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-PrimeSCale model code metadata and software requirements accompanying the publication
-
Keuper, Wild et al, 2020, Nature Geoscience:
Rhizosphere priming amplifies carbon loss from northern circumpolar permafrost soils

For software related communication, contact matti.kummu@aalto.fi


1. MATLAB requirements

This software is tested under MATLAB R2017b and MATLAB R2019b, but it should run under many other versions without changes.

The following toolboxes are used:
Distributed Computing Toolbox
Mapping Toolbox
Optimization Toolbox
Statistics Toolbox


2. Main scripts

PrimeSCale_model_input.m
metadata of the input data for the model, as well as scripts to transfer the vectorised spatial data to map format (with f_priming_back2map.m function script) as well as export those as GeoTIFF

PrimeSCale_model_v1_2020_06.m
model script itself, prepares data for a given scenario, runs the model function (f_priming_model_function.m) as well as collects the output. 

PrimeSCale_combine_composites_2020_06.m
combines the model output composites for all the ran scenarios. Provides also example scripts for plotting the resulting maps.


3. Input data

All input data is collected to a single .mat file:
v_PrimeSCale_input_data.mat
 (list and metadata of the files is provided in PrimeSCale_model_input.m)
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4. External open source software

4.1. ColorBrewer

The model uses ColorBrewer for producing color tables. MATLAB version of ColorBrewer
is available at the MathWorks File Exchange:
https://se.mathworks.com/matlabcentral/fileexchange/34087-cbrewer-colorbrewer-schemes-for-matlab

To expedite installation, the package is included with the software.
The ColorBrewer software is subject to the following copyright:

Copyright (c) 2015, Charles Robert
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
  list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
  this list of conditions and the following disclaimer in the documentation
  and/or other materials provided with the distribution
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Additionally, the ColorBrewer product includes color specifications 
and designs developed by Cynthia Brewer (http://colorbrewer.org/).

4.2. truncnormrnd function

The model uses truncnormrnd function by Chad Fulton.
https://github.com/ChadFulton/opw_forecast/blob/master/matlab/truncnormrnd.m

The code refers to a comp.soft-sys.matlab message by John D'Errico 
(see https://groups.google.com/forum/#!topic/comp.soft-sys.matlab/_WXo4FhVP4g) 
potentially as the original source. 

No copyright message was provided by either author. The function is provided 
as a part of the model source code.
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