Bayesian Palaeoclimate Reconstruction from Pollen data with Bclim

Introduction

This vignette contains the code and associated descriptions to re-create the plots given in the Parnell et al submitted paper Joint palaeoclimate reconstruction from pollen data via forward models and climate histories. It is not meant to be a completed vignette, and it is not a complete instruction manual yet. If you spot bugs or mistakes please post to the GitHub repository. Some of the code below takes a long time to run, so you can shortcut the steps by downloading the resulting files from my website. The places where this is relevant are all given in the code below.

Installation

The stable version can be downloaded at the R command prompt with:

install.packages('Bclim')

The latest version, which usually contains extra bug fixes, or experimental functions which might not work well yet, is available via:

devtools::install_github('andrewcparnell/Bclim')

Note that for the above you need to have installed the devtools package.

If the installation has worked correctly no error should be returned upon typing:

library(Bclim)

Roya

To create the plots for Roya we first need to create a chronology using the Bchron package before we can run Bclim on it.

We run the Bchron step with:

library(Bchron)

# load in dates
Roya_dates = read.table(system.file("extdata", 
                                    "Roya.dat", 
                                    package = "Bclim"), 
                        header=TRUE)

# Load in the pollen depths
Roya_depths = read.table(system.file("extdata", 
                                     "Roya_pollen_depths.txt", 
                                     package = "Bclim"))

# Run Bchron
Roya_chron = with(Roya_dates,
                  Bchronology(ages=Age, 
                              ageSds=sd, 
                              positions=Depth, 
                              positionThickness=Thickness, 
                              id=id, 
                              predictPositions=Roya_depths$V1,
                              thin = 4))

We can check convergence with:

# Check convergence
summary(Roya_chron,type='convergence') # Good

## Convergence check (watch for too many small p-values): 
##           p-value
## Outlier 6 0.00514
## Outlier 2 0.02317
## Roya_1    0.03916
## Roya_2    0.05741
## Roya_6    0.09877
## RateVar   0.11563
## Roya_3    0.15197
## Roya_4    0.23676
## Outlier 5 0.25522
## Outlier 3 0.28771
## Outlier 1 0.32119
## RateMean  0.33938
## Outlier 4 0.34662
## Roya_5    0.47743

And plot the chronology with

# Plot
plot(Roya_chron,xlab='Age (cal BP)',ylab='Depth (cm)',main='Laguna de la Roya',las=1)

We can now run Bclim with:

# Load in the pollen data
Roya_pollen = read.table(system.file("extdata",
                                    "Roya_pollen.txt",
                                    package = "Bclim"),
                        header=TRUE)

# Extract the chronologies - Bclim requires them in thousands of years
Roya_chronologies = Roya_chron$thetaPredict/1000

# Run the single layer climate clouds
Roya_layers = layer_clouds(Roya_pollen)

# Run the climate histories function - 
Roya_histories = climate_histories(layer_clouds = Roya_layers,
                              chronology = Roya_chronologies,
                              time_grid = seq(0,16,by=0.1))

We can plot a single layer of the climate clouds:

# Plot a single layer cloud if required - plot layer 50
par(mar=c(3,3,2,1), mgp=c(2,.7,0), tck=-.01,las=1)
plot(Roya_histories$layer_clouds,layer=50, dims=2:3, main='Layer 50',xlab='MTCO',ylab='AET/PET',col=terrain.colors(30))

Plot the climate histories:

# Plot the climate histories
par(mar=c(3,3,2,1), mgp=c(2,.7,0), tck=-.01,las=1)
plot(Roya_histories, most_representative = 3, chron=Roya_chronologies,xlab='Age (k cal years BP)',ylab='GDD5',main='Roya GDD5')
legend('topleft',legend=c('Layer clouds','Climate ribbon','Representative histories'),pch=15,col=c('blue','red','green'))

plot(Roya_histories,dim=2,most_representative = 3,chron=Roya_chronologies,xlab='Age (k cal years BP)',ylab='MTCO',main='Roya MTCO')
legend('bottomleft',legend=c('Layer clouds','Climate ribbon','Representative histories'),pch=15,col=c('blue','red','green'))

par(mar=c(3,3,2,1), mgp=c(2,.7,0), tck=-.01,las=1)
plot(Roya_histories,dim=3,most_representative = 3, chron=Roya_chronologies,xlab='Age (k cal years BP)',ylab='AET/PET',main='Roya AET/PET')
legend('bottomleft',legend=c('Layer clouds','Climate ribbon','Representative histories'),pch=15,col=c('blue','red','green'))

We can summarise the histories with e.g. (results not shown)

# Summarise the histories if required
summary(Roya_histories,dim=3)

And finally create the plots of the first differences:

### Create the plot of first differences
# This might one day become a function in Bclim

# Somewhere to store the differences
diffs = vector('list',length=3)
clim_names = c('GDD5','MTCO','AET/PET')

# Loop through each climate dimension
for(i in 1:3) {
  diffs[[i]] = -apply(Roya_histories$histories[,,i],1,'diff')
}
diff_means = lapply(diffs,'rowMeans')
diff_sds = lapply(diffs,function(x) apply(x,1,'sd'))
diff_snr = lapply(mapply("/",diff_means,diff_sds,SIMPLIFY = FALSE),'abs')
df = data.frame(tg=rep(Roya_histories$time_grid[-1],3),
                diff_means=unlist(diff_means),
                diff_sds=unlist(diff_sds),
                SNR=unlist(diff_snr),
                clim_var=rep(clim_names,
                             each=length(Roya_histories$time_grid)-1))
df$clim_var = factor(df$clim_var,levels=clim_names,ordered=TRUE)

# Create the plot using ggplot2
library(ggplot2)
limits = aes(ymax = diff_means + diff_sds, ymin= diff_means - diff_sds)
p = ggplot(df,aes(x=tg,y=diff_means,colour=SNR)) + 
  geom_linerange(limits) + 
  geom_line(colour='black') +
  facet_grid(clim_var ~ .,scales='free_y')+ xlab('Age (k cal yrs BP)') + 
  ylab('First difference') + 
  ggtitle('Roya: centennial first difference means +/- 1 standard deviation') + 
  scale_x_continuous(breaks=seq(0,16,by=1))+theme_bw() + 
  geom_hline(aes(yintercept=0)) + 
  scale_colour_gradientn(colours=rev(heat.colors(3)))
print(p)