pyholos 0.0.1__py3-none-any.whl

pyholos/resources/holos/main_tables.py

@@ -0,0 +1,493 @@
+from pathlib import Path
+
+from pandas import DataFrame
+
+from pyholos.components.animals.common import AnimalType, BeddingMaterialType
+from pyholos.components.land_management.common import TillageType
+from pyholos.config import PathsHolosResources
+from pyholos.core_constants import CoreConstants
+from pyholos.soil import SoilFunctionalCategory
+
+
+class _HolosTable:
+    def __init__(
+            self,
+            name: str,
+            data: list | DataFrame,
+            path: Path
+    ):
+        self.name = name
+        self.data = data
+        self.path = path
+
+    def write_data_to_csv(
+            self,
+            comments: list[str] | str = None
+    ) -> None:
+        if comments is None:
+            comments = []
+        elif isinstance(comments, str):
+            comments = [comments]
+
+        comments.insert(0, f'This table was automatically generated using "{Path(__file__).name}"')
+
+        with self.path.open(mode='w', newline='') as f:
+            for comment in comments:
+                f.write(f'# {comment}\n')
+            f.write('#\n')
+
+            DataFrame.from_records(self.data).to_csv(f, sep=',', decimal='.', index=False)
+
+
+def set_table_16():
+    table_16 = _HolosTable(
+        name='Table_16_Livestock_Coefficients_BeefAndDairy_Cattle_Provider',
+        data=[
+            # Beef Cattle Data Sources :
+
+            # BaselineMaintenanceCoefficient = IPCC (2019, Table 10.4)
+            # GainCoefficient = IPCC (2019, Eq. 10.6)
+            # DefaultInitialWeight = Sheppard et al. (2015) , A.Alemu(pers.comm, 2022)
+            # DefaultFinalWeight = Sheppard et al. (2015) , A.Alemu(pers.comm, 2022)
+
+            dict(
+                AnimalType=AnimalType.beef_calf.value,
+                BaselineMaintenanceCoefficient=CoreConstants.NotApplicable,
+                GainCoefficient=CoreConstants.NotApplicable,
+                DefaultInitialWeight=39,
+                DefaultFinalWeight=260
+            ),
+            dict(
+                AnimalType=AnimalType.beef_cow_lactating.value,
+                BaselineMaintenanceCoefficient=0.386,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=610,
+                DefaultFinalWeight=610
+            ),
+            dict(
+                AnimalType=AnimalType.beef_cow_dry.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=610,
+                DefaultFinalWeight=610
+            ),
+            dict(
+                AnimalType=AnimalType.beef_bulls.value,
+                BaselineMaintenanceCoefficient=0.370,
+                GainCoefficient=1.2,
+                DefaultInitialWeight=900,
+                DefaultFinalWeight=900
+            ),
+            dict(
+                AnimalType=AnimalType.beef_backgrounder_steer.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=1,
+                DefaultInitialWeight=250,
+                DefaultFinalWeight=380
+            ),
+            # Aklilu says these two animal groups have the same values
+            dict(
+                AnimalType=AnimalType.beef_backgrounder_heifer.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=240,
+                DefaultFinalWeight=360
+            ),
+            dict(
+                AnimalType=AnimalType.beef_replacement_heifers.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=240,
+                DefaultFinalWeight=360
+            ),
+            dict(
+                AnimalType=AnimalType.beef_finishing_steer.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=1.0,
+                DefaultInitialWeight=310,
+                DefaultFinalWeight=610
+            ),
+            dict(
+                AnimalType=AnimalType.beef_finishing_heifer.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=300,
+                DefaultFinalWeight=580
+            ),
+
+            # """
+            # Dairy Cattle
+            # Footnote 1
+            # Dairy Cattle Data Sources :
+            # BaselineMaintenanceCoefficient = IPCC (2019, Table 10.4)
+            # GainCoefficient = IPCC (2019, Eq. 10.6)
+            # DefaultInitialWeight = Lactanet (2020)
+            # DefaultFinalWeight = Lactanet (2020)
+            # """
+
+            dict(
+                AnimalType=AnimalType.dairy_lactating_cow.value,
+                BaselineMaintenanceCoefficient=0.386,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=687,
+                DefaultFinalWeight=687
+            ),
+            dict(
+                AnimalType=AnimalType.dairy_dry_cow.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=687,
+                DefaultFinalWeight=687
+            ),
+            dict(
+                AnimalType=AnimalType.dairy_heifers.value,
+                BaselineMaintenanceCoefficient=0.322,
+                GainCoefficient=0.8,
+                DefaultInitialWeight=637,
+                DefaultFinalWeight=687
+            ),
+            dict(
+                AnimalType=AnimalType.dairy_bulls.value,
+                BaselineMaintenanceCoefficient=0.37,
+                GainCoefficient=1.2,
+                DefaultInitialWeight=1200,
+                DefaultFinalWeight=1200
+            ),
+            dict(
+                AnimalType=AnimalType.dairy_calves.value,
+                BaselineMaintenanceCoefficient=0,
+                GainCoefficient=0,
+                DefaultInitialWeight=45,
+                DefaultFinalWeight=127
+            )
+        ],
+        path=PathsHolosResources.Table_16_Livestock_Coefficients_BeefAndDairy_Cattle_Provider
+    )
+
+    table_16.write_data_to_csv(
+        comments=[
+            'Table 16. Livestock coefficients for beef cattle and dairy cattle.',
+            'source: https://github.com/holos-aafc/Holos/blob/396f1ab9bc7247e6d78766f9445c14d2eb7c0d9d/H.Core/Providers/Animals/Table_16_Livestock_Coefficients_BeefAndDairy_Cattle_Provider.cs#L13',
+            '',
+            'The value of "DefaultFinalWeight" was modified from 260 kg to 90 kg, according to the default values set in the GUI.'
+        ])
+
+
+def set_table_30():
+    """
+
+    Holos Source Code Footnotes:
+        Footnote 1: C, N and P composition values for straw (barley) and wood-chip bedding are averages of data recorded in 1998 and 1999 in Larney et al. (2008);
+                straw bedding application rates for beef cattle are from Chai et al. (2014), originally based on Larney et al. (2008) and Gilhespy et al. (2009)
+        *    Footnote 2: Wood-chip bedding is a mixture of sawdust and bark peelings derived from 80% lodgepole pine (Pinus contorta var. latifolia  Engelm.) and 20% white
+                spruce [Picea glauca (Moench)Voss].
+        *    Footnote 3: “Drylot” refers to milking parlours, yards and exercise lots.
+        *    Footnote 4: Values for bedding amounts are based on minimum values for recommended bedding per 450 kg animal weight from Lorimor et al. (2004, Table 13).
+                We assumed an average dairy cow weight of 687 kg (Lactanet, 2020) (sand for freestall barn: 15.9 kg/450 kg * 687 kg = 24.3 kg head-1 day-1;
+                shavings and sawdust for tie-stall barn: 1.4 kg/450 kg * 687 kg = 1.9 kg head-1 day-1) – due to a lack of available data, bedding application
+                rates for sand for freestall barns and shavings and sawdust for freestall barns were also applied to other dairy housing types. For swine, calculations
+                assumed an average weight for sows and boars of 198 kg (ECCC, 2022) (chopped straw: 1.8 kg/450 kg * 198 kg = 0.79 kg head-1 day-1;
+                long straw: 1.6 kg/450 kg * 198 kg = 0.7 kg head-1 day-1). For poultry we assumed an average weight of 0.9 kg for broilers, 1.8 kg for layers,
+                and 6.8 kg for turkeys (ECCC, 2022). For sawdust bedding this gave application rates of: broilers – 0.7 kg/450 kg * 0.9 kg =  = 0.0014 kg head-1 day-1;
+                for layers – 0.7 kg/450 kg * 1.8 kg = 0.0028 kg head-1 day-1; for turkeys – 0.7 kg/450 kg * 6.8 kg = 0.011 kg head-1 day-1.
+        *    Footnote 5: Dairy manure soilds separated from manure liquid using a screw press and composted and dried; also sometimes referred to as recycled manure solids,
+                dried manure solids, undigested feedstuffs or more commonly compost bedding (OMAFRA, 2015). Values from Misselbrook and Powell (2005, Table 1).
+        *    Footnote 6: Values for long and chopped straw follow Chai et al. (2016) and are originally from Rotz et al. (2013).
+        *    Footnote 7: Due to a lack of data, total C, total N, total P and C:N ratio values for wood-chip bedding from Larney et al. (2008) are used for wood shavings
+                and sawdust bedding for dairy cattle, sheep, swine and poultry.
+        *    Footnote 8: Bedding application rates for sheep were obtained from the Canadian Sheep Foundation (2021), and applied to all bedding options. The application
+                rate of 0.57 was calculated as the midpoint of the recommended 0.45-0.68 kg head-1 day-1 range provided.
+        *    Footnote 9: Following Chai et al. (2016), a total N content value of 0.0057 (derived from Larney et al., 2008) was used for chopped straw bedding for dairy
+                cattle; due to a lack of data, the total C, total N, total P and C:N ratio values for straw bedding from Larney et al. (2008) were applied to
+                long- and chopped-straw bedding for dairy cows, swine and poultry.
+        *    Footnote 10: Bedding options for sheep were identified from the Canadian Sheep Foundation (2021). Nutrient concentration values for straw and wood shavings
+                for beef cattle were used for sheep in a drylot/corral and barn.
+        *    Footnote 11: For Other livestock, straw was assumed to be the main bedding type and total C, total N, total P and C:N ratio values for straw bedding from
+                Larney et al. (2008) were applied. For llamas and alpacas and goats, the bedding application rate for sheep was used; for deer and elk, horses,
+                mules and bison, the bedding application rate for beef cattle (feedlot) was used as no data for these animals groups was available.
+        *   Footnote  12: Values for moisture content of bedding from Ferraz et al. (2020). The moisture content for straw is the mean of values for barley straw (9.8%)
+                and wheat straw (9.33%); the moisture content for sawdust is the value for dried sawdust.
+
+    """
+    table_30 = _HolosTable(
+        name='Table_30_Default_Bedding_Material_Composition_Provider',
+        data=[
+            # Beef
+            dict(
+                AnimalType=AnimalType.beef.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,  # Footnote 1
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5,
+                MoistureContent=9.57  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.beef.value,
+                BeddingMaterial=BeddingMaterialType.wood_chip.value,  # Footnotes 1, 2
+                TotalNitrogenKilogramsDryMatter=0.00185,
+                TotalCarbonKilogramsDryMatter=0.506,
+                TotalPhosphorusKilogramsDryMatter=0.000275,
+                CarbonToNitrogenRatio=329.5,
+                MoistureContent=12.82  # Footnote12
+            ),
+            # Dairy
+            dict(
+                AnimalType=AnimalType.dairy.value,
+                BeddingMaterial=BeddingMaterialType.sand.value,  # Footnote 4
+
+                # set all following values to 0 to mimic the behavior in cs code
+                TotalNitrogenKilogramsDryMatter=0,
+                TotalCarbonKilogramsDryMatter=0,
+                TotalPhosphorusKilogramsDryMatter=0,
+                CarbonToNitrogenRatio=0,
+                MoistureContent=0  # Footnote12
+            ),
+            dict(
+                AnimalType=AnimalType.dairy.value,
+                BeddingMaterial=BeddingMaterialType.separated_manure_solid.value,  # Footnote 5
+                TotalNitrogenKilogramsDryMatter=0.033,
+                TotalCarbonKilogramsDryMatter=0.395,
+                TotalPhosphorusKilogramsDryMatter=0,
+                CarbonToNitrogenRatio=12,
+                MoistureContent=0
+            ),
+            dict(
+                AnimalType=AnimalType.dairy.value,
+                BeddingMaterial=BeddingMaterialType.straw_long.value,  # Footnote 6
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5,
+                MoistureContent=9.57  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.dairy.value,
+                BeddingMaterial=BeddingMaterialType.straw_chopped.value,  # Footnote 6
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5,
+                MoistureContent=9.57  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.dairy.value,
+                BeddingMaterial=BeddingMaterialType.shavings.value,  # Footnotes 4, 7
+                TotalNitrogenKilogramsDryMatter=0.00185,
+                TotalCarbonKilogramsDryMatter=0.506,
+                TotalPhosphorusKilogramsDryMatter=0.000275,
+                CarbonToNitrogenRatio=329.5,
+                MoistureContent=10.09  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.dairy.value,
+                BeddingMaterial=BeddingMaterialType.sawdust.value,  # Footnotes 4, 7
+                TotalNitrogenKilogramsDryMatter=0.00185,
+                TotalCarbonKilogramsDryMatter=0.506,
+                TotalPhosphorusKilogramsDryMatter=0.000275,
+                CarbonToNitrogenRatio=329.5,
+                MoistureContent=10.99  # Footnote 12
+            ),
+            # Swine
+            dict(
+                AnimalType=AnimalType.swine.value,
+                BeddingMaterial=BeddingMaterialType.straw_long.value,  # Footnotes 4, 9
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5,
+                MoistureContent=9.57  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.swine.value,
+                BeddingMaterial=BeddingMaterialType.straw_chopped.value,  # Footnotes 4, 9
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5,
+                MoistureContent=9.57  # Footnote 12
+            ),
+            # Sheep
+            dict(
+                AnimalType=AnimalType.sheep.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,  # Footnote 7
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5,
+                MoistureContent=9.57  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.sheep.value,
+                BeddingMaterial=BeddingMaterialType.shavings.value,  # Footnote 7
+                TotalNitrogenKilogramsDryMatter=0.00185,
+                TotalCarbonKilogramsDryMatter=0.506,
+                TotalPhosphorusKilogramsDryMatter=0.000275,
+                CarbonToNitrogenRatio=329.5,
+                MoistureContent=10.09  # Footnote 12
+            ),
+            # Poultry
+            dict(
+                AnimalType=AnimalType.poultry.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,  # Footnote 9
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5,
+                MoistureContent=9.57  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.poultry.value,
+                BeddingMaterial=BeddingMaterialType.shavings.value,  # Footnote 9
+                TotalNitrogenKilogramsDryMatter=0.00185,
+                TotalCarbonKilogramsDryMatter=0.506,
+                TotalPhosphorusKilogramsDryMatter=0.000275,
+                CarbonToNitrogenRatio=329.5,
+                MoistureContent=10.09  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.poultry.value,
+                BeddingMaterial=BeddingMaterialType.sawdust.value,  # Footnotes 4, 7
+                TotalNitrogenKilogramsDryMatter=0.00185,
+                TotalCarbonKilogramsDryMatter=0.506,
+                TotalPhosphorusKilogramsDryMatter=0.000275,
+                CarbonToNitrogenRatio=329.5,
+                MoistureContent=10.99  # Footnote 12
+            ),
+            # Other Livestock
+            dict(
+                AnimalType=AnimalType.llamas.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.alpacas.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.deer.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.elk.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.goats.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.horses.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.mules.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            ),
+            dict(
+                AnimalType=AnimalType.bison.value,
+                BeddingMaterial=BeddingMaterialType.straw.value,
+                MoistureContent=9.57,
+                TotalNitrogenKilogramsDryMatter=0.0057,
+                TotalCarbonKilogramsDryMatter=0.447,
+                TotalPhosphorusKilogramsDryMatter=0.000635,
+                CarbonToNitrogenRatio=90.5  # Footnote 12
+            )
+        ],
+        path=PathsHolosResources.Table_30_Default_Bedding_Material_Composition_Provider)
+    table_30.write_data_to_csv(
+        comments=[
+            'Table 30. Default bedding application rates and composition of bedding materials for all livestock groups.',
+            'source: https://github.com/holos-aafc/Holos/blob/396f1ab9bc7247e6d78766f9445c14d2eb7c0d9d/H.Core/Providers/Animals/Table_30_Default_Bedding_Material_Composition_Provider.cs#L15'
+        ])
+    pass
+
+
+def set_tillage_factor_table():
+    table_tillage = _HolosTable(
+        name='Table_Tillage_Factor',
+        data=[
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.Brown,
+                TillageType=TillageType.Intensive,
+                TillageFactor=1),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.Brown,
+                TillageType=TillageType.Reduced,
+                TillageFactor=0.9),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.Brown,
+                TillageType=TillageType.NoTill,
+                TillageFactor=0.8),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.DarkBrown,
+                TillageType=TillageType.Intensive,
+                TillageFactor=1),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.DarkBrown,
+                TillageType=TillageType.Reduced,
+                TillageFactor=0.85),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.DarkBrown,
+                TillageType=TillageType.NoTill,
+                TillageFactor=0.7),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.Black,
+                TillageType=TillageType.Intensive,
+                TillageFactor=1),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.Black,
+                TillageType=TillageType.Reduced,
+                TillageFactor=0.8),
+            dict(
+                SoilFunctionalCategory=SoilFunctionalCategory.Black,
+                TillageType=TillageType.NoTill,
+                TillageFactor=0.6)
+
+        ],
+        path=PathsHolosResources.Table_Tillage_Factor)
+
+    table_tillage.write_data_to_csv(
+        comments=[
+            'Holos source code: https://github.com/holos-aafc/Holos/blob/e644d8e52446faefe3d7503565a723563bba61fe/H.Core/Calculators/Tillage/TillageFactorCalculator.cs#L27',
+        ])
+
+
+if __name__ == '__main__':
+    set_table_16()
+    set_table_30()
+    set_tillage_factor_table()