This directory contains the supplemental materials for the Schmidt, Mann and Rutherford 
comment on the McShane and Wyner (2010, AOAS) paper.

The code is turnkey if you have R installed:
http://www.r-project.org/
Some extra packages may be required: lars, rjags, coda, lattice etc.

EIV reconstructions are from Mann et al (2008):
http://www.meteo.psu.edu/~mann/supplements/MultiproxyMeans07/

Pseudo-proxies are from Mann et al (2006):
http://www.meteo.psu.edu/~mann/PseudoproxyJGR06/
(including later corrections).

All figures and analysis can be generated using 
R_master_file_SMR_response_to_MW.txt

Files:

*.pdf    Figures output by the code used in the paper

R_*      R code, called via the master file, or can be called independently
           Note, there are some dependencies, so calling must be in the right
           order              

actual_proxy_list    List of 59 proxies actually used in 1000 AD EIV reconstruction 
                       by Mann et al (2008)  

data_allproxy1209.R  Original data files from M&W (derived from Mann et al 08)
data_instfilled.R
data_instrument.R

grid_csm       Grid of modern temperature simulations from CSM 
grid_gkss      Grid of modern temperature simulations from GKSS
 
nh_csm         NH mean from the CSM simulation 
nh_gkss        NH mean from the GKSS simulation
 
csmproxynorm_104red    59/104 pseudo-proxies generated from the GKSS/CSM model
csmproxynorm_59red       simulations with red noise
gkssproxynorm_104red
gkssproxynorm_59red

csmnhrecon_104red_long_eiv   Results of the EIV hybrid/no-hybrid methods with 59/104
csmnhrecon_59red_long_eiv      pseudo-proxies drawn from the CSM model using a long
                               calibration interval  
csmnhrecon_104red_long_nohybrid_eiv  
csmnhrecon_59red_long_nohybrid_eiv

gkssnhrecon_104red_long_eiv  Results of the EIV hybrid/no-hybrid methods with 59/104
gkssnhrecon_59red_long_eiv     pseudo-proxies drawn from the GKSS model using a long
                               calibration interval
gkssnhrecon_104red_long_nohybrid_eiv
gkssnhrecon_59red_long_nohybrid_eiv

cru_nh_smooth   Lowpassed CRU NH temperatures
proxylow/       Directory containing lowpassed proxy arrays, stepwise every hundred years
                  proxylow9 corresponds to the frozen 1000AD network          

eiv_crunhgl_froz      EIV reconstruction of NH CRU data from Mann et al (2008), 
                        frozen 1000 AD network
eiv_crunhglno7_froz   EIV reconstruction of NH CRU, frozen 1000 AD network, 
                        no Tiljander proxies
eiv_crunhglno7_froz_20yrsmooth 
                      EIV reconstruction of NH CRU, frozen 1000 AD network, 
                        no Tiljander proxies, lowpass input data

bayesmodel/   Directory containing code and data associated with the MCMC 
                emulation in figs. 1b/c
  *.pdf       PDF figures generated by the R code
  R_*         Code called by R_master_file_SMR_response_to_MW.txt in above directory
  model*.bug  Specification of the MCMC model (using jags) for different numbers of PCs
  rjags_data_*.txt    Setup data for jags/MCMC calculations for different numbers of PCs
  bayes_recon_*.R     Output data from the jags code