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Users

  • Getting started with pyrealm
    • Prerequisites
      • Using the command line
      • Installing prerequisites
    • Installing pyrealm
    • Running the worked examples
    • pyrealm developers
  • Using arrays in pyrealm
    • Array shapes
    • Xarray inputs
  • The P Model module
    • Shared components in the P Model module
      • Photosynthetic environment
        • Photorespiratory compensation point (\(\Gamma^*\))
        • Michaelis-Menten coefficient for photosynthesis (\(K_{mm}\))
        • Relative viscosity of water (\(\eta^*\))
        • Partial pressure of \(\ce{CO2}\) (\(c_a\))
        • Absorbed irradiation (\(I_{abs}\))
      • Optimal \(\chi\) and leaf \(\ce{CO2}\)
        • The prentice14 method
        • The c4 method
        • The c4_no_gamma method
        • The lavergne20_c3 and lavergne20_c4 methods
        • The rootzone stress methods
      • Quantum yield efficiency of photosynthesis
        • Temperature dependent \(\phi_0\)
        • Fixed \(\phi_0\)
        • Temperature and aridity effects on \(\phi_0\)
      • \(J_{max}\) limitation
      • Arrhenius scaling in the P Model
        • Scaling of \(V_{cmax}\) and \(J_{max}\)
        • Using different Arrhenius scaling
      • Soil moisture effects
        • Alternative approaches
        • The calculate_soilmstress_stocker() penalty factor
        • The calculate_soilmstress_mengoli() penalty factor
      • Extreme forcing values
        • Realistic input values
        • Temperature dependence of quantum yield efficiency
        • Photorespiratory compensation point (\(\Gamma^*\))
        • Michaelis-Menten coefficient for photosynthesis (\(K_{mm}\))
        • Relative viscosity of water (\(\eta^*\))
      • Using the Two Leaf, Two Stream model
        • Fitting big leaf models
        • Estimating solar elevation and irradiances
        • Assimilation under the two leaf, two stream model
    • The Standard P Model
      • Worked examples
        • Simple point estimate
        • 3D grid example
      • P Model predictions
        • Efficiency outputs
        • Productivity outputs
        • Scaling with absorbed irradiance
    • The subdaily P Model
      • Subdaily P Model calculations
        • Example dataset
        • Photosynthetic environment
        • Calculation of GPP using fast and slow responses
      • Estimating acclimation
        • The acclimation model
        • Estimating realised responses
        • Interpolation of realised values to subdaily timescales
      • Missing data in the subdaily model
        • Sources of missing data
      • Worked example of the Subdaily P Model
        • Instantaneous C3 and C4 P Models
        • Subdaily P Models
        • Time series predictions
        • Converting models
    • C3 / C4 Competition
      • Step 1: Proportional GPP advantage
      • Step 2: Convert GPP advantage to the fraction of C4 plants
      • Step 3: Account for shading by C3 trees
      • Step 4: Filtering cold areas and cropland
      • Predicted GPP and expected isotopic signatures
      • Worked example
        • Code
        • Figures
    • Isotopic discrimination
      • Calculation of values
  • The demography module
    • Plant Functional Types and Traits
      • Plant traits
      • Plant Functional Types
      • The Flora class
      • The StemTraits class
    • The T Model module
      • Stem allometry
      • Productivity allocation
    • The tree crown model
      • Crown traits
        • Canopy shape
        • Projected crown and leaf area
      • Calculating crown model traits in pyrealm
      • Crown calculations in pyrealm
        • Calculating crown profiles
        • Visualising crown profiles
        • Visualising crown and leaf projected areas
      • Plotting tools for crown shapes
    • Plant Communities
    • The canopy model
      • Vertically structured canopies
        • Community definition
        • Community projected crown area
        • Crown and canopy gap fractions
    • Light capture in the canopy
      • Light capture in a simple model
      • Light capture in a vertically structured canopy
        • Calculation of light transmission terms
      • Numerical examples of light capture calculation
        • Input data
        • Layer-wise simulation
        • Matrix approach
      • Implementation in pyrealm
        • Calculation of light capture for a community
  • The splash submodule
    • Example data
    • Running the splash model
      • Initialising a SplashModel
      • Estimating initial soil moisture
      • Calculating water balance
  • The phenology module
    • Estimating maximum annual \(f_{APAR}\)
      • Example calculations
        • Direct calculation from annual values
        • Calculation from a fitted PModel
    • Phenology
      • Phenology methods
        • The zhou method
        • The zhu method
      • Example calculations
        • Direct calculation for daily assimilation values
      • Calculation from a fitted PModel
        • Fortnightly data
        • Subdaily data
  • Package constants
    • Creating constant class instances
    • Exporting and reloading parameter sets
  • Hygrometric functions
    • Saturated vapour pressure
    • Vapour pressure to VPD
    • Relative humidity to VPD
    • Specific humidity to VPD
  • Water density and viscosity
    • Water density
    • Water viscosity
    • Effect on GPP predictions
  • Versions and migration
    • Migration from 1.0 to version 2.0
      • Renamed functions
      • Water viscosity and density
      • The PModelEnvironment class
      • The quantum yield of photosynthesis (\(\phi_0\))
      • Arrhenius scaling of \(J_{max}\) and \(V_{cmax}\)
      • Method choices in the Subdaily PModel
      • The Acclimation Model
      • Code comparison
      • Duplication of results from version 1.0
      • Supporting functions for the P Model
    • Changes Log

API

  • The constants module
    • C3C4Const
      • C3C4Const.adv_to_frac_k
      • C3C4Const.adv_to_frac_q
      • C3C4Const.c3_forest_closure_gpp
      • C3C4Const.gpp_to_tc_a
      • C3C4Const.gpp_to_tc_b
      • C3C4Const.gpp_to_tc_c
    • ConstantsClass
      • ConstantsClass.from_dict()
      • ConstantsClass.from_json()
      • ConstantsClass.to_dict()
      • ConstantsClass.to_json()
    • CoreConst
      • CoreConst.chen_ca
      • CoreConst.chen_cb
      • CoreConst.chen_ko
      • CoreConst.chen_po
      • CoreConst.day_seconds
      • CoreConst.density_jones_harris_kappa
      • CoreConst.density_jones_harris_rho
      • CoreConst.density_kell
      • CoreConst.equation_of_time_coef
      • CoreConst.fisher_dial_Po
      • CoreConst.fisher_dial_Vinf
      • CoreConst.fisher_dial_lambda
      • CoreConst.huber_H_i
      • CoreConst.huber_H_ij
      • CoreConst.huber_mu_ast
      • CoreConst.huber_rho_ast
      • CoreConst.huber_tk_ast
      • CoreConst.k_CtoK
      • CoreConst.k_Cw
      • CoreConst.k_G
      • CoreConst.k_L
      • CoreConst.k_Ma
      • CoreConst.k_Mv
      • CoreConst.k_Po
      • CoreConst.k_R
      • CoreConst.k_To
      • CoreConst.k_c_molmass
      • CoreConst.k_co
      • CoreConst.k_pir
      • CoreConst.k_w
      • CoreConst.k_water_molmass
      • CoreConst.magnus_coef
      • CoreConst.magnus_option
      • CoreConst.mwr
      • CoreConst.net_longwave_radiation_coef
      • CoreConst.shortwave_albedo
      • CoreConst.solar_constant
      • CoreConst.solar_eccentricity
      • CoreConst.solar_obliquity
      • CoreConst.solar_perihelion
      • CoreConst.swdown_to_ppfd_factor
      • CoreConst.transmissivity_coef
      • CoreConst.viscosity_daubert_danner
      • CoreConst.viscosity_girifalco
      • CoreConst.viscosity_reid
      • CoreConst.viscosity_viswanath_natarajan
      • CoreConst.viscosity_vogel
      • CoreConst.visible_light_albedo
      • CoreConst.water_density_method
      • CoreConst.water_viscosity_method
    • IsotopesConst
      • IsotopesConst.badeck_postfrac
      • IsotopesConst.farquhar_a
      • IsotopesConst.farquhar_b
      • IsotopesConst.farquhar_b2
      • IsotopesConst.farquhar_f
      • IsotopesConst.frank_postfrac
      • IsotopesConst.lavergne_delta13_a
      • IsotopesConst.lavergne_delta13_b
      • IsotopesConst.vonCaemmerer_b4
      • IsotopesConst.vonCaemmerer_phi
      • IsotopesConst.vonCaemmerer_s
    • PModelConst
      • PModelConst.arrhenius_jmax
      • PModelConst.arrhenius_vcmax
      • PModelConst.bernacchi_gs
      • PModelConst.bernacchi_kmm
      • PModelConst.beta_cost_ratio_c3
      • PModelConst.beta_cost_ratio_c4
      • PModelConst.heskel_rd
      • PModelConst.kphio_C3
      • PModelConst.kphio_C4
      • PModelConst.lavergne_2020_c3
      • PModelConst.lavergne_2020_c4
      • PModelConst.maximum_phi0
      • PModelConst.sandoval_kinetics
      • PModelConst.sandoval_peak_phio
      • PModelConst.smith19_coef
      • PModelConst.soilmstress_mengoli
      • PModelConst.soilmstress_stocker
      • PModelConst.tc_ref
      • PModelConst.tk_ref
      • PModelConst.wang17_c
    • PhenologyConst
      • PhenologyConst.calculate_f0()
      • PhenologyConst.f0_coefficients
      • PhenologyConst.k
      • PhenologyConst.sigma
      • PhenologyConst.z
    • TModelTraits
      • TModelTraits.a_hd
      • TModelTraits.ca_ratio
      • TModelTraits.h_max
      • TModelTraits.lai
      • TModelTraits.par_ext
      • TModelTraits.resp_f
      • TModelTraits.resp_r
      • TModelTraits.resp_s
      • TModelTraits.rho_s
      • TModelTraits.sla
      • TModelTraits.tau_f
      • TModelTraits.tau_r
      • TModelTraits.yld
      • TModelTraits.zeta
    • The ConstantsClass base class
      • ConstantsClass
        • ConstantsClass.from_dict()
        • ConstantsClass.from_json()
        • ConstantsClass.to_dict()
        • ConstantsClass.to_json()
    • Core constants
      • CoreConst
        • CoreConst.chen_ca
        • CoreConst.chen_cb
        • CoreConst.chen_ko
        • CoreConst.chen_po
        • CoreConst.day_seconds
        • CoreConst.density_jones_harris_kappa
        • CoreConst.density_jones_harris_rho
        • CoreConst.density_kell
        • CoreConst.equation_of_time_coef
        • CoreConst.fisher_dial_Po
        • CoreConst.fisher_dial_Vinf
        • CoreConst.fisher_dial_lambda
        • CoreConst.huber_H_i
        • CoreConst.huber_H_ij
        • CoreConst.huber_mu_ast
        • CoreConst.huber_rho_ast
        • CoreConst.huber_tk_ast
        • CoreConst.k_CtoK
        • CoreConst.k_Cw
        • CoreConst.k_G
        • CoreConst.k_L
        • CoreConst.k_Ma
        • CoreConst.k_Mv
        • CoreConst.k_Po
        • CoreConst.k_R
        • CoreConst.k_To
        • CoreConst.k_c_molmass
        • CoreConst.k_co
        • CoreConst.k_pir
        • CoreConst.k_w
        • CoreConst.k_water_molmass
        • CoreConst.magnus_coef
        • CoreConst.magnus_option
        • CoreConst.mwr
        • CoreConst.net_longwave_radiation_coef
        • CoreConst.shortwave_albedo
        • CoreConst.solar_constant
        • CoreConst.solar_eccentricity
        • CoreConst.solar_obliquity
        • CoreConst.solar_perihelion
        • CoreConst.swdown_to_ppfd_factor
        • CoreConst.transmissivity_coef
        • CoreConst.viscosity_daubert_danner
        • CoreConst.viscosity_girifalco
        • CoreConst.viscosity_reid
        • CoreConst.viscosity_viswanath_natarajan
        • CoreConst.viscosity_vogel
        • CoreConst.visible_light_albedo
        • CoreConst.water_density_method
        • CoreConst.water_viscosity_method
    • P Model constants
      • PModelConst
        • PModelConst.arrhenius_jmax
        • PModelConst.arrhenius_vcmax
        • PModelConst.bernacchi_gs
        • PModelConst.bernacchi_kmm
        • PModelConst.beta_cost_ratio_c3
        • PModelConst.beta_cost_ratio_c4
        • PModelConst.heskel_rd
        • PModelConst.kphio_C3
        • PModelConst.kphio_C4
        • PModelConst.lavergne_2020_c3
        • PModelConst.lavergne_2020_c4
        • PModelConst.maximum_phi0
        • PModelConst.sandoval_kinetics
        • PModelConst.sandoval_peak_phio
        • PModelConst.smith19_coef
        • PModelConst.soilmstress_mengoli
        • PModelConst.soilmstress_stocker
        • PModelConst.tc_ref
        • PModelConst.tk_ref
        • PModelConst.wang17_c
    • T Model traits
      • TModelTraits
        • TModelTraits.a_hd
        • TModelTraits.ca_ratio
        • TModelTraits.h_max
        • TModelTraits.lai
        • TModelTraits.par_ext
        • TModelTraits.resp_f
        • TModelTraits.resp_r
        • TModelTraits.resp_s
        • TModelTraits.rho_s
        • TModelTraits.sla
        • TModelTraits.tau_f
        • TModelTraits.tau_r
        • TModelTraits.yld
        • TModelTraits.zeta
    • Isotopic discrimination constants
      • IsotopesConst
        • IsotopesConst.badeck_postfrac
        • IsotopesConst.farquhar_a
        • IsotopesConst.farquhar_b
        • IsotopesConst.farquhar_b2
        • IsotopesConst.farquhar_f
        • IsotopesConst.frank_postfrac
        • IsotopesConst.lavergne_delta13_a
        • IsotopesConst.lavergne_delta13_b
        • IsotopesConst.vonCaemmerer_b4
        • IsotopesConst.vonCaemmerer_phi
        • IsotopesConst.vonCaemmerer_s
    • C3/C4 competition constants
      • C3C4Const
        • C3C4Const.adv_to_frac_k
        • C3C4Const.adv_to_frac_q
        • C3C4Const.c3_forest_closure_gpp
        • C3C4Const.gpp_to_tc_a
        • C3C4Const.gpp_to_tc_b
        • C3C4Const.gpp_to_tc_c
    • Two leaf model constants
      • TwoLeafConst
        • TwoLeafConst.atmos_transmission_par
        • TwoLeafConst.atmospheric_scattering_coef
        • TwoLeafConst.diffuse_extinction_coef
        • TwoLeafConst.diffuse_reflectance
        • TwoLeafConst.direct_beam_extinction_numerator
        • TwoLeafConst.horizontal_leaf_reflectance
        • TwoLeafConst.jmax25_wullschleger_coef
        • TwoLeafConst.leaf_scattering_coef
        • TwoLeafConst.scattered_beam_extinction_numerator
        • TwoLeafConst.solar_obscurity_angle
        • TwoLeafConst.vcmax_lloyd_coef
    • Phenology constants
      • PhenologyConst
        • PhenologyConst.calculate_f0()
        • PhenologyConst.f0_coefficients
        • PhenologyConst.k
        • PhenologyConst.sigma
        • PhenologyConst.z
      • PhenologyConstNew
        • PhenologyConstNew.cai_f0_coefficients
        • PhenologyConstNew.cai_sigma
        • PhenologyConstNew.cai_z
        • PhenologyConstNew.k
        • PhenologyConstNew.zhou_alpha
        • PhenologyConstNew.zhu_A0_quantile
        • PhenologyConstNew.zhu_budyko
        • PhenologyConstNew.zhu_f0
        • PhenologyConstNew.zhu_lagcoef
        • PhenologyConstNew.zhu_lagmax
        • PhenologyConstNew.zhu_min_a0
        • PhenologyConstNew.zhu_z
  • The core module
    • The bounds submodule
      • Bounds
        • Bounds.interval_type
        • Bounds.lower
        • Bounds.unit
        • Bounds.upper
        • Bounds.var_name
      • BoundsChecker
        • BoundsChecker.check()
        • BoundsChecker.update()
    • The calendar submodule
      • Calendar
        • Calendar.dates
        • Calendar.days_in_year
        • Calendar.julian_day
        • Calendar.year
      • CalendarDay
        • CalendarDay.date
        • CalendarDay.days_in_year
        • CalendarDay.julian_day
        • CalendarDay.year
    • The datasets submodule
      • _populate_pooch_registry()
      • get_pyrealm_data()
      • DATASETS
    • The hygro submodule
      • calculate_enthalpy_vaporisation()
      • calculate_psychrometric_constant()
      • calculate_saturation_vapour_pressure_slope()
      • calculate_specific_heat()
      • calculate_vp_sat()
      • convert_rh_to_vpd()
      • convert_sh_to_vp()
      • convert_sh_to_vpd()
      • convert_vp_to_vpd()
    • The pressure submodule
      • calculate_patm()
    • The solar submodule
      • SolarPositions
        • SolarPositions.get_local_standard_meridian()
        • SolarPositions.core_const
        • SolarPositions.datetime
        • SolarPositions.day_angle
        • SolarPositions.decimal_time
        • SolarPositions.declination
        • SolarPositions.equation_of_time
        • SolarPositions.hour_angle
        • SolarPositions.latitude
        • SolarPositions.latitude_rad
        • SolarPositions.local_standard_meridian
        • SolarPositions.longitude
        • SolarPositions.longitude_rad
        • SolarPositions.ordinal_date
        • SolarPositions.solar_elevation
        • SolarPositions.solar_noon
      • calculate_daily_solar_radiation()
      • calculate_day_angle()
      • calculate_daytime_net_radiation()
      • calculate_distance_factor()
      • calculate_equation_of_time()
      • calculate_heliocentric_longitudes()
      • calculate_local_hour_angle()
      • calculate_net_longwave_radiation()
      • calculate_net_radiation_crossover_hour_angle()
      • calculate_nighttime_net_radiation()
      • calculate_ppfd()
      • calculate_ppfd_from_tau_rd()
      • calculate_ru_rv_intermediates()
      • calculate_rw_intermediate()
      • calculate_solar_declination()
      • calculate_solar_declination_angle()
      • calculate_solar_elevation()
      • calculate_solar_noon()
      • calculate_sunset_hour_angle()
      • calculate_transmissivity()
    • The time_series submodule
      • AnnualValueCalculator
        • AnnualValueCalculator.get_annual_means()
        • AnnualValueCalculator.get_annual_totals()
        • AnnualValueCalculator.datetimes
        • AnnualValueCalculator.duration_seconds
        • AnnualValueCalculator.duration_weights
        • AnnualValueCalculator.endpoint
        • AnnualValueCalculator.fractional_weights
        • AnnualValueCalculator.indexing
        • AnnualValueCalculator.n_obs
        • AnnualValueCalculator.shape
        • AnnualValueCalculator.subset_mask
        • AnnualValueCalculator.subset_mask_by_year
        • AnnualValueCalculator.year_completeness
        • AnnualValueCalculator.year_n_days
        • AnnualValueCalculator.year_n_growing_days
        • AnnualValueCalculator.year_total_seconds
        • AnnualValueCalculator.years
      • broadcast_time()
    • The utilities submodule
      • check_input_shapes()
      • evaluate_horner_polynomial()
      • exponential_moving_average()
      • summarize_attrs()
    • The water submodule
      • calculate_density_h2o()
      • calculate_density_h2o_chen()
      • calculate_density_h2o_fisher()
      • calculate_density_h2o_jones_harris_eq6()
      • calculate_density_h2o_jones_harris_eq8()
      • calculate_density_h2o_kell()
      • calculate_viscosity_h2o()
      • calculate_viscosity_h2o_daubert_danner()
      • calculate_viscosity_h2o_girifalco()
      • calculate_viscosity_h2o_huber()
      • calculate_viscosity_h2o_reid()
      • calculate_viscosity_h2o_viswanath_natarajan()
      • calculate_viscosity_h2o_vogel()
      • calculate_water_molar_volume()
      • convert_water_mm_to_moles()
      • convert_water_moles_to_mm()
      • register_density_method()
      • register_viscosity_method()
      • DENSITY_FUNCTION_SIGNATURE
      • DENSITY_METHODS
      • VISCOSITY_FUNCTION_SIGNATURE
      • VISCOSITY_METHODS
    • The xarray submodule
      • get_common_dims()
      • is_arraytype()
      • xarray_inputs()
      • ArrayType
  • The demography module
    • The core module
      • CohortMethods
        • CohortMethods.add_cohort_data()
        • CohortMethods.drop_cohort_data()
      • PandasExporter
        • PandasExporter.to_pandas()
    • The flora module
      • Flora
        • Flora.from_csv()
        • Flora.from_json()
        • Flora.from_toml()
        • Flora.get_stem_traits()
        • Flora.a_hd
        • Flora.ca_ratio
        • Flora.f_g
        • Flora.gpp_topslice
        • Flora.h_max
        • Flora.lai
        • Flora.m
        • Flora.n
        • Flora.n_pfts
        • Flora.name
        • Flora.p_foliage_for_reproductive_tissue
        • Flora.par_ext
        • Flora.pft_dict
        • Flora.pft_indices
        • Flora.pfts
        • Flora.q_m
        • Flora.resp_f
        • Flora.resp_r
        • Flora.resp_rt
        • Flora.resp_s
        • Flora.rho_s
        • Flora.sla
        • Flora.tau_f
        • Flora.tau_r
        • Flora.tau_rt
        • Flora.yld
        • Flora.z_max_prop
        • Flora.zeta
      • PlantFunctionalType
        • PlantFunctionalType.a_hd
        • PlantFunctionalType.ca_ratio
        • PlantFunctionalType.f_g
        • PlantFunctionalType.gpp_topslice
        • PlantFunctionalType.h_max
        • PlantFunctionalType.lai
        • PlantFunctionalType.m
        • PlantFunctionalType.n
        • PlantFunctionalType.name
        • PlantFunctionalType.p_foliage_for_reproductive_tissue
        • PlantFunctionalType.par_ext
        • PlantFunctionalType.q_m
        • PlantFunctionalType.resp_f
        • PlantFunctionalType.resp_r
        • PlantFunctionalType.resp_rt
        • PlantFunctionalType.resp_s
        • PlantFunctionalType.rho_s
        • PlantFunctionalType.sla
        • PlantFunctionalType.tau_f
        • PlantFunctionalType.tau_r
        • PlantFunctionalType.tau_rt
        • PlantFunctionalType.yld
        • PlantFunctionalType.z_max_prop
        • PlantFunctionalType.zeta
      • PlantFunctionalTypeSchema
      • PlantFunctionalTypeStrict
        • PlantFunctionalTypeStrict.a_hd
        • PlantFunctionalTypeStrict.ca_ratio
        • PlantFunctionalTypeStrict.f_g
        • PlantFunctionalTypeStrict.gpp_topslice
        • PlantFunctionalTypeStrict.h_max
        • PlantFunctionalTypeStrict.lai
        • PlantFunctionalTypeStrict.m
        • PlantFunctionalTypeStrict.n
        • PlantFunctionalTypeStrict.name
        • PlantFunctionalTypeStrict.p_foliage_for_reproductive_tissue
        • PlantFunctionalTypeStrict.par_ext
        • PlantFunctionalTypeStrict.q_m
        • PlantFunctionalTypeStrict.resp_f
        • PlantFunctionalTypeStrict.resp_r
        • PlantFunctionalTypeStrict.resp_rt
        • PlantFunctionalTypeStrict.resp_s
        • PlantFunctionalTypeStrict.rho_s
        • PlantFunctionalTypeStrict.sla
        • PlantFunctionalTypeStrict.tau_f
        • PlantFunctionalTypeStrict.tau_r
        • PlantFunctionalTypeStrict.tau_rt
        • PlantFunctionalTypeStrict.yld
        • PlantFunctionalTypeStrict.z_max_prop
        • PlantFunctionalTypeStrict.zeta
      • StemTraits
        • StemTraits.a_hd
        • StemTraits.ca_ratio
        • StemTraits.f_g
        • StemTraits.gpp_topslice
        • StemTraits.h_max
        • StemTraits.lai
        • StemTraits.m
        • StemTraits.n
        • StemTraits.name
        • StemTraits.p_foliage_for_reproductive_tissue
        • StemTraits.par_ext
        • StemTraits.q_m
        • StemTraits.resp_f
        • StemTraits.resp_r
        • StemTraits.resp_rt
        • StemTraits.resp_s
        • StemTraits.rho_s
        • StemTraits.sla
        • StemTraits.tau_f
        • StemTraits.tau_r
        • StemTraits.tau_rt
        • StemTraits.validate
        • StemTraits.yld
        • StemTraits.z_max_prop
        • StemTraits.zeta
      • calculate_crown_q_m()
      • calculate_crown_z_max_proportion()
    • The tmodel module
      • StemAllocation
        • StemAllocation.delta_dbh
        • StemAllocation.delta_fine_root_mass
        • StemAllocation.delta_foliage_mass
        • StemAllocation.delta_stem_mass
        • StemAllocation.fine_root_respiration
        • StemAllocation.fine_root_turnover
        • StemAllocation.foliar_respiration
        • StemAllocation.gpp_topslice
        • StemAllocation.leaf_turnover
        • StemAllocation.npp
        • StemAllocation.reproductive_tissue_respiration
        • StemAllocation.reproductive_tissue_turnover
        • StemAllocation.sapwood_respiration
        • StemAllocation.stem_allometry
        • StemAllocation.stem_traits
        • StemAllocation.topslice_whole_crown_gpp
        • StemAllocation.validate
        • StemAllocation.whole_crown_gpp
      • StemAllometry
        • StemAllometry.at_dbh
        • StemAllometry.crown_area
        • StemAllometry.crown_fraction
        • StemAllometry.crown_r0
        • StemAllometry.crown_z_max
        • StemAllometry.dbh
        • StemAllometry.fine_root_mass
        • StemAllometry.foliage_mass
        • StemAllometry.reproductive_tissue_mass
        • StemAllometry.sapwood_mass
        • StemAllometry.stem_height
        • StemAllometry.stem_mass
        • StemAllometry.stem_traits
        • StemAllometry.validate
      • calculate_crown_areas()
      • calculate_crown_fractions()
      • calculate_crown_r0()
      • calculate_crown_z_max()
      • calculate_dbh_from_height()
      • calculate_fine_root_masses()
      • calculate_fine_root_respiration()
      • calculate_fine_root_turnover()
      • calculate_foliage_masses()
      • calculate_foliage_turnover()
      • calculate_foliar_respiration()
      • calculate_gpp_topslice()
      • calculate_growth_increments()
      • calculate_heights()
      • calculate_net_primary_productivity()
      • calculate_reproductive_tissue_mass()
      • calculate_reproductive_tissue_respiration()
      • calculate_reproductive_tissue_turnover()
      • calculate_sapwood_masses()
      • calculate_sapwood_respiration()
      • calculate_stem_masses()
      • calculate_whole_crown_gpp()
    • The crown module
      • CrownProfile
        • CrownProfile.crown_radius
        • CrownProfile.projected_crown_area
        • CrownProfile.projected_crown_radius
        • CrownProfile.projected_leaf_area
        • CrownProfile.projected_leaf_radius
        • CrownProfile.relative_crown_radius
        • CrownProfile.stem_allometry
        • CrownProfile.stem_traits
        • CrownProfile.validate
        • CrownProfile.z
      • calculate_crown_radius()
      • calculate_relative_crown_radius_at_z()
      • calculate_stem_projected_crown_area_at_z()
      • calculate_stem_projected_leaf_area_at_z()
      • get_crown_xy()
    • The community module
      • Worked example
      • CohortSchema
      • Cohorts
        • Cohorts.cohort_id
        • Cohorts.dbh_values
      • Community
        • Community.add_cohorts()
        • Community.drop_cohorts()
        • Community.from_csv()
        • Community.from_json()
        • Community.from_toml()
      • CommunityCSVDataSchema
        • CommunityCSVDataSchema.convert_to_community_args()
        • CommunityCSVDataSchema.validate_consistent_cell_data()
      • CommunityStructuredDataSchema
        • CommunityStructuredDataSchema.convert_to_community_args()
    • The canopy module
      • Canopy
        • Canopy.canopy_gap_fraction
        • Canopy.cohort_data
        • Canopy.community_data
        • Canopy.crown_profile
        • Canopy.filled_community_area
        • Canopy.heights
        • Canopy.max_stem_height
        • Canopy.n_cohorts
        • Canopy.n_layers
        • Canopy.solver_tolerance
      • CohortCanopyData
        • CohortCanopyData.cell_area
        • CohortCanopyData.cohort_absorption
        • CohortCanopyData.community_data
        • CohortCanopyData.fapar
        • CohortCanopyData.lai
        • CohortCanopyData.n_individuals
        • CohortCanopyData.par_ext
        • CohortCanopyData.projected_leaf_area
        • CohortCanopyData.stem_leaf_area
      • CommunityCanopyData
        • CommunityCanopyData.absorption
        • CommunityCanopyData.average_layer_absorption
        • CommunityCanopyData.average_layer_fapar
        • CommunityCanopyData.average_layer_lai
        • CommunityCanopyData.cell_area
        • CommunityCanopyData.cohort_leaf_area
        • CommunityCanopyData.leaf_area_index
        • CommunityCanopyData.transmission_profile
        • CommunityCanopyData.transmission_to_ground
      • fit_perfect_plasticity_approximation()
      • solve_canopy_area_filling_height()
  • The phenology module
    • The FAPAR limitation module
      • FaparLimitation
        • FaparLimitation.from_pmodel()
        • FaparLimitation.summarize()
        • FaparLimitation.annual_growing_season_length
        • FaparLimitation.annual_mean_ca
        • FaparLimitation.annual_mean_chi
        • FaparLimitation.annual_mean_vpd
        • FaparLimitation.annual_total_potential_gpp
        • FaparLimitation.annual_total_precip
        • FaparLimitation.lai_max
        • FaparLimitation.years
      • FaparLimitationMethodABC
        • FaparLimitationMethodABC.calculate_maximum_fapar()
        • FaparLimitationMethodABC.set_z_and_f0()
        • FaparLimitationMethodABC.attrs
        • FaparLimitationMethodABC.method
        • FaparLimitationMethodABC.requires
      • FaparLimitationMethodCai
        • FaparLimitationMethodCai.calculate_maximum_fapar()
        • FaparLimitationMethodCai.set_z_and_f0()
        • FaparLimitationMethodCai.attrs
        • FaparLimitationMethodCai.energy_limited
        • FaparLimitationMethodCai.method
        • FaparLimitationMethodCai.requires
      • FaparLimitationMethodZhu
        • FaparLimitationMethodZhu.calculate_maximum_fapar()
        • FaparLimitationMethodZhu.set_z_and_f0()
        • FaparLimitationMethodZhu.attrs
        • FaparLimitationMethodZhu.method
        • FaparLimitationMethodZhu.requires
      • FAPAR_LIMITATION_METHOD_CLASS_REGISTRY
    • The Phenology module
      • Phenology
        • Phenology.from_pmodel()
        • Phenology.fapar_limitation
      • PhenologyMethodABC
        • PhenologyMethodABC.attrs
        • PhenologyMethodABC.method
        • PhenologyMethodABC.requires
      • PhenologyMethodZhou
        • PhenologyMethodZhou.attrs
        • PhenologyMethodZhou.lai_to_gpp_ratio_m
        • PhenologyMethodZhou.method
        • PhenologyMethodZhou.requires
      • PhenologyMethodZhu
        • PhenologyMethodZhu.attrs
        • PhenologyMethodZhu.lai_to_gpp_ratio_m
        • PhenologyMethodZhu.method
        • PhenologyMethodZhu.requires
      • PHENOLOGY_METHOD_CLASS_REGISTRY
  • The pmodel module
    • The pmodel_environment submodule
      • PModelEnvironment
        • PModelEnvironment.summarize()
        • PModelEnvironment.ca
        • PModelEnvironment.co2
        • PModelEnvironment.core_const
        • PModelEnvironment.fapar
        • PModelEnvironment.gammastar
        • PModelEnvironment.kmm
        • PModelEnvironment.ns_star
        • PModelEnvironment.patm
        • PModelEnvironment.pmodel_const
        • PModelEnvironment.ppfd
        • PModelEnvironment.shape
        • PModelEnvironment.tc
        • PModelEnvironment.tk
        • PModelEnvironment.vpd
    • The jmax_limitation submodule
      • JmaxLimitationABC
        • JmaxLimitationABC._calculate_limitation_terms()
        • JmaxLimitationABC.summarize()
        • JmaxLimitationABC.data_attrs
        • JmaxLimitationABC.f_j
        • JmaxLimitationABC.f_v
        • JmaxLimitationABC.method
        • JmaxLimitationABC.optchi
        • JmaxLimitationABC.pmodel_const
        • JmaxLimitationABC.shape
      • JmaxLimitationNone
        • JmaxLimitationNone._calculate_limitation_terms()
        • JmaxLimitationNone.summarize()
        • JmaxLimitationNone.data_attrs
        • JmaxLimitationNone.f_j
        • JmaxLimitationNone.f_v
        • JmaxLimitationNone.method
        • JmaxLimitationNone.optchi
        • JmaxLimitationNone.pmodel_const
        • JmaxLimitationNone.shape
      • JmaxLimitationSmith19
        • JmaxLimitationSmith19._calculate_limitation_terms()
        • JmaxLimitationSmith19.summarize()
        • JmaxLimitationSmith19.data_attrs
        • JmaxLimitationSmith19.f_j
        • JmaxLimitationSmith19.f_v
        • JmaxLimitationSmith19.method
        • JmaxLimitationSmith19.omega
        • JmaxLimitationSmith19.omega_star
        • JmaxLimitationSmith19.optchi
        • JmaxLimitationSmith19.pmodel_const
        • JmaxLimitationSmith19.shape
      • JmaxLimitationWang17
        • JmaxLimitationWang17._calculate_limitation_terms()
        • JmaxLimitationWang17.summarize()
        • JmaxLimitationWang17.data_attrs
        • JmaxLimitationWang17.f_j
        • JmaxLimitationWang17.f_v
        • JmaxLimitationWang17.method
        • JmaxLimitationWang17.optchi
        • JmaxLimitationWang17.pmodel_const
        • JmaxLimitationWang17.shape
      • JMAX_LIMITATION_CLASS_REGISTRY
    • The optimal_chi submodule
      • OptimalChiABC
        • OptimalChiABC.estimate_chi()
        • OptimalChiABC.set_beta()
        • OptimalChiABC.summarize()
        • OptimalChiABC.beta
        • OptimalChiABC.chi
        • OptimalChiABC.ci
        • OptimalChiABC.env
        • OptimalChiABC.is_c4
        • OptimalChiABC.mc
        • OptimalChiABC.method
        • OptimalChiABC.mj
        • OptimalChiABC.mjoc
        • OptimalChiABC.pmodel_const
        • OptimalChiABC.required_env_variables
        • OptimalChiABC.shape
        • OptimalChiABC.xi
      • OptimalChiC4
        • OptimalChiC4.estimate_chi()
        • OptimalChiC4.set_beta()
        • OptimalChiC4.summarize()
        • OptimalChiC4.beta
        • OptimalChiC4.chi
        • OptimalChiC4.ci
        • OptimalChiC4.env
        • OptimalChiC4.is_c4
        • OptimalChiC4.mc
        • OptimalChiC4.method
        • OptimalChiC4.mj
        • OptimalChiC4.mjoc
        • OptimalChiC4.pmodel_const
        • OptimalChiC4.required_env_variables
        • OptimalChiC4.shape
        • OptimalChiC4.xi
      • OptimalChiC4NoGamma
        • OptimalChiC4NoGamma.estimate_chi()
        • OptimalChiC4NoGamma.set_beta()
        • OptimalChiC4NoGamma.summarize()
        • OptimalChiC4NoGamma.beta
        • OptimalChiC4NoGamma.chi
        • OptimalChiC4NoGamma.ci
        • OptimalChiC4NoGamma.env
        • OptimalChiC4NoGamma.is_c4
        • OptimalChiC4NoGamma.mc
        • OptimalChiC4NoGamma.method
        • OptimalChiC4NoGamma.mj
        • OptimalChiC4NoGamma.mjoc
        • OptimalChiC4NoGamma.pmodel_const
        • OptimalChiC4NoGamma.required_env_variables
        • OptimalChiC4NoGamma.shape
        • OptimalChiC4NoGamma.xi
      • OptimalChiC4NoGammaRootzoneStress
        • OptimalChiC4NoGammaRootzoneStress.estimate_chi()
        • OptimalChiC4NoGammaRootzoneStress.set_beta()
        • OptimalChiC4NoGammaRootzoneStress.summarize()
        • OptimalChiC4NoGammaRootzoneStress.beta
        • OptimalChiC4NoGammaRootzoneStress.chi
        • OptimalChiC4NoGammaRootzoneStress.ci
        • OptimalChiC4NoGammaRootzoneStress.env
        • OptimalChiC4NoGammaRootzoneStress.is_c4
        • OptimalChiC4NoGammaRootzoneStress.mc
        • OptimalChiC4NoGammaRootzoneStress.method
        • OptimalChiC4NoGammaRootzoneStress.mj
        • OptimalChiC4NoGammaRootzoneStress.mjoc
        • OptimalChiC4NoGammaRootzoneStress.pmodel_const
        • OptimalChiC4NoGammaRootzoneStress.required_env_variables
        • OptimalChiC4NoGammaRootzoneStress.shape
        • OptimalChiC4NoGammaRootzoneStress.xi
      • OptimalChiC4RootzoneStress
        • OptimalChiC4RootzoneStress.estimate_chi()
        • OptimalChiC4RootzoneStress.set_beta()
        • OptimalChiC4RootzoneStress.summarize()
        • OptimalChiC4RootzoneStress.beta
        • OptimalChiC4RootzoneStress.chi
        • OptimalChiC4RootzoneStress.ci
        • OptimalChiC4RootzoneStress.env
        • OptimalChiC4RootzoneStress.is_c4
        • OptimalChiC4RootzoneStress.mc
        • OptimalChiC4RootzoneStress.method
        • OptimalChiC4RootzoneStress.mj
        • OptimalChiC4RootzoneStress.mjoc
        • OptimalChiC4RootzoneStress.pmodel_const
        • OptimalChiC4RootzoneStress.required_env_variables
        • OptimalChiC4RootzoneStress.shape
        • OptimalChiC4RootzoneStress.xi
      • OptimalChiLavergne20C3
        • OptimalChiLavergne20C3.estimate_chi()
        • OptimalChiLavergne20C3.set_beta()
        • OptimalChiLavergne20C3.summarize()
        • OptimalChiLavergne20C3.beta
        • OptimalChiLavergne20C3.chi
        • OptimalChiLavergne20C3.ci
        • OptimalChiLavergne20C3.env
        • OptimalChiLavergne20C3.is_c4
        • OptimalChiLavergne20C3.mc
        • OptimalChiLavergne20C3.method
        • OptimalChiLavergne20C3.mj
        • OptimalChiLavergne20C3.mjoc
        • OptimalChiLavergne20C3.pmodel_const
        • OptimalChiLavergne20C3.required_env_variables
        • OptimalChiLavergne20C3.shape
        • OptimalChiLavergne20C3.xi
      • OptimalChiLavergne20C4
        • OptimalChiLavergne20C4.estimate_chi()
        • OptimalChiLavergne20C4.set_beta()
        • OptimalChiLavergne20C4.summarize()
        • OptimalChiLavergne20C4.beta
        • OptimalChiLavergne20C4.chi
        • OptimalChiLavergne20C4.ci
        • OptimalChiLavergne20C4.env
        • OptimalChiLavergne20C4.is_c4
        • OptimalChiLavergne20C4.mc
        • OptimalChiLavergne20C4.method
        • OptimalChiLavergne20C4.mj
        • OptimalChiLavergne20C4.mjoc
        • OptimalChiLavergne20C4.pmodel_const
        • OptimalChiLavergne20C4.required_env_variables
        • OptimalChiLavergne20C4.shape
        • OptimalChiLavergne20C4.xi
      • OptimalChiPrentice14
        • OptimalChiPrentice14.estimate_chi()
        • OptimalChiPrentice14.set_beta()
        • OptimalChiPrentice14.summarize()
        • OptimalChiPrentice14.beta
        • OptimalChiPrentice14.chi
        • OptimalChiPrentice14.ci
        • OptimalChiPrentice14.env
        • OptimalChiPrentice14.is_c4
        • OptimalChiPrentice14.mc
        • OptimalChiPrentice14.method
        • OptimalChiPrentice14.mj
        • OptimalChiPrentice14.mjoc
        • OptimalChiPrentice14.pmodel_const
        • OptimalChiPrentice14.required_env_variables
        • OptimalChiPrentice14.shape
        • OptimalChiPrentice14.xi
      • OptimalChiPrentice14RootzoneStress
        • OptimalChiPrentice14RootzoneStress.estimate_chi()
        • OptimalChiPrentice14RootzoneStress.set_beta()
        • OptimalChiPrentice14RootzoneStress.summarize()
        • OptimalChiPrentice14RootzoneStress.beta
        • OptimalChiPrentice14RootzoneStress.chi
        • OptimalChiPrentice14RootzoneStress.ci
        • OptimalChiPrentice14RootzoneStress.env
        • OptimalChiPrentice14RootzoneStress.is_c4
        • OptimalChiPrentice14RootzoneStress.mc
        • OptimalChiPrentice14RootzoneStress.method
        • OptimalChiPrentice14RootzoneStress.mj
        • OptimalChiPrentice14RootzoneStress.mjoc
        • OptimalChiPrentice14RootzoneStress.pmodel_const
        • OptimalChiPrentice14RootzoneStress.required_env_variables
        • OptimalChiPrentice14RootzoneStress.shape
        • OptimalChiPrentice14RootzoneStress.xi
      • OPTIMAL_CHI_CLASS_REGISTRY
    • The arrhenius submodule
      • ArrheniusFactorABC
        • ArrheniusFactorABC.calculate_arrhenius_factor()
        • ArrheniusFactorABC.env
        • ArrheniusFactorABC.method
        • ArrheniusFactorABC.required_coefficients
        • ArrheniusFactorABC.required_env_variables
      • KattgeKnorrArrhenius
        • KattgeKnorrArrhenius.calculate_arrhenius_factor()
        • KattgeKnorrArrhenius.env
        • KattgeKnorrArrhenius.method
        • KattgeKnorrArrhenius.required_coefficients
        • KattgeKnorrArrhenius.required_env_variables
      • SimpleArrhenius
        • SimpleArrhenius.calculate_arrhenius_factor()
        • SimpleArrhenius.env
        • SimpleArrhenius.method
        • SimpleArrhenius.required_coefficients
        • SimpleArrhenius.required_env_variables
      • ARRHENIUS_METHOD_REGISTRY
    • The quantum_yield submodule
      • QuantumYieldABC
        • QuantumYieldABC.summarize()
        • QuantumYieldABC.array_reference_kphio_ok
        • QuantumYieldABC.env
        • QuantumYieldABC.kphio
        • QuantumYieldABC.method
        • QuantumYieldABC.reference_kphio
        • QuantumYieldABC.required_env_variables
        • QuantumYieldABC.shape
        • QuantumYieldABC.use_c4
      • QuantumYieldFixed
        • QuantumYieldFixed.summarize()
        • QuantumYieldFixed.array_reference_kphio_ok
        • QuantumYieldFixed.env
        • QuantumYieldFixed.kphio
        • QuantumYieldFixed.method
        • QuantumYieldFixed.reference_kphio
        • QuantumYieldFixed.required_env_variables
        • QuantumYieldFixed.shape
        • QuantumYieldFixed.use_c4
      • QuantumYieldSandoval
        • QuantumYieldSandoval.peak_quantum_yield()
        • QuantumYieldSandoval.summarize()
        • QuantumYieldSandoval.array_reference_kphio_ok
        • QuantumYieldSandoval.env
        • QuantumYieldSandoval.kphio
        • QuantumYieldSandoval.method
        • QuantumYieldSandoval.reference_kphio
        • QuantumYieldSandoval.required_env_variables
        • QuantumYieldSandoval.shape
        • QuantumYieldSandoval.use_c4
      • QuantumYieldTemperature
        • QuantumYieldTemperature.summarize()
        • QuantumYieldTemperature.array_reference_kphio_ok
        • QuantumYieldTemperature.env
        • QuantumYieldTemperature.kphio
        • QuantumYieldTemperature.method
        • QuantumYieldTemperature.reference_kphio
        • QuantumYieldTemperature.required_env_variables
        • QuantumYieldTemperature.shape
        • QuantumYieldTemperature.use_c4
      • QUANTUM_YIELD_CLASS_REGISTRY
    • The functions submodule
      • calculate_co2_to_ca()
      • calculate_ftemp_inst_rd()
      • calculate_gammastar()
      • calculate_kattge_knorr_arrhenius_factor()
      • calculate_kmm()
      • calculate_ns_star()
      • calculate_simple_arrhenius_factor()
      • calculate_soilmstress_mengoli()
      • calculate_soilmstress_stocker()
    • The isotopes submodule
      • CarbonIsotopes
        • CarbonIsotopes.calculate_c3_discrimination()
        • CarbonIsotopes.calculate_c4_discrimination()
        • CarbonIsotopes.calculate_c4_discrimination_vonC()
        • CarbonIsotopes.summarize()
        • CarbonIsotopes.Delta13C
        • CarbonIsotopes.Delta13C_simple
        • CarbonIsotopes.Delta14C
        • CarbonIsotopes.c4
        • CarbonIsotopes.d13C_leaf
        • CarbonIsotopes.d13C_wood
        • CarbonIsotopes.d14C_leaf
        • CarbonIsotopes.isotopes_const
        • CarbonIsotopes.shape
    • The competition submodule
      • C3C4Competition
        • C3C4Competition.estimate_isotopic_discrimination()
        • C3C4Competition.summarize()
        • C3C4Competition.Delta13C_C3
        • C3C4Competition.Delta13C_C4
        • C3C4Competition.d13C_C3
        • C3C4Competition.d13C_C4
        • C3C4Competition.frac_c4
        • C3C4Competition.gpp_adv_c4
        • C3C4Competition.gpp_c3_contrib
        • C3C4Competition.gpp_c4_contrib
      • calculate_tree_proportion()
      • convert_gpp_advantage_to_c4_fraction()
    • The acclimation submodule
      • AcclimationModel
        • AcclimationModel.apply_acclimation()
        • AcclimationModel.fill_daily_to_subdaily()
        • AcclimationModel.get_daily_means()
        • AcclimationModel.get_window_values()
        • AcclimationModel.set_include()
        • AcclimationModel.set_nearest()
        • AcclimationModel.set_window()
        • AcclimationModel.allow_holdover
        • AcclimationModel.allow_partial_data
        • AcclimationModel.alpha
        • AcclimationModel.datetimes
        • AcclimationModel.fill_method
        • AcclimationModel.include
        • AcclimationModel.n_days
        • AcclimationModel.n_obs
        • AcclimationModel.observation_dates
        • AcclimationModel.observation_times
        • AcclimationModel.padded_datetimes
        • AcclimationModel.padding
        • AcclimationModel.sample_datetimes
        • AcclimationModel.sample_datetimes_max
        • AcclimationModel.sample_datetimes_mean
        • AcclimationModel.spacing
        • AcclimationModel.update_point
    • The two_leaf submodule
      • TwoLeafAssimilation
        • TwoLeafAssimilation.A_shade
        • TwoLeafAssimilation.A_sun
        • TwoLeafAssimilation.Aj_shade
        • TwoLeafAssimilation.Aj_sun
        • TwoLeafAssimilation.Av_shade
        • TwoLeafAssimilation.Av_sun
        • TwoLeafAssimilation.J_shade
        • TwoLeafAssimilation.J_sun
        • TwoLeafAssimilation.Jmax25_shade
        • TwoLeafAssimilation.Jmax25_sun
        • TwoLeafAssimilation.Jmax_shade
        • TwoLeafAssimilation.Jmax_sun
        • TwoLeafAssimilation.Vcmax25_canopy
        • TwoLeafAssimilation.Vcmax25_shade
        • TwoLeafAssimilation.Vcmax25_sun
        • TwoLeafAssimilation.Vcmax_shade
        • TwoLeafAssimilation.Vcmax_sun
        • TwoLeafAssimilation.canopy_extinction_coef
        • TwoLeafAssimilation.gpp
        • TwoLeafAssimilation.irradiance
        • TwoLeafAssimilation.pmodel
      • TwoLeafIrradiance
        • TwoLeafIrradiance.beam_extinction_coef
        • TwoLeafIrradiance.beam_irradiance
        • TwoLeafIrradiance.beam_reflectance
        • TwoLeafIrradiance.canopy_irradiance
        • TwoLeafIrradiance.core_constants
        • TwoLeafIrradiance.diffuse_irradiance
        • TwoLeafIrradiance.fraction_of_diffuse_radiation
        • TwoLeafIrradiance.leaf_area_index
        • TwoLeafIrradiance.patm
        • TwoLeafIrradiance.ppfd
        • TwoLeafIrradiance.scattered_beam_extinction_coef
        • TwoLeafIrradiance.shaded_absorbed_irradiance
        • TwoLeafIrradiance.solar_elevation
        • TwoLeafIrradiance.sunlit_absorbed_irradiance
        • TwoLeafIrradiance.sunlit_beam_irradiance
        • TwoLeafIrradiance.sunlit_diffuse_irradiance
        • TwoLeafIrradiance.sunlit_scattered_irradiance
        • TwoLeafIrradiance.two_leaf_constants
      • calculate_beam_extinction_coef()
      • calculate_beam_reflectance()
      • calculate_canopy_extinction_coef()
      • calculate_canopy_irradiance()
      • calculate_canopy_vcmax25()
      • calculate_electron_transport_rate()
      • calculate_fraction_of_diffuse_radiation()
      • calculate_jmax25()
      • calculate_sun_vcmax25()
      • calculate_sunlit_beam_irradiance()
      • calculate_sunlit_diffuse_irradiance()
      • calculate_sunlit_scattered_irradiance()
    • The pmodel submodule
      • PModel
        • PModel.apply_gpp_conversion_factor()
        • PModel.apply_gpp_penalty_factor()
        • PModel.remove_gpp_penalty_factor()
        • PModel.summarize()
        • PModel.to_subdaily()
        • PModel.A_c
        • PModel.A_j
        • PModel.J
        • PModel.c4
        • PModel.core_const
        • PModel.env
        • PModel.gpp
        • PModel.gpp_conversion_factor
        • PModel.gpp_penalty_factor
        • PModel.gs
        • PModel.iwue
        • PModel.jmax
        • PModel.jmax25
        • PModel.jmaxlim
        • PModel.kphio
        • PModel.lue
        • PModel.method_arrhenius
        • PModel.method_jmaxlim
        • PModel.method_kphio
        • PModel.method_optchi
        • PModel.optchi
        • PModel.pmodel_const
        • PModel.reference_kphio
        • PModel.shape
        • PModel.vcmax
        • PModel.vcmax25
      • PModelABC
        • PModelABC.apply_gpp_conversion_factor()
        • PModelABC.apply_gpp_penalty_factor()
        • PModelABC.remove_gpp_penalty_factor()
        • PModelABC.summarize()
        • PModelABC.A_c
        • PModelABC.A_j
        • PModelABC.J
        • PModelABC.c4
        • PModelABC.core_const
        • PModelABC.env
        • PModelABC.gpp
        • PModelABC.gpp_conversion_factor
        • PModelABC.gpp_penalty_factor
        • PModelABC.gs
        • PModelABC.iwue
        • PModelABC.jmax
        • PModelABC.jmax25
        • PModelABC.jmaxlim
        • PModelABC.kphio
        • PModelABC.lue
        • PModelABC.method_arrhenius
        • PModelABC.method_jmaxlim
        • PModelABC.method_kphio
        • PModelABC.method_optchi
        • PModelABC.optchi
        • PModelABC.pmodel_const
        • PModelABC.reference_kphio
        • PModelABC.shape
        • PModelABC.vcmax
        • PModelABC.vcmax25
      • SubdailyPModel
        • SubdailyPModel.apply_gpp_conversion_factor()
        • SubdailyPModel.apply_gpp_penalty_factor()
        • SubdailyPModel.remove_gpp_penalty_factor()
        • SubdailyPModel.summarize()
        • SubdailyPModel.A_c
        • SubdailyPModel.A_j
        • SubdailyPModel.J
        • SubdailyPModel.acclim_model
        • SubdailyPModel.c4
        • SubdailyPModel.core_const
        • SubdailyPModel.env
        • SubdailyPModel.gpp
        • SubdailyPModel.gpp_conversion_factor
        • SubdailyPModel.gpp_penalty_factor
        • SubdailyPModel.gs
        • SubdailyPModel.iwue
        • SubdailyPModel.jmax
        • SubdailyPModel.jmax25
        • SubdailyPModel.jmax25_daily_optimal
        • SubdailyPModel.jmax25_daily_realised
        • SubdailyPModel.jmaxlim
        • SubdailyPModel.kphio
        • SubdailyPModel.lue
        • SubdailyPModel.method_arrhenius
        • SubdailyPModel.method_jmaxlim
        • SubdailyPModel.method_kphio
        • SubdailyPModel.method_optchi
        • SubdailyPModel.optchi
        • SubdailyPModel.pmodel_acclim
        • SubdailyPModel.pmodel_const
        • SubdailyPModel.previous_realised
        • SubdailyPModel.reference_kphio
        • SubdailyPModel.shape
        • SubdailyPModel.vcmax
        • SubdailyPModel.vcmax25
        • SubdailyPModel.vcmax25_daily_optimal
        • SubdailyPModel.vcmax25_daily_realised
        • SubdailyPModel.xi_daily_optimal
        • SubdailyPModel.xi_daily_realised
  • The pyrealm package
  • The splash module
    • The DailySolarFluxes submodule
      • DailySolarFluxes
        • DailySolarFluxes.crossover_hour_angle
        • DailySolarFluxes.daily_ppfd
        • DailySolarFluxes.daily_solar_radiation
        • DailySolarFluxes.daytime_net_radiation
        • DailySolarFluxes.declination
        • DailySolarFluxes.distance_factor
        • DailySolarFluxes.lambda_
        • DailySolarFluxes.net_longwave_radiation
        • DailySolarFluxes.nighttime_net_radiation
        • DailySolarFluxes.nu
        • DailySolarFluxes.ru
        • DailySolarFluxes.rv
        • DailySolarFluxes.rw
        • DailySolarFluxes.sunset_hour_angle
        • DailySolarFluxes.transmissivity
    • The DailyEvapFluxes submodule
      • DailyEvapFluxes
        • DailyEvapFluxes.estimate_aet()
        • DailyEvapFluxes.cond
        • DailyEvapFluxes.econ
        • DailyEvapFluxes.eet_d
        • DailyEvapFluxes.lv
        • DailyEvapFluxes.pet_d
        • DailyEvapFluxes.psy
        • DailyEvapFluxes.pw
        • DailyEvapFluxes.rx
        • DailyEvapFluxes.sat
    • The SplashModel submodule
      • SplashModel
        • SplashModel.calculate_soil_moisture()
        • SplashModel.estimate_daily_water_balance()
        • SplashModel.estimate_initial_soil_moisture()
        • SplashModel.dates
        • SplashModel.elv
        • SplashModel.evap
        • SplashModel.kWm
        • SplashModel.lat
        • SplashModel.pa
        • SplashModel.pn
        • SplashModel.sf
        • SplashModel.shape
        • SplashModel.solar
        • SplashModel.tc

Development

  • Developing pyrealm
    • What is a package contributor?
    • Contributing code
    • The package development environment
      • Python environment
      • Package management
      • Installing pyrealm
      • Updating poetry and package versions
      • Installing and using pre-commit
      • Static typing with mypy
      • Package testing
      • Code profiling
      • The pyrealm-build-data package
      • Documentation
      • GitHub Actions
      • Package version releases
    • Setup script example
  • Code quality and static typing
    • Using pre-commit
      • The pre-commit configuration
      • Output and configuration
      • Updating pre-commit
    • Typing with mypy
    • Suppressing checking
  • Documentation
    • Documentation guide
      • MyST Markdown
      • Table of contents
      • Docstrings
      • Referencing
    • Building the documentation
  • Package testing
    • Using pytest
    • Using doctest
    • Using pytest-coverage and codecov
    • Resolving errors in the array inputs tests
      • Debugging
  • Profiling and benchmarking
    • Latest performance results
    • Running code profiling
      • Scaling of the profiling with problem size
    • Benchmarking code performance
      • Simple benchmarking
      • Advanced benchmarking
      • Resolving failed benchmarking
    • Updating performance results
  • GitHub Actions
    • pre-commit_autoupdate.yaml
    • pyrealm_ci.yaml
    • pyrealm_publish.yaml
  • Package release process
    • Generate the code commit to be released
    • Create the GitHub release
    • Publish the package on Zenodo
    • Publish the package on PyPI
      • Manual publication
      • Trusted publishing
  • The pyrealm_build_data package
    • The bigleaf submodule
    • The community submodule
    • The rpmodel submodule
      • Test inputs
      • Simple rpmodel benchmarking
      • Global array test
    • The sandoval_kphio submodule
    • The splash submodule
      • Benchmark test data
      • Original time series
      • Gridded time series
    • The subdaily submodule
    • The t_model submodule
    • The two_leaf submodule
    • The uk_data submodule
    • The phenology submodule

Reference

  • Bibliography
  • Glossary
pyrealm: Ecosystem Models in Python
  • Search

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