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License, copyright and attributions updates

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# Finn Cereal Models
**Model for net blotch (Pyrenophora teres), tan spot (pyrenophora triciti-repentis), and stagonospora blotch (s. nodorum)**
This is a mechanistic model that can be used for three fungal diseases in cereals: the barley net
blotch caused by *Pyrenophora teres*, the wheat tan spot caused by *Pyrenophora triciti-repentis*,
and the wheat stagonospora blotch caused by *S. nodorum*.
All three diseases included in the model can be modeled similarly, but only one disease,
shown in the model title, is being modeled at a time.
The model is based on explicitly modeling the progress of diseases separately on each location.
The principal entities and phenomena used in the model are *the disease*, *the field*, *the cultivar*,
and *the weather*. The output of the model provides the farmer with information when the situation on
their field has been beneficial for disease development and thus there is an elevated risk of a disease
outbreak. Modeling each disease is based on the same, mechanistic modeling approach. However, as the optimal
circumstances for the progress of each disease are different, each disease needs to be modelled individually.
The model gives two types of results: the daily risk and the accumulated risk. Of these the accumulated risk
value is the one to keep an eye on. The accumulated risk tells how likely it is that the net blotch is going
to infect the crop; the higher the accumulated risk value the higher the likehood of infection.
**An accumulated risk value of 50 or more is a cause for concern.**
**An accumulated risk value of 100 or more is a cause for heightened concern.**
To set up the model, the following information is required:
* A weather data source, such as a weather station, integrated to the VIPS system
* The sowing date for the field in question
* The preceding crop on the field
* The tillage method used on the field
* The susceptibility of the crop on the field
As can be seen from the list, the model is field-specific, and therefore needs to be set up separately for
each field where the disease situation is being monitored.
## References and attributions
This model is based on and uses to a large extent code that was originally written in the context of research work published in
* Markus Stocker, Jussi Nikander, Hanna Huitu, Marja Jalli, Markku
Koistinen, Mauno Rönkkö, and Mikko Kolehmainen (2016). Representing
Situational Knowledge for Disease Outbreaks in Agriculture. Journal of
Agricultural Informatics, 7(2):29-39. https://doi.org/10.17700/jai.2016.7.2.290
* Markus Stocker (2015). Situation Awareness in Environmental
Monitoring. Doctoral Dissertation (PhD). Publications of the
University of Eastern Finland. Dissertations in Forestry and Natural
Sciences No 192, University of Eastern Finland. ISBN:
978-952-61-1907-6. http://urn.fi/URN:ISBN:978-952-61-1908-3
...@@ -93,9 +93,15 @@ public class FinnCerealModels extends I18nImpl implements Model { ...@@ -93,9 +93,15 @@ public class FinnCerealModels extends I18nImpl implements Model {
@Override @Override
public String getLicense() { public String getLicense() {
return "Copyright (c) 2016-2019 Natural Resources Institute Finland\n" + return "Copyright (c) 2016-2019 Natural Resources Institute Finland\n" +
"This file is part of the Finnish cereal models package." + "This program is free software: you can redistribute it and/or modify\n" +
"The Finnish cereal models package is free software: you can distribute and/or modify it\n" + " it under the terms of the GNU Affero General Public License as published by\n" +
"under the terms of the GNU Lesser General Public License (LGPL) version 3, or any later version."; " the Free Software Foundation, either version 3 of the License, or\n" +
" (at your option) any later version.\n" +
"\n" +
" This program is distributed in the hope that it will be useful,\n" +
" but WITHOUT ANY WARRANTY; without even the implied warranty of\n" +
" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n" +
" GNU Affero General Public License for more details.";
} }
@Override @Override
......
...@@ -37,6 +37,10 @@ import no.nibio.vips.model.ModelExcecutionException; ...@@ -37,6 +37,10 @@ import no.nibio.vips.model.ModelExcecutionException;
import no.nibio.vips.util.WeatherElements; import no.nibio.vips.util.WeatherElements;
import no.nibio.vips.util.test.WeatherDataFileReader; import no.nibio.vips.util.test.WeatherDataFileReader;
/**
*
* @author Jussi Nikander <jussi.nikander@aalto.fi>
*/
public class FinnCerealModelsTest { public class FinnCerealModelsTest {
private static boolean printOutput = true; private static boolean printOutput = true;
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; ...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: AccumulatedRisk
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
...@@ -15,18 +29,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; ...@@ -15,18 +29,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: BaseRisk
* </p>
* <p>
* Description: (A+B)*C
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: DailyRisk
* </p>
* <p>
* Description: (A+B)*C*D*E*F*G
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
...@@ -18,18 +32,7 @@ import com.fasterxml.jackson.databind.JsonNode; ...@@ -18,18 +32,7 @@ import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: DiseasePressureModel
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; ...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: DiseaseProgress
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; ...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: InfectionProbability
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: Measure
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title:
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: Risk
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; ...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: SporeDevelopment
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.JsonNode; ...@@ -16,18 +30,7 @@ import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title: SporeSpreading
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
/* /*
* Copyright (C) 2014 see CREDITS.txt * Copyright (c) 2018 LUKE <https://www.luke.fi>
* All rights reserved. *
* This file is part of FinnCerealModels.
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/ */
package fi.uef.envi.mtt.model.diseasepressure; package fi.uef.envi.mtt.model.diseasepressure;
/** /**
* <p> * Copyright (c) 2018 LUKE <https://www.luke.fi>
* Title:
* </p>
* <p>
* Description:
* </p>
* <p>
* Project:
* </p>
* <p>
* Copyright: Copyright (C) 2014
* </p>
* *
* @author Markus Stocker * @author Markus Stocker
*/ */
......
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