diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..badfc42ed7c104ee8e9d8129564cee9ddb00db30 --- /dev/null +++ b/README.md @@ -0,0 +1,88 @@ +# PrimeSCale model + +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) + + +## 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. \ No newline at end of file