Bclim (version 2.3.1)

BclimCompile: Compiles results from other Bclim stages

Description

This function is designed to compile results from other Bclim stages.

Usage

BclimCompile(Layers, Mixtures, MCMC, Interpolations, core.name = "Core")

Arguments

Layers

Output from the function BclimLayer

Mixtures

Output from the function BclimMixSer or BclimMixPar

MCMC

Output from the function BclimMCMC

Interpolations

Output from the function BclimInterp

core.name

A character string giving the name of the core

Value

• A list of class Bclim is returned with the following components:
• time.grid
  The time grid used for interpolation
• core.name
  The name of the core
• clim.interp
  The interpolated values of climate for the 3 climate dimensions
• vol.interp
  The interpolated volatilities for the 3 climate dimensions
• MDP
  The marginal data posteriors for each layer in the core
• ScMean
  The raw climate means (used for standardisation purposes)
• ScVar
  The raw climate variances (used for standardisation purposes)
• clim.dims
  The names of the different climate dimensions
• n
  The number of layers in the core
• m
  The number of climate dimensions (always 3)
• n.samp
  The number of samples created for the MDPs
• Chronsfile
  The location of the chronologies file
• nchron
  The number of chronologies
• chron.store
  The chronologies used for creating the posterior distributions of climate

Details

A Bclim run can be separated into 4 stages: 1 - Turning each individual pollen layer into climate marginal data posteriors, 2 - Approximating the marginal data posteriors as mixtures of Gaussians, 3 - Running an MCMC stage to estimate climates and climate volatilities, 4 - Interpolating the climates and volatilities onto a regular grid. This function takes the output from each of these functions and returns a Bclim list object that can be further manipulated.

References

See Arxiv paper at http://arxiv.org/abs/1206.5009.

See Also

The output here can be used as an input to plotBclim and plotBclimVol. For advanced use of Bclim, see the functions referenced at the top of this file.

Examples

# Set the working directory using setwd (not shown)

# Download and load in the response surfaces:
url1 <- 'http://mathsci.ucd.ie/~parnell_a/required.data3D.RData'
download.file(url1,'required_data3D.RData')

# and now the pollen
url2 <- 'http://mathsci.ucd.ie/~parnell_a/SlugganPollen.txt'
download.file(url2,'SlugganPollen.txt')

# and finally the chronologies
url3 <- 'http://mathsci.ucd.ie/~parnell_a/Sluggan_2chrons.txt'
download.file(url3,'Slugganchrons.txt')

# Create variables which state the locations of the pollen and chronologies
pollen.loc <- paste(getwd(),'/SlugganPollen.txt',sep='')
chron.loc <- paste(getwd(),'/Slugganchrons.txt',sep='')

# Load in the response surfaces
load('required.data3D.RData')

## note that all of these functions have further options you can change with
step1 <- BclimLayer(pollen.loc,required.data3D=required.data3D)
step2 <- BclimMixSer(step1) 
# See also the parallelised version BclimMixPar if you have doMC and foreach installed
step3 <- BclimMCMC(step2,chron.loc) 
# You should probably do some convergence checking after this step
step4 <- BclimInterp(step2,step3) 
results <- BclimCompile(step1,step2,step3,step4,core.name="Sluggan Moss")

# Create a plot of MTCO (dim=2)
plotBclim(results,dim=2)

# Create a volatility plot
plotBclimVol(results,dim=2)