master.sh

#! /bin/bash
# SPDX-FileContributor: Kai Wirtz <kai.wirtz@hereon.de>
# SPDX-License-Identifier: GPL-3.0-or-later
# SPDX-FileCopyrightText: 2023-2024 Helmholtz-Zentrum hereon GmbH

# Last change Aug 26, 2024
# master bash script for the joint analysis of archaeological C14 and paleo-climate proxy data
# edit scdir='out/'; and 'addpath('~/tools/m_map');' in load_pars.m

# Prepare the R environment by installing all required packages
Rscript environment.r

#  reads C14_europe_*  saves eurogrid_*.bin
Rscript grid_growth.r
# on HPC: sbatch --array=1-64 slurm.sh

Rscript collect.r # loads bin/eurogrid_1-64, writes bin/eurodat_all
Rscript cluster.r # in parallel mode slumclust.sh
#  forms regions using an extended kmeans algorithm with optimized total number of clusters (for each RegionPatch)
#  saves clusti.mat

# region kriging on a grid  - based on cluster points
matlab -nodesktop -r "try; make_grid; catch; end; quit" > LogFile 2> ErrorLogFile

# calculates Summed Probability Density (SPD) and related growth (RGR) for each region and time slice
Rscript spd_growth.r  # reads clusti, writes AllPop for time slices
# using an array of methods and time slice:
#    sbatch --array=0-101 slurmspd.sh (for 6 SPD methods: 6*17=102, start with 0!)

# pooled method
Rscript spd_pooled.r #reads C14_europe0 (or C14_EA, C14_NIreland), writes AllPop_all

# -------------------------------------
# collect and plot RGR
# plot_RGR    : reads AllPop_i writes AllPop_tag_all avg_rgr_ (avg_rgr_all all major methods)  RGR_MethComp.png
# -------------------------------------
# process climate proxy data
# proxy_dtw   : applies DTW ; reads paleoclimate time-series from paleoclim/ ; writes dtwpca/dtwpca2*
# integrate and smooth most time-series
# collect_ts
matlab -nodesktop -r "try; plot_RGR; proxy_dtw; collect_ts; catch; end; quit" > LogFile 2> ErrorLogFile

#plot_varmap_slice %reads AllPop_i

Rscript glmloop.r #  runs GLM for boom/bust probability with 1-4 input variables

# plot time series
# reads target_ts_0; writes  target_ts_1
# combine climate and RGR
matlab -nodesktop -r "try; plot_RGR; overlap_ts; catch; end; quit" > LogFile 2> ErrorLogFile