# this file gives the overall sequence of R calculations for the figures used in the
# Schmidt, Mann and Rutherford comment on the McShane and Wyner (2010) paper.
# Code is adapted from McShane and Wyner (2010) along with input from 
# http://probabilitynotes.wordpress.com for the MCMC emulation.
# Please report any problems or errors to Gavin Schmidt <gschmidt@giss.nasa.gov>
# NOTE: THE FILE R_les_proxy.txt HAS BEEN CORRECTED (SEE FILE FOR DETAILS) (DEC 16 2010)

### Fig 1, (c.f. fig 14 in MW) and Figs. S1, S2

source("R_recon_orig.txt")
source("R_add_eiv+cru.txt")
yhat_orig_ann = yhat
yhat_orig_sm = yhat_sm
pc_sdev_orig = proxy_pc$sdev

tilj="no"
source("R_recon_correct_proxies_notilj.txt")
yhat_correct_ann = yhat
yhat_correct_sm = yhat_sm
pc_sdev_correct_notilj = proxy_pc$sdev

# plot fig 1a
pdffile="SMR_fig1a.pdf"
title1="Impact of proper proxy selection + no Tiljander"
yhat_orig = yhat_orig_sm 
yhat_correct = yhat_correct_sm 
source("R_SMR_fig1aS1.txt")

print("Fig 1a done...")

### plot fig S1 (as fig1a but this time including Tiljander proxies). 
tilj="yes"
source("R_recon_correct_proxies_notilj.txt")
yhat_correct2_ann = yhat
yhat_correct2_sm = yhat_sm
pc_sdev_correct = proxy_pc$sdev

pdffile="SMR_figS1.pdf"
title1="Impact of proper proxy selection (incl. Tiljander)" 
yhat_orig = yhat_orig_sm 
yhat_correct = yhat_correct2_sm 
source("R_SMR_fig1aS1.txt")

print("Fig S1 done...")

### plot fig S2 (as fig 1a but with annual data)
pdffile="SMR_figS2.pdf"
title1="Impact of proper proxy selection + no Tiljander"
yhat_orig = yhat_orig_ann
yhat_correct = yhat_correct_ann 
source("R_SMR_figS2.txt")

print("Fig S2 done...")

### plot fig S3 (impact of using lowpassed data and different calibration interval)

endyr=1980 
source("R_recon_lowpass.txt") 
yhat2=yhat 
ppc_out2=ppc_out 
endyr=1995
source("R_recon_lowpass.txt")

pdffile="SMR_figS3.pdf"
source("R_SMR_figS3.txt")

print("Fig S3 done...")

### plot fig S4 (log eigenvalue spectra for the proxy PC networks)
# needs previous calculated pc_sdev_* arrays
# CORRECTED VERSION (DEC 16 2010) SEE FILE FOR DETAILS
pdffile="SMR_figS4_corr.pdf"
source("R_les_proxy.txt")

print("Fig S4 done...")

### plots for fig 2: Two versions of pseudo proxy tests with two different models
# data for table S1 is also produced 
# pseudo_GKSS_59.pdf  and pseudo_CSM_59.pdf
# pseudo_GKSS_104.pdf  and pseudo_CSM_104.pdf

num=59        # 59 proxy network
src="GKSS"    # choice of simulation
source("R_pseudo.txt")
src="CSM"
source("R_pseudo.txt")

num=104       # 104 proxy network
src="GKSS"    # choice of simulation
source("R_pseudo.txt")
src="CSM"
source("R_pseudo.txt")

print("Fig 2 done...")

### plots for fig 1b/1c
# Use MCMC techniques to estimate errors in reconstructions using
# correct proxy selection and no Tiljander proxies, with OLS PC10 and OLS PC4
# Note that this is a stochastic calculation and exact reproducibilty from one
# run of jags to another is not expected.

# set up PCs and input data
numpc <- 10
source("bayesmodel/R_bayes_setup.txt")
source("bayesmodel/R_jags.txt")

# first plot
pdffile1="SMR_fig1b.pdf"
source("bayesmodel/R_SMR_fig1bc.txt")
source("bayesmodel/R_posterior_probs.txt")

# set up case for OLS PC4
numpc <- 4
source("bayesmodel/R_bayes_setup.txt")
source("bayesmodel/R_jags.txt")

# second plot
pdffile1="SMR_fig1c.pdf"
source("bayesmodel/R_SMR_fig1bc.txt")
source("bayesmodel/R_posterior_probs.txt")

print("Figs 1b/c done...")