ) ) # Sites included before 2016-01-01
plot( pfSiteSel(update_date > "2018-01-01" ) ) # Sites included since 2018-01-01

The map above that is used to display all GCD charcoal sites has been produced by adapting the code available at https://seethedatablog.wordpress.com/2016/12/23/r-simple-world-map-robinson-ggplot/ please follow that link for additional references and explanations. The modified code is copied below:

# ======================================================================================
# Create a simple world map in Robinson projection with labeled graticules using ggplot
# ======================================================================================

# Set a working directory with setwd() or work with an RStudio project

# __________ Set libraries
library(rgdal) # for spTransform() & project()
library(ggplot2) # for ggplot()
library(paleofire) #

setwd("somewhere...")

# __________ Load ready to use data from GitHub
load(url("https://github.com/valentinitnelav/RandomScripts/blob/master/NaturalEarth.RData?raw=true"))
# This will load 6 objects:
# xbl.X & lbl.Y are two data.frames that contain labels for graticule lines
# They can be created with the code at this link:
# https://gist.github.com/valentinitnelav/8992f09b4c7e206d39d00e813d2bddb1
# NE_box is a SpatialPolygonsDataFrame object and represents a bounding box for Earth
# NE_countries is a SpatialPolygonsDataFrame object representing countries
# NE_graticules is a SpatialLinesDataFrame object that represents 10 dg latitude lines and 20 dg longitude lines
# (for creating graticules check also the graticule package or gridlines fun. from sp package)
# (or check this gist: https://gist.github.com/valentinitnelav/a7871128d58097e9d227f7a04e00134f)
# NE_places - SpatialPointsDataFrame with city and town points
# NOTE: data downloaded from http://www.naturalearthdata.com/
# here is a sample script how to download, unzip and read such shapefiles:
# https://gist.github.com/valentinitnelav/a415f3fbfd90f72ea06b5411fb16df16

# __________ Project from long-lat (unprojected data) to Robinson projection
# spTransform() is used for shapefiles and project() in the case of data frames
# for more PROJ.4 strings check the followings
# http://proj4.org/projections/index.html
# https://epsg.io/

PROJ <- "+proj=robin +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"
# or use the short form "+proj=robin"
NE_countries_rob <- spTransform(NE_countries, CRSobj = PROJ)
NE_graticules_rob <- spTransform(NE_graticules, CRSobj = PROJ)
NE_box_rob <- spTransform(NE_box, CRSobj = PROJ)

# Add lakes http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/physical/ne_10m_lakes.zip

download.file("http://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/physical/ne_10m_lakes.zip", destfile="ne_10m_lakes.zip")
unzip("ne_10m_lakes.zip")
NE_lakes <- readOGR('ne_10m_lakes.shp',
'ne_10m_lakes')
NE_lakes <- spTransform(NE_lakes, CRSobj = PROJ)
NE_lakes <- NE_lakes[NE_lakes@data$scalerank==0,]

# project long-lat coordinates for graticule label data frames
# (two extra columns with projected XY are created)
prj.coord <- project(cbind(lbl.Y$lon, lbl.Y$lat), proj=PROJ)
lbl.Y.prj <- cbind(prj.coord, lbl.Y)
names(lbl.Y.prj)[1:2] <- c("X.prj","Y.prj")

prj.coord <- project(cbind(lbl.X$lon, lbl.X$lat), proj=PROJ)
lbl.X.prj <- cbind(prj.coord, lbl.X)
names(lbl.X.prj)[1:2] <- c("X.prj","Y.prj")

# Project GCD sites

gcd_rob=project(cbind(paleofiresites$long,paleofiresites$lat),PROJ)
gcd=data.frame(long=gcd_rob[,1],lat=gcd_rob[,2],GCD_version=paleofiresites$gcd_version)

# __________ Plot layers
ggplot() +
# add Natural Earth countries projected to Robinson, give black border and fill with gray
geom_polygon(data=NE_box_rob, aes(x=long, y=lat), colour="black", fill="grey90", size = 0.25) +
geom_polygon(data=NE_countries_rob, aes(long,lat, group=group), colour="black", fill="white", size = 0.25) +
geom_polygon(data=NE_lakes, aes(long,lat, group=group), colour="black", fill="white", size = 0.25) +
# Note: "Regions defined for each Polygons" warning has to do with fortify transformation. Might get deprecated in future!
# alternatively, use use map_data(NE_countries) to transform to data frame and then use project() to change to desired projection.
# add Natural Earth box projected to Robinson
geom_polygon(data=NE_box_rob, aes(x=long, y=lat), colour="black", fill="transparent", size = 0.25) +
# add graticules projected to Robinson
geom_path(data=NE_graticules_rob, aes(long, lat, group=group), linetype="dotted", color="grey50", size = 0.25) +
# add graticule labels - latitude and longitude
geom_text(data = lbl.Y.prj, aes(x = X.prj, y = Y.prj, label = lbl), color="grey50", size=2) +
geom_text(data = lbl.X.prj, aes(x = X.prj, y = Y.prj, label = lbl), color="grey50", size=2) +
# the default, ratio = 1 in coord_fixed ensures that one unit on the x-axis is the same length as one unit on the y-axis
geom_point(data=gcd, aes(long,lat, col= GCD_version),pch=2)+
coord_fixed(ratio = 1) +
# remove the background and default gridlines
theme_void()+
theme(legend.title = element_text(colour="black", size=8, face="bold"), # adjust legend title
legend.position = c(0.1, 0.2), # relative position of legend
plot.margin = unit(c(t=0, r=0, b=0, l=0), unit="cm"),
legend.background = element_rect(fill="white",
size=0.5, linetype="solid",
colour ="black")) # adjust margins

# save to pdf and png file
ggsave("map_draft_1.pdf", width=28, height=13.5, units="cm")
ggsave("map_1.png", width=26, height=13.5, units="cm", dpi=300)

# REFERENCES:
# This link was useful for graticule idea
# http://stackoverflow.com/questions/38532070/how-to-add-lines-of-longitude-and-latitude-on-a-map-using-ggplot2
# Working with shapefiles, projections and world maps in ggplot
# http://rpsychologist.com/working-with-shapefiles-projections-and-world-maps-in-ggplot

ggplot2 pollen diagram (and dendrogram)

Posted on May 17, 2017May 26, 2017 by Olivier | Posted in Code & Data, R

In R, excellent packages provide ways to plot pollen or more generally stratigraphic diagrams. The two main tools come from the rioja package with “strat.plot” and the analogue package with “Stratiplot”. Althought those two functions are very comprehensive (you can include a dendrogram, pollen zones, etc.), easy to use, and highly customizable; I was still wondering if there is a way in R to plot a simple pollen diagram using only general plot syntax an preferably ggplot2. I came up with this simple solution that involve only ggplot2 syntax. Probably there is a possibility to add a dendrogram with grid.arrange and to overlay additionnal information but right now this approach seems sufficient to cover my very basic plotting needs:

library(ggplot2)
library(grid)
library(neotoma)
library(analogue)
## Loading required package: vegan
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.4-1
## analogue version 0.17-0

First extract data from Neotoma using neotoma package, we will have a look at “Le Grand Etang de Suze-La-Rousse” in Provençal Drome by: “Argant, J. 1990. Climat et environnement au Quaternaire dans le bassin du Rhône d’après les données palynologiques. Documents du Laboratoire de Géologie de Lyon 3:1-199.”

suze <- get_site(sitename = 'Le Grand Etang%')
suze_pollen=get_dataset(suze)
suze_data=get_download(suze_pollen)

# head(suze_data[[1]]$counts)

core.pct <- data.frame(tran(suze_data[[1]]$counts, method = 'percent'))

age <- suze_data[[1]]$sample.meta$age
core.pct <- chooseTaxa(core.pct, max.abun = 10) 

Stratiplot(age ~ ., core.pct, sort = 'wa', type = 'poly',
 ylab ='Years Before Present')
           

Now we create a simple data.frame with information for plotting a pollen diagram in ggplot2:

df=data.frame(yr=rep(age,ncol(core.pct)),
 per=as.vector(as.matrix(core.pct)),
 taxa=as.factor(rep(colnames(core.pct),each=nrow(core.pct))))

We define a theme without gridlines, etc. and elements that will decrease readability of the diagram

theme_new <- theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), # remove grids
 panel.background = element_blank(), axis.line = element_line(colour = "black"),
 strip.text.x = element_text(size=10, angle=90, vjust=0), # Taxa names 
 strip.background = element_blank(),
 strip.text.y = element_text(angle = 0),
 legend.position="none",panel.border = element_blank(),
 axis.text.x=element_text(angle=45,hjust=1)) # Axis tick label angle

And finally the pollen diagram:

ggplot(df)+
 geom_line(aes(yr,per))+
 geom_area(aes(yr,per))+
 scale_x_reverse(breaks =seq(0,100000,1000))+
 scale_y_continuous(breaks =seq(0,100,10))+
 xlab("Age (cal. BP)")+ylab("%")+
 coord_flip()+
 theme_new+
 facet_grid(~df$taxa,scales = "free", space = "free")

Add an exageration line (the quick and dirty way):

df$exag=df$per*10
id=unique(df$taxa)
for(i in 1:length(id)){
 uplim=which(df$exag[df$taxa==id[i]]>max(df$per[df$taxa==id[i]]))
 df$exag[df$taxa==id[i]][uplim]<-max(df$per[df$taxa==id[i]])
} 

diag=ggplot(df)+
 geom_line(aes(yr,per))+
 geom_area(aes(yr,exag,fill=taxa))+
 geom_area(aes(yr,per))+
 scale_x_reverse(breaks =seq(0,1e8,1000))+
 scale_y_continuous(breaks =seq(0,100,10))+
 xlab("Age (cal. BP)")+ylab("%")+
 coord_flip(xlim=c(3000,14000))+
 theme_new+
 facet_grid(~df$taxa,scales = "free", space = "free")

diag

 

Because only ggplot2 syntax is used you can play around and add geom_point, geom_bar layouts etc. and customize your diagram the way you want with the theme() function.

UPDATE: Adding a dendrogram is not straightforward but definitively doable. We will use a combinason of rioja and ggdendro package such as:

diss <- dist(sqrt(core.pct/100)^2)
clust <- chclust(diss, method="coniss")
# bstick(clust) # optionnally look at number of optimal zones

Now we will use ggdendro and modify its output in order to inject ages that will replace sample numbers:

dendro <- as.dendrogram(clust)
ddata <- dendro_data(dendro, type="rectangle")

## MOD the segment data frame for age instead of value order -----------------------
ddata$segments->yo
yo$xx=NA
yo$xxend=NA

for(i in 1:length(age)){
 yo$xx[which(yo$x == i)]=age[i]
 yo$xxend[which(yo$xend == i)]=age[i]
 da=age[i+1]-age[i]
 yo$xx[yo$x>i & yo$x<i+1]<-age[i]+(yo$x[yo$x>i & yo$x<i+1]-i)*da
 yo$xxend[yo$xend>i & yo$xend<i+1]<-age[i]+(yo$xend[yo$xend>i & yo$xend<i+1]-i)*da
} # Please dont ask....
ddata$segments$x<-yo$xx
ddata$segments$xend<-yo$xxend

# -----------------------------------------------------------------------------------

We finally can plot the dendrogram along with the diagram with gridExtra

dendro=ggplot(segment(ddata)) +
 geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) +
 coord_flip(xlim=c(3000,14000)) +
 ylab("Distance")+
 scale_x_reverse(breaks =seq(0,1e8,1000))+
 theme_new+theme(axis.title.y=element_blank(),
 axis.text.y=element_blank(),
 axis.ticks.y=element_blank(),
 axis.line.y = element_blank())


g1 = ggplotGrob(diag)
g2 = ggplotGrob(dendro)
g2$heights[5:7]<-g1$heights[6:8] # Important to align plots!
grid.arrange(g1, g2, widths =c(1,0.3),ncol=2,newpage = TRUE)

You can follow the overall logic to add any type of additional plot as long as its a ggplot2 object!