From 19424c3b979e69dc582b23537ee72c923a85ab0c Mon Sep 17 00:00:00 2001 From: David Orme Date: Fri, 13 Sep 2024 12:46:34 +0100 Subject: [PATCH 1/8] Expand set of tmodel regression test data --- .../t_model/pft_definitions.csv | 4 + .../t_model/rtmodel_output_alt_one.csv | 101 ++++++++++++++++++ .../t_model/rtmodel_output_alt_two.csv | 101 ++++++++++++++++++ .../t_model/rtmodel_output_default.csv | 101 ++++++++++++++++++ .../t_model/rtmodel_test_outputs.r | 41 +++---- .../test_t_model_functions_against_rtmodel.py | 97 +++++++++++++++++ 6 files changed, 427 insertions(+), 18 deletions(-) create mode 100644 pyrealm_build_data/t_model/pft_definitions.csv create mode 100644 pyrealm_build_data/t_model/rtmodel_output_alt_one.csv create mode 100644 pyrealm_build_data/t_model/rtmodel_output_alt_two.csv create mode 100644 pyrealm_build_data/t_model/rtmodel_output_default.csv create mode 100644 tests/regression/demography/test_t_model_functions_against_rtmodel.py diff --git a/pyrealm_build_data/t_model/pft_definitions.csv b/pyrealm_build_data/t_model/pft_definitions.csv new file mode 100644 index 00000000..c83124d4 --- /dev/null +++ b/pyrealm_build_data/t_model/pft_definitions.csv @@ -0,0 +1,4 @@ +name,d,a,cr,Hm,rho,L,sigma,tf,tr,K,y,zeta,rr,rs +default,0.1,116,390.43,25.33,200,1.8,14,4,1.04,0.5,0.6,0.17,0.913,0.044 +alt_one,0.04,124,351.62,15.33,400,4,10,2,0.95,0.6,0.5,0.22,0.813,0.034 +alt_two,0.6,102,406.12,45.33,100,1,21,8,2.1,0.4,0.7,0.15,0.962,0.054 diff --git a/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv b/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv new file mode 100644 index 00000000..da151d5a --- /dev/null +++ b/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv @@ -0,0 +1,101 @@ +"dD","D","H","Ac","Wf","Ws","Wss","GPP","Rm1","Rm2","dWs","dWfr" 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a/pyrealm_build_data/t_model/rtmodel_test_outputs.r +++ b/pyrealm_build_data/t_model/rtmodel_test_outputs.r @@ -87,21 +87,26 @@ tmodel <- function(P0, year, a, cr, Hm, rho, rr, return(output) } -tmodel_run <- tmodel(rep(7, 100), seq(100), - d = 0.1, - a = 116.0, - cr = 390.43, - Hm = 25.33, - rho = 200.0, - L = 1.8, - sigma = 14.0, - tf = 4.0, - tr = 1.04, - K = 0.5, - y = 0.6, - zeta = 0.17, - rr = 0.913, - rs = 0.044 -) - -write.csv(tmodel_run, "rtmodel_output.csv", row.names = FALSE) +# Load alternative plant functional types +pfts <- read.csv("pft_definitions.csv") + +for (pft_idx in seq_len(nrow(pfts))) { + # Get the PFT + pft <- as.list(pfts[pft_idx, ]) + + # Seperate off the name + name <- pft[["name"]] + pft[["name"]] <- NULL + + # Get GPP sequence + n_years <- 100 + pft[["P0"]] <- rnorm(n_years, mean = 7) + pft[["year"]] <- seq(n_years) + + tmodel_run <- do.call(tmodel, pft) + + write.csv(tmodel_run, + sprintf("rtmodel_output_%s.csv", name), + row.names = FALSE + ) +} diff --git a/tests/regression/demography/test_t_model_functions_against_rtmodel.py b/tests/regression/demography/test_t_model_functions_against_rtmodel.py new file mode 100644 index 00000000..1d994de3 --- /dev/null +++ b/tests/regression/demography/test_t_model_functions_against_rtmodel.py @@ -0,0 +1,97 @@ +"""Test TModel class. + +Tests the init, grow_ttree and other methods of TModel. +""" + +from importlib import resources + +import numpy as np +import pandas as pd +import pytest + +# Fixtures: inputs and expected values from the original implementation in R + + +@pytest.fixture(scope="module") +def rvalues(): + """Fixture to load test inputs from file. + + This is a time series of growth using the default trait values in R, mapped to the + internal property names used in TTree + """ + from pyrealm.demography.flora import PlantFunctionalType + + # Load the PFT definitions and rename to pyrealm attributes + pfts_path = resources.files("pyrealm_build_data.t_model") / "pft_definitions.csv" + pft_definitions = pd.read_csv(pfts_path) + + pft_definitions = pft_definitions.rename( + columns={ + "name": "alt_two", + "d": 0.6, + "a": 102, + "cr": 406.12, + "Hm": 45.33, + "rho": 100, + "L": 1.0, + "sigma": 21, + "tf": 8, + "tr": 2.1, + "K": 0.4, + "y": 0.7, + "zeta": 0.15, + "rr": 0.962, + "rs": 0.054, + } + ) + + datapath = resources.files("pyrealm_build_data.t_model") / "rtmodel_output.csv" + data = pd.read_csv(datapath) + + data = data.rename( + columns={ + "dD": "delta_d", + "D": "diameter", + "H": "height", + "Ac": "crown_area", + "Wf": "mass_fol", + "Ws": "mass_stm", + "Wss": "mass_swd", + "GPP": "gpp_actual", + "Rm1": "resp_swd", + "Rm2": "resp_frt", + "dWs": "delta_mass_stm", + "dWfr": "delta_mass_frt", + } + ) + + # Get the default PFT traits, which should match the settings used for the + # regression data set. + default_pft = PlantFunctionalType() + + # Fix some scaling differences: + # The R tmodel implementation rescales reported delta_d as a radial increase in + # millimetres, not diameter increase in metres + data["delta_d"] = data["delta_d"] / 500 + + # The R tmodel implementation slices off foliar respiration costs from GPP before + # doing anything - the pyrealm.tmodel implementation keeps this cost within the tree + # calculation, so proportionally inflate the GPP to make it match + data["gpp_actual"] = data["gpp_actual"] / (1 - default_pft.resp_f) + + return data + + +def test_calculate_heights(rvalues): + """Tests happy path for calculation of heights of tree from diameter.""" + + from pyrealm.demography.t_model_functions import calculate_heights + + pft_h_max_values = np.array([25.33, 15.33]) + pft_a_hd_values = np.array([116.0, 116.0]) + diameters_at_breast_height = np.array([0.2, 0.6]) + expected_heights = np.array([15.19414157, 15.16639589]) + actual_heights = calculate_heights( + pft_h_max_values, pft_a_hd_values, diameters_at_breast_height + ) + assert np.allclose(actual_heights, expected_heights, decimal=8) From e808947cd077cab8b47c3351a9ef5d973c4e6c04 Mon Sep 17 00:00:00 2001 From: David Orme Date: Fri, 13 Sep 2024 13:21:30 +0100 Subject: [PATCH 2/8] Regression tests for multiple PFTs for existing demography.t_model functions --- .../t_model/rtmodel_output_alt_one.csv | 202 ++++++++--------- .../t_model/rtmodel_output_alt_two.csv | 202 ++++++++--------- .../t_model/rtmodel_output_default.csv | 202 ++++++++--------- .../t_model/rtmodel_test_outputs.r | 6 +- .../test_t_model_functions_against_rtmodel.py | 203 +++++++++++++----- tests/regression/tmodel/test_tmodel.py | 1 + 6 files changed, 451 insertions(+), 365 deletions(-) diff --git a/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv b/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv index da151d5a..6e9785b0 100644 --- a/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv +++ b/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv @@ -1,101 +1,101 @@ -"dD","D","H","Ac","Wf","Ws","Wss","GPP","Rm1","Rm2","dWs","dWfr" 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"Ac", "Wf", "Ws", "Wss", + "dD", "D", "H", "fc", "Ac", "Wf", "Ws", "Wss", "GPP", "Rm1", "Rm2", "dWs", "dWfr" ) # you can decide which index you want output dD <- 0 @@ -80,7 +80,7 @@ tmodel <- function(P0, year, a, cr, Hm, rho, rr, a * d * (1 - H / Hm) + H )) * (1 / sigma + zeta) * dD output[i, ] <- c( - dD / 2 * 1000, d, H, Ac, Wf, Ws, Wss, GPP, Rm1, Rm2, dWs, dWfr + dD / 2 * 1000, d, H, fc, Ac, Wf, Ws, Wss, GPP, Rm1, Rm2, dWs, dWfr ) } diff --git a/tests/regression/demography/test_t_model_functions_against_rtmodel.py b/tests/regression/demography/test_t_model_functions_against_rtmodel.py index 1d994de3..218b3a07 100644 --- a/tests/regression/demography/test_t_model_functions_against_rtmodel.py +++ b/tests/regression/demography/test_t_model_functions_against_rtmodel.py @@ -5,9 +5,9 @@ from importlib import resources -import numpy as np import pandas as pd import pytest +from numpy.testing import assert_array_almost_equal # Fixtures: inputs and expected values from the original implementation in R @@ -16,8 +16,8 @@ def rvalues(): """Fixture to load test inputs from file. - This is a time series of growth using the default trait values in R, mapped to the - internal property names used in TTree + The regression test inputs consist of time series of growth from an initial DBH + using a small set of different plant functional type definitions. """ from pyrealm.demography.flora import PlantFunctionalType @@ -25,73 +25,158 @@ def rvalues(): pfts_path = resources.files("pyrealm_build_data.t_model") / "pft_definitions.csv" pft_definitions = pd.read_csv(pfts_path) + # Map the PFT trait args from the R implementation to pyrealm pft_definitions = pft_definitions.rename( columns={ - "name": "alt_two", - "d": 0.6, - "a": 102, - "cr": 406.12, - "Hm": 45.33, - "rho": 100, - "L": 1.0, - "sigma": 21, - "tf": 8, - "tr": 2.1, - "K": 0.4, - "y": 0.7, - "zeta": 0.15, - "rr": 0.962, - "rs": 0.054, + "a": "a_hd", + "cr": "ca_ratio", + "Hm": "h_max", + "rho": "rho_s", + "L": "lai", + "sigma": "sla", + "tf": "tau_f", + "tr": "tau_r", + "K": "par_ext", + "y": "yld", + "rr": "resp_r", + "rs": "resp_s", } ) - datapath = resources.files("pyrealm_build_data.t_model") / "rtmodel_output.csv" - data = pd.read_csv(datapath) + # Convert to dicts for creating PFT instances + pft_definitions = pft_definitions.to_dict(orient="records") + + return_value = [] + + # Loop over the PFT definitions + for pft_args in pft_definitions: + # Record the starting DBH and create the PFT instances + dbh_init = pft_args.pop("d") + pft = PlantFunctionalType(**pft_args) + + # Load the appropriate output file and then remap the field names + datapath = ( + resources.files("pyrealm_build_data.t_model") + / f"rtmodel_output_{pft.name}.csv" + ) + data = pd.read_csv(datapath) + + data = data.rename( + columns={ + "dD": "delta_d", + "D": "diameter", + "H": "height", + "fc": "crown_fraction", + "Ac": "crown_area", + "Wf": "mass_fol", + "Ws": "mass_stm", + "Wss": "mass_swd", + "GPP": "gpp_actual", + "Rm1": "resp_swd", + "Rm2": "resp_frt", + "dWs": "delta_mass_stm", + "dWfr": "delta_mass_frt", + } + ) + + # Fix some scaling differences: + # The R tmodel implementation rescales reported delta_d as a radial increase in + # millimetres, not diameter increase in metres + data["delta_d"] = data["delta_d"] / 500 + + # The R tmodel implementation slices off foliar respiration costs from GPP + # before doing anything - the pyrealm.tmodel implementation keeps this cost + # within the tree calculation, so proportionally inflate the GPP to make it + # match + data["gpp_actual"] = data["gpp_actual"] / (1 - pft.resp_f) + + # Add a tuple of the inputs and outputs to the return list. + return_value.append((pft, dbh_init, data)) + + return return_value - data = data.rename( - columns={ - "dD": "delta_d", - "D": "diameter", - "H": "height", - "Ac": "crown_area", - "Wf": "mass_fol", - "Ws": "mass_stm", - "Wss": "mass_swd", - "GPP": "gpp_actual", - "Rm1": "resp_swd", - "Rm2": "resp_frt", - "dWs": "delta_mass_stm", - "dWfr": "delta_mass_frt", - } - ) - # Get the default PFT traits, which should match the settings used for the - # regression data set. - default_pft = PlantFunctionalType() +def test_calculate_heights(rvalues): + """Test calculation of heights of tree from diameter.""" - # Fix some scaling differences: - # The R tmodel implementation rescales reported delta_d as a radial increase in - # millimetres, not diameter increase in metres - data["delta_d"] = data["delta_d"] / 500 + from pyrealm.demography.t_model_functions import calculate_heights - # The R tmodel implementation slices off foliar respiration costs from GPP before - # doing anything - the pyrealm.tmodel implementation keeps this cost within the tree - # calculation, so proportionally inflate the GPP to make it match - data["gpp_actual"] = data["gpp_actual"] / (1 - default_pft.resp_f) + for pft, _, data in rvalues: + actual_heights = calculate_heights( + h_max=pft.h_max, a_hd=pft.a_hd, dbh=data["diameter"] + ) - return data + assert_array_almost_equal(actual_heights, data["height"], decimal=8) -def test_calculate_heights(rvalues): - """Tests happy path for calculation of heights of tree from diameter.""" +def test_calculate_crown_areas(rvalues): + """Tests calculation of crown areas of trees.""" + from pyrealm.demography.t_model_functions import calculate_crown_areas - from pyrealm.demography.t_model_functions import calculate_heights + for pft, _, data in rvalues: + actual_crown_areas = calculate_crown_areas( + ca_ratio=pft.ca_ratio, + a_hd=pft.a_hd, + dbh=data["diameter"], + height=data["height"], + ) - pft_h_max_values = np.array([25.33, 15.33]) - pft_a_hd_values = np.array([116.0, 116.0]) - diameters_at_breast_height = np.array([0.2, 0.6]) - expected_heights = np.array([15.19414157, 15.16639589]) - actual_heights = calculate_heights( - pft_h_max_values, pft_a_hd_values, diameters_at_breast_height - ) - assert np.allclose(actual_heights, expected_heights, decimal=8) + assert_array_almost_equal(actual_crown_areas, data["crown_area"], decimal=8) + + +def test_calculate_crown_fractions(rvalues): + """Tests calculation of crown fractions of trees.""" + + from pyrealm.demography.t_model_functions import calculate_crown_fractions + + for pft, _, data in rvalues: + actual_crown_fractions = calculate_crown_fractions( + a_hd=pft.a_hd, + dbh=data["diameter"], + height=data["height"], + ) + assert_array_almost_equal( + actual_crown_fractions, data["crown_fraction"], decimal=8 + ) + + +def test_calculate_stem_masses(rvalues): + """Tests happy path for calculation of stem masses of trees.""" + + from pyrealm.demography.t_model_functions import calculate_stem_masses + + for pft, _, data in rvalues: + actual_stem_masses = calculate_stem_masses( + dbh=data["diameter"], + height=data["height"], + rho_s=pft.rho_s, + ) + assert_array_almost_equal(actual_stem_masses, data["mass_stm"], decimal=8) + + +def test_calculate_foliage_masses(rvalues): + """Tests calculation of foliage masses of trees.""" + + from pyrealm.demography.t_model_functions import calculate_foliage_masses + + for pft, _, data in rvalues: + actual_foliage_masses = calculate_foliage_masses( + crown_area=data["crown_area"], lai=pft.lai, sla=pft.sla + ) + assert_array_almost_equal(actual_foliage_masses, data["mass_fol"], decimal=8) + + +def test_calculate_sapwood_masses(rvalues): + """Tests calculation of sapwood masses of trees.""" + + from pyrealm.demography.t_model_functions import calculate_sapwood_masses + + for pft, _, data in rvalues: + actual_sapwood_masses = calculate_sapwood_masses( + crown_area=data["crown_area"], + height=data["height"], + crown_fraction=data["crown_fraction"], + ca_ratio=pft.ca_ratio, + rho_s=pft.rho_s, + ) + assert_array_almost_equal(actual_sapwood_masses, data["mass_swd"], decimal=8) diff --git a/tests/regression/tmodel/test_tmodel.py b/tests/regression/tmodel/test_tmodel.py index 6c7d2f3d..8aa1e33a 100644 --- a/tests/regression/tmodel/test_tmodel.py +++ b/tests/regression/tmodel/test_tmodel.py @@ -32,6 +32,7 @@ def rvalues(): ("dD", "delta_d"), ("D", "diameter"), ("H", "height"), + ("fc", "crown_fraction"), ("Ac", "crown_area"), ("Wf", "mass_fol"), ("Ws", "mass_stm"), From 0e60479bab80389eda9790825a20f996329e3cdf Mon Sep 17 00:00:00 2001 From: David Orme Date: Fri, 13 Sep 2024 17:30:43 +0100 Subject: [PATCH 3/8] First draft of T Model growth functions and regression tests --- pyrealm/demography/t_model_functions.py | 102 +++++++++ .../t_model/rtmodel_output_alt_one.csv | 202 +++++++++--------- .../t_model/rtmodel_output_alt_two.csv | 202 +++++++++--------- .../t_model/rtmodel_output_default.csv | 202 +++++++++--------- .../t_model/rtmodel_test_outputs.r | 8 +- .../test_t_model_functions_against_rtmodel.py | 179 +++++++++++++++- tests/regression/tmodel/test_tmodel.py | 1 + 7 files changed, 581 insertions(+), 315 deletions(-) diff --git a/pyrealm/demography/t_model_functions.py b/pyrealm/demography/t_model_functions.py index 9c2fd903..82f64d24 100644 --- a/pyrealm/demography/t_model_functions.py +++ b/pyrealm/demography/t_model_functions.py @@ -145,6 +145,108 @@ def calculate_sapwood_masses( return crown_area * rho_s * height * (1 - crown_fraction / 2) / ca_ratio +def calculate_whole_crown_gpp( + potential_gpp: Series, crown_area: Series, par_ext: Series, lai: Series +) -> Series: + r"""Calculate whole crown gross primary productivity. + + Given an estimate of potential gross primary productivity (GPP) per metre squared + (:math:`P_0`), this function scales the GPP up to the whole crown, given the crown + area (:math:`A_c`) and leaf area index (:math:`L`) and the extinction coefficient + (:math:`k`) :cite:p:`{Equation 12, }Li:2014bc`:. + + .. math:: + + P = P_0 A_c (1 - e^{-kL}) + + Args: + potential_gpp: Potential GPP per metre squared + crown_area: The crown area in metres squared + par_ext: The extinction coefficient + lai: The leaf area index + """ + + return potential_gpp * crown_area * (1 - np.exp(-(par_ext * lai))) + + +def calculate_sapwood_respiration(resp_s: Series, sapwood_mass: Series) -> Series: + """TODO docstring.""" + return sapwood_mass * resp_s + + +def calculate_foliar_respiration(resp_f: Series, whole_crown_gpp: Series) -> Series: + """TODO docstring.""" + return whole_crown_gpp * resp_f + + +def calculate_fine_root_respiration( + zeta: Series, sla: Series, resp_r: Series, foliage_mass: Series +) -> Series: + """TODO docstring.""" + + return zeta * sla * foliage_mass * resp_r + + +def calculate_net_primary_productivity( + yld: Series, + whole_crown_gpp: Series, + foliar_respiration: Series, + fine_root_respiration: Series, + sapwood_respiration: Series, +) -> Series: + """TODO docstring.""" + + return yld * ( + whole_crown_gpp + - foliar_respiration + - fine_root_respiration + - sapwood_respiration + ) + + +def calculate_foliage_and_fine_root_turnover( + lai: Series, + sla: Series, + tau_f: Series, + zeta: Series, + tau_r: Series, + crown_area: Series, +) -> Series: + """TODO docstring.""" + + return crown_area * lai * ((1 / (sla * tau_f)) + (zeta / tau_r)) + + +def calculate_growth_increments( + rho_s: Series, + a_hd: Series, + h_max: Series, + lai: Series, + ca_ratio: Series, + sla: Series, + zeta: Series, + npp: Series, + turnover: Series, + dbh: Series, + height: Series, +) -> tuple[Series, Series, Series]: + """TODO docstring.""" + # relative increments - these are used to calculate delta_d and + # then scaled by delta_d to give actual increments + dSdD = np.pi / 8 * rho_s * dbh * (a_hd * dbh * (1 - (height / h_max)) + 2 * height) + + dFdD = ( + lai + * ((np.pi * ca_ratio) / (4 * a_hd)) + * (a_hd * dbh * (1 - height / h_max) + height) + * (1 / sla + zeta) + ) + + delta_d = (npp - turnover) / (dSdD + dFdD) + + return (delta_d, dSdD * delta_d, dFdD * delta_d) + + def calculate_canopy_q_m(m: float, n: float) -> float: """Calculate a q_m value. diff --git a/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv b/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv index 6e9785b0..2df8e17c 100644 --- a/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv +++ b/pyrealm_build_data/t_model/rtmodel_output_alt_one.csv @@ -1,101 +1,101 @@ -"dD","D","H","fc","Ac","Wf","Ws","Wss","GPP","Rm1","Rm2","dWs","dWfr" 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+6.57297094426391,12.7425793906757,2.46847656936885,25.3296880046465,0.0884591662971433,165.285182870947,21.2509520834075,12122.0965952848,2049.76541915996,644.711447770915,90.1896784430382,46.1770438201194,305.006835304655,53.944724519419,250.320435350945,0.741675434290741 diff --git a/pyrealm_build_data/t_model/rtmodel_test_outputs.r b/pyrealm_build_data/t_model/rtmodel_test_outputs.r index 70e9cb4a..bf19857a 100644 --- a/pyrealm_build_data/t_model/rtmodel_test_outputs.r +++ b/pyrealm_build_data/t_model/rtmodel_test_outputs.r @@ -12,10 +12,10 @@ tmodel <- function(P0, year, a, cr, Hm, rho, rr, P0 <- P0 * (1 - 0.1) aa <- length(year) # simulate years output <- matrix() - output <- matrix(NA, nrow = aa, ncol = 13, byrow = T) + output <- matrix(NA, nrow = aa, ncol = 16, byrow = T) colnames(output) <- c( - "dD", "D", "H", "fc", "Ac", "Wf", "Ws", "Wss", - "GPP", "Rm1", "Rm2", "dWs", "dWfr" + "P0", "dD", "D", "H", "fc", "Ac", "Wf", "Ws", "Wss", + "GPP", "Rm1", "Rm2", "NPP", "turnover", "dWs", "dWfr" ) # you can decide which index you want output dD <- 0 NPP1 <- NA @@ -80,7 +80,7 @@ tmodel <- function(P0, year, a, cr, Hm, rho, rr, a * d * (1 - H / Hm) + H )) * (1 / sigma + zeta) * dD output[i, ] <- c( - dD / 2 * 1000, d, H, fc, Ac, Wf, Ws, Wss, GPP, Rm1, Rm2, dWs, dWfr + P0[i], dD / 2 * 1000, d, H, fc, Ac, Wf, Ws, Wss, GPP, Rm1, Rm2, NPP1, NPP2, dWs, dWfr ) } diff --git a/tests/regression/demography/test_t_model_functions_against_rtmodel.py b/tests/regression/demography/test_t_model_functions_against_rtmodel.py index 218b3a07..cb62efbc 100644 --- a/tests/regression/demography/test_t_model_functions_against_rtmodel.py +++ b/tests/regression/demography/test_t_model_functions_against_rtmodel.py @@ -1,6 +1,8 @@ -"""Test TModel class. +"""Regression tests of the demography.t_model functions. -Tests the init, grow_ttree and other methods of TModel. +The original R implementation has been used to generate a set of predicted growth +trajectories across a set of PFT definitions (default from the original paper and then +two fairly randomly chosen variants). """ from importlib import resources @@ -71,7 +73,8 @@ def rvalues(): "Wf": "mass_fol", "Ws": "mass_stm", "Wss": "mass_swd", - "GPP": "gpp_actual", + "P0": "potential_gpp", + "GPP": "crown_gpp", "Rm1": "resp_swd", "Rm2": "resp_frt", "dWs": "delta_mass_stm", @@ -84,11 +87,11 @@ def rvalues(): # millimetres, not diameter increase in metres data["delta_d"] = data["delta_d"] / 500 - # The R tmodel implementation slices off foliar respiration costs from GPP - # before doing anything - the pyrealm.tmodel implementation keeps this cost - # within the tree calculation, so proportionally inflate the GPP to make it - # match - data["gpp_actual"] = data["gpp_actual"] / (1 - pft.resp_f) + # The reported P0 in the R tmodel outputs has already had fixed foliar + # respiration costs removed before calculating anything. The pyrealm + # implementation has this as a PFT trait, so in some tests the potential GPP + # will need to be proportionally scaled up to make them match, but this is not + # true for _all_ tests so the values here are left untouched. # Add a tuple of the inputs and outputs to the return list. return_value.append((pft, dbh_init, data)) @@ -180,3 +183,163 @@ def test_calculate_sapwood_masses(rvalues): rho_s=pft.rho_s, ) assert_array_almost_equal(actual_sapwood_masses, data["mass_swd"], decimal=8) + + +def test_calculate_whole_crown_gpp(rvalues): + """Tests calculation of sapwood masses of trees. + + Note that this test can used reported P0 from R directly - no need to correct for + foliar respiration. + """ + + from pyrealm.demography.t_model_functions import calculate_whole_crown_gpp + + for pft, _, data in rvalues: + actual_whole_crown_gpp = calculate_whole_crown_gpp( + potential_gpp=data["potential_gpp"], + crown_area=data["crown_area"], + par_ext=pft.par_ext, + lai=pft.lai, + ) + assert_array_almost_equal(actual_whole_crown_gpp, data["crown_gpp"], decimal=8) + + +def test_calculate_sapwood_respiration(rvalues): + """Tests calculation of sapwood respiration of trees.""" + + from pyrealm.demography.t_model_functions import calculate_sapwood_respiration + + for pft, _, data in rvalues: + actual_sapwood_respiration = calculate_sapwood_respiration( + sapwood_mass=data["mass_swd"], + resp_s=pft.resp_s, + ) + assert_array_almost_equal( + actual_sapwood_respiration, data["resp_swd"], decimal=8 + ) + + +def test_calculate_foliar_respiration(rvalues): + """Tests calculation of foliar respiration of trees. + + This is implemented as a fixed proportion of GPP - and the reported values from R + are automatically penalised by this proportion beforehand, so this test looks + circular but is important to validate this difference. + """ + + from pyrealm.demography.t_model_functions import calculate_foliar_respiration + + for pft, _, data in rvalues: + actual_foliar_respiration = calculate_foliar_respiration( + whole_crown_gpp=data["crown_gpp"], + resp_f=pft.resp_f, + ) + assert_array_almost_equal( + actual_foliar_respiration, + data["crown_gpp"] * pft.resp_f, + decimal=8, + ) + + +def test_calculate_fine_root_respiration(rvalues): + """Tests calculation of fine root respiration of trees.""" + + from pyrealm.demography.t_model_functions import calculate_fine_root_respiration + + for pft, _, data in rvalues: + actual_fine_root_respiration = calculate_fine_root_respiration( + zeta=pft.zeta, + sla=pft.sla, + resp_r=pft.resp_r, + foliage_mass=data["mass_fol"], + ) + assert_array_almost_equal( + actual_fine_root_respiration, + data["resp_frt"], + decimal=8, + ) + + +def test_calculate_net_primary_productivity(rvalues): + """Tests calculation of fine root respiration of trees. + + Again - this test has to account for the R implementation removing foliar + respiration from potential GPP before calculating crown GPP. + """ + + from pyrealm.demography.t_model_functions import calculate_net_primary_productivity + + for pft, _, data in rvalues: + actual_npp = calculate_net_primary_productivity( + yld=pft.yld, + whole_crown_gpp=data["crown_gpp"] / (1 - pft.resp_f), + foliar_respiration=data["crown_gpp"] / (1 - pft.resp_f) * pft.resp_f, + fine_root_respiration=data["resp_frt"], + sapwood_respiration=data["resp_swd"], + ) + assert_array_almost_equal( + actual_npp, + data["NPP"], + decimal=8, + ) + + +def test_calculate_foliage_and_fine_root_turnover(rvalues): + """Tests calculation of fine root respiration of trees.""" + + from pyrealm.demography.t_model_functions import ( + calculate_foliage_and_fine_root_turnover, + ) + + for pft, _, data in rvalues: + actual_turnover = calculate_foliage_and_fine_root_turnover( + lai=pft.lai, + sla=pft.sla, + tau_f=pft.tau_f, + zeta=pft.zeta, + tau_r=pft.tau_r, + crown_area=data["crown_area"], + ) + assert_array_almost_equal( + actual_turnover, + data["turnover"], + decimal=8, + ) + + +def test_calculate_growth_increments(rvalues): + """Tests calculation of fine root respiration of trees.""" + + from pyrealm.demography.t_model_functions import ( + calculate_growth_increments, + ) + + for pft, _, data in rvalues: + delta_dbh, delta_mass_stem, delta_mass_fine_root = calculate_growth_increments( + rho_s=pft.rho_s, + a_hd=pft.a_hd, + h_max=pft.h_max, + lai=pft.lai, + ca_ratio=pft.ca_ratio, + sla=pft.sla, + zeta=pft.zeta, + npp=data["NPP"], + turnover=data["turnover"], + dbh=data["diameter"], + height=data["height"], + ) + assert_array_almost_equal( + delta_dbh, + data["delta_d"], + decimal=8, + ) + assert_array_almost_equal( + delta_mass_stem, + data["delta_mass_stm"], + decimal=8, + ) + assert_array_almost_equal( + delta_mass_fine_root, + data["delta_mass_frt"], + decimal=8, + ) diff --git a/tests/regression/tmodel/test_tmodel.py b/tests/regression/tmodel/test_tmodel.py index 8aa1e33a..cbe95afd 100644 --- a/tests/regression/tmodel/test_tmodel.py +++ b/tests/regression/tmodel/test_tmodel.py @@ -37,6 +37,7 @@ def rvalues(): ("Wf", "mass_fol"), ("Ws", "mass_stm"), ("Wss", "mass_swd"), + ("P0", "potential_gpp"), ("GPP", "gpp_actual"), ("Rm1", "resp_swd"), ("Rm2", "resp_frt"), From 2b94a2c6877cd7ea21e369b6095a7ca6a809c952 Mon Sep 17 00:00:00 2001 From: David Orme Date: Fri, 13 Sep 2024 22:05:01 +0100 Subject: [PATCH 4/8] Docstring updates to T model functions --- pyrealm/demography/t_model_functions.py | 185 +++++++++++++++--- .../test_t_model_functions_against_rtmodel.py | 3 +- 2 files changed, 163 insertions(+), 25 deletions(-) diff --git a/pyrealm/demography/t_model_functions.py b/pyrealm/demography/t_model_functions.py index 82f64d24..b3e20818 100644 --- a/pyrealm/demography/t_model_functions.py +++ b/pyrealm/demography/t_model_functions.py @@ -101,7 +101,7 @@ def calculate_foliage_masses(sla: Series, lai: Series, crown_area: Series) -> Se The foliage mass (:math:`W_{f}`) is calculated from the crown area (:math:`A_{c}`), along with the specific leaf area (:math:`\sigma`) and leaf area index (:math:`L`) - of the plant functional type :cite:p:`Li:2014bc`: + of the plant functional type :cite:p:`Li:2014bc`. .. math:: @@ -128,7 +128,7 @@ def calculate_sapwood_masses( The sapwood mass (:math:`W_{\cdot s}`) is calculated from the individual crown area (:math:`A_{c}`), height :math:`H` and canopy fraction (:math:`f_{c}`) along with the wood density (:math:`\rho_s`) and crown area ratio :math:`A_{c}` of the plant - functional type :cite:p:`{Equation 14, }Li:2014bc`: + functional type :cite:p:`{Equation 14, }Li:2014bc`. .. math:: @@ -150,10 +150,11 @@ def calculate_whole_crown_gpp( ) -> Series: r"""Calculate whole crown gross primary productivity. - Given an estimate of potential gross primary productivity (GPP) per metre squared - (:math:`P_0`), this function scales the GPP up to the whole crown, given the crown - area (:math:`A_c`) and leaf area index (:math:`L`) and the extinction coefficient - (:math:`k`) :cite:p:`{Equation 12, }Li:2014bc`:. + This function calculates individual GPP across the whole crown, given the + individual potential gross primary productivity (GPP) per metre squared + (:math:`P_0`) and crown area (:math:`A_c`), along with the leaf area index + (:math:`L`) and the extinction coefficient (:math:`k`) of the plant functional type + :cite:p:`{Equation 12, }Li:2014bc`. .. math:: @@ -170,19 +171,60 @@ def calculate_whole_crown_gpp( def calculate_sapwood_respiration(resp_s: Series, sapwood_mass: Series) -> Series: - """TODO docstring.""" + r"""Calculate sapwood respiration. + + Calculates the total sapwood respiration (:math:`R_{\cdot s}`) given the individual + sapwood mass (:math:`W_{\cdot s}`) and the sapwood respiration rate of the plant + functional type (:math:`r_{s}`) :cite:p:`{see Equation 13, }Li:2014bc`. + + .. math:: + R_{\cdot s} = W_{\cdot s} \, r_s + + Args: + resp_s: The sapwood respiration rate + sapwood_mass: The individual sapwood mass + """ return sapwood_mass * resp_s def calculate_foliar_respiration(resp_f: Series, whole_crown_gpp: Series) -> Series: - """TODO docstring.""" + r"""Calculate foliar respiration. + + Calculates the total foliar respiration (:math:`R_{f}`) given the individual crown + GPP (:math:`P`) and the foliar respiration rate of the plant functional type + (:math:`r_{f}`). :cite:t:`Li:2014bc` remove foliar respiration as a constant + proportion of potential GPP before calculating GPP for the crown, but ``pyrealm`` + treats this proportion as part of the definition of plant functional types. + + .. math:: + R_{f} = P \, r_f + + Args: + resp_f: The foliar respiration rate + whole_crown_gpp: The individual whole crown GPP. + """ return whole_crown_gpp * resp_f def calculate_fine_root_respiration( zeta: Series, sla: Series, resp_r: Series, foliage_mass: Series ) -> Series: - """TODO docstring.""" + r"""Calculate foliar respiration. + + Calculates the total fine root respiration (:math:`R_{r}`) given the individual + foliage mass (:math:`W_f`), along with the fine root respiration rate (:math:`r_r`), + the ratio of fine root mass to foliage area (:math:`\zeta`) and the specific leaf + area (:math:`\sigma`) :cite:p:`{see Equation 13, }Li:2014bc` + + .. math:: + R_{r} = \zeta \sigma W_f r_r + + Args: + zeta: The ratio of fine root mass to foliage area. + sla: The specific leaf area + resp_r: The respiration rate of fine roots. + foliage_mass: The individual foliage mass. + """ return zeta * sla * foliage_mass * resp_r @@ -194,7 +236,28 @@ def calculate_net_primary_productivity( fine_root_respiration: Series, sapwood_respiration: Series, ) -> Series: - """TODO docstring.""" + r"""Calculate net primary productivity. + + The net primary productivity (NPP, :math:`P_{net}`) is calculated as a plant + functional type specific yield proportion (:math:`y`) of the total GPP (:math:`P`) + for the individual minus respiration (:math:`R_m`), as the sum of the respiration + costs for foliage (:math:`R_f`), fine roots (:math:`R_r`) and sapwood + (:math:`R_s`). + + .. math:: + P_{net} = y (P - R_m) = y (P - W_{\cdot s} r_s - \zeta \sigma W_f r_r - P r_f) + + Note that this differs from Equation 13 of :cite:t:`Li:2014bc`, which removes foliar + respiration from potential GPP. This approach is equivalent but allows the foliar + respiration to vary between plant functional types. + + Args: + yld: The yield proportion. + whole_crown_gpp: The total GPP for the crown. + foliar_respiration: The total foliar respiration. + fine_root_respiration: The total fine root respiration + sapwood_respiration: The total sapwood respiration. + """ return yld * ( whole_crown_gpp @@ -205,16 +268,34 @@ def calculate_net_primary_productivity( def calculate_foliage_and_fine_root_turnover( - lai: Series, sla: Series, - tau_f: Series, zeta: Series, + tau_f: Series, tau_r: Series, - crown_area: Series, + foliage_mass: Series, ) -> Series: - """TODO docstring.""" + r"""Calculate turnover costs. - return crown_area * lai * ((1 / (sla * tau_f)) + (zeta / tau_r)) + This function calculates the costs associated with the turnover of fine roots and + foliage. This is calculated from the total foliage mass of individuals + (:math:`W_f`), along with the specific leaf area (:math:`\sigma`) and fine root mass + to foliar area ratio (:math:`\zeta`) and the turnover times of foliage + (:math:`\tau_f`) and fine roots (:math:`\tau_r`) of the plant functional type + :cite:p:`{see Equation 15, }Li:2014bc`. + + .. math:: + + T = W_f \left( \frac{1}{\tau_f} + \frac{\sigma \zeta}{\tau_f} \right) + + Args: + sla: The specific leaf area + zeta: The ratio of fine root mass to foliage area. + tau_f: The turnover time of foliage + tau_r: The turnover time of fine roots + foliage_mass: The foliage mass + """ + + return foliage_mass * ((1 / tau_f) + (sla * zeta / tau_r)) def calculate_growth_increments( @@ -230,21 +311,80 @@ def calculate_growth_increments( dbh: Series, height: Series, ) -> tuple[Series, Series, Series]: - """TODO docstring.""" - # relative increments - these are used to calculate delta_d and - # then scaled by delta_d to give actual increments - dSdD = np.pi / 8 * rho_s * dbh * (a_hd * dbh * (1 - (height / h_max)) + 2 * height) + r"""Calculate growth increments. + + Given an estimate of net primary productivity (:math:`P_{net}`), less associated + turnover costs (:math:`T`), the remaining productivity can be allocated to growth + and hence estimate resulting increments in: + + * the stem diameter (:math:`\Delta D`), + * the stem mass (:math:`\Delta W_s`), and + * the foliar mass (:math:`\Delta W_f`). + + + The stem diameter increment can be calculated using the available productivity for + growth and the rates of change in stem (:math:`\textrm{d}W_s / \textrm{d}t`) and + foliar masses (:math:`\textrm{d}W_f / \textrm{d}t`): + + .. math:: + + \Delta D = \frac{P_{net} - T}{ \textrm{d}W_s / \textrm{d}t + + \textrm{d}W_f / \textrm{d}t} + + The rates of change in stem and foliar mass can be calculated as: + + .. math:: + :nowrap: + + \[ + \begin{align*} + \textrm{d}W_s / \textrm{d}t &= \frac{\pi}{8} \rho_s D + \left(a D \left(1 - \frac{H}{H_{m}} + 2 H \right) \right) \\ + + \textrm{d}W_f / \textrm{d}t &= L \frac{\pi c}{4 a} \left(a D \left( 1 - + \frac{H}{H_{m}} + H \right) \right) \frac{1}{\sigma + \zeta} + \end{align*} + \] + + given the current stem diameter (:math:`D`) and height (:math:`H`) and the following + plant functional type traits: + + * the specific leaf area (:math:`\sigma`), + * the leaf area index (:math:`L`), + * the wood density of the PFT (:math:`\rho_s`), + * the maximum height (:math:`H_{m}`), + * the initial slope of the height/diameter relationship (:math:`a`), + * the crown area ratio (:math:`c`), and + * the ratio of fine root mass to leaf area (:math:`\zeta`). + + The resulting incremental changes in stem mass and foliar mass can then be + calculated as: + + .. math:: + :nowrap: + + \[ + \begin{align*} + \Delta W_s &= \textrm{d}W_s / \textrm{d}t \, \Delta D\\ + \Delta W_f &= \textrm{d}W_f / \textrm{d}t \, \Delta D + \end{align*} + \] + + """ + # Rates of change in stem and foliar + dWsdt = np.pi / 8 * rho_s * dbh * (a_hd * dbh * (1 - (height / h_max)) + 2 * height) - dFdD = ( + dWfdt = ( lai * ((np.pi * ca_ratio) / (4 * a_hd)) * (a_hd * dbh * (1 - height / h_max) + height) * (1 / sla + zeta) ) - delta_d = (npp - turnover) / (dSdD + dFdD) + # Increment of diameter at breast height + delta_d = (npp - turnover) / (dWsdt + dWfdt) - return (delta_d, dSdD * delta_d, dFdD * delta_d) + return (delta_d, dWsdt * delta_d, dWfdt * delta_d) def calculate_canopy_q_m(m: float, n: float) -> float: @@ -303,7 +443,6 @@ def calculate_canopy_z_max(z_max_prop: Series, height: Series) -> Series: z_max_prop: Canopy shape parameter of the PFT height: Crown area of individuals """ - """Calculate z_m, the height of maximum crown radius.""" return height * z_max_prop diff --git a/tests/regression/demography/test_t_model_functions_against_rtmodel.py b/tests/regression/demography/test_t_model_functions_against_rtmodel.py index cb62efbc..6b75df6b 100644 --- a/tests/regression/demography/test_t_model_functions_against_rtmodel.py +++ b/tests/regression/demography/test_t_model_functions_against_rtmodel.py @@ -293,12 +293,11 @@ def test_calculate_foliage_and_fine_root_turnover(rvalues): for pft, _, data in rvalues: actual_turnover = calculate_foliage_and_fine_root_turnover( - lai=pft.lai, sla=pft.sla, tau_f=pft.tau_f, zeta=pft.zeta, tau_r=pft.tau_r, - crown_area=data["crown_area"], + foliage_mass=data["mass_fol"], ) assert_array_almost_equal( actual_turnover, From c9339ce304d2b6c6a9efb9f47440536b2ab1f4f4 Mon Sep 17 00:00:00 2001 From: David Orme Date: Sat, 14 Sep 2024 12:35:07 +0100 Subject: [PATCH 5/8] Adding missing args --- pyrealm/demography/t_model_functions.py | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/pyrealm/demography/t_model_functions.py b/pyrealm/demography/t_model_functions.py index b3e20818..6e985e13 100644 --- a/pyrealm/demography/t_model_functions.py +++ b/pyrealm/demography/t_model_functions.py @@ -220,9 +220,9 @@ def calculate_fine_root_respiration( R_{r} = \zeta \sigma W_f r_r Args: - zeta: The ratio of fine root mass to foliage area. - sla: The specific leaf area - resp_r: The respiration rate of fine roots. + zeta: The ratio of fine root mass to foliage area of the PFT. + sla: The specific leaf area of the PFT. + resp_r: The respiration rate of fine roots of the PFT. foliage_mass: The individual foliage mass. """ @@ -370,6 +370,18 @@ def calculate_growth_increments( \end{align*} \] + Args: + rho_s: Wood density of the PFT + a_hd: Initial slope of the height/diameter relationship of the PFT + h_max: Maximum height of the PFT + lai: Leaf area index of the PFT + ca_ratio: Crown area ratio of the PFT + sla: Specific leaf area of the PFT + zeta: The ratio of fine root mass to foliage area of the PFT + npp: Net primary productivity of individuals + turnover: Fine root and foliage turnover cost of individuals + dbh: Diameter at breast height of individuals + height: Stem height of individuals """ # Rates of change in stem and foliar dWsdt = np.pi / 8 * rho_s * dbh * (a_hd * dbh * (1 - (height / h_max)) + 2 * height) From 8737728512ef516008fc9fc42760d1b2858e3873 Mon Sep 17 00:00:00 2001 From: David Orme Date: Sat, 14 Sep 2024 12:52:10 +0100 Subject: [PATCH 6/8] Minor text updates --- .../demography/test_t_model_functions_against_rtmodel.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tests/regression/demography/test_t_model_functions_against_rtmodel.py b/tests/regression/demography/test_t_model_functions_against_rtmodel.py index 6b75df6b..0582daa2 100644 --- a/tests/regression/demography/test_t_model_functions_against_rtmodel.py +++ b/tests/regression/demography/test_t_model_functions_against_rtmodel.py @@ -19,7 +19,9 @@ def rvalues(): """Fixture to load test inputs from file. The regression test inputs consist of time series of growth from an initial DBH - using a small set of different plant functional type definitions. + run using the original R implementation of the T model, for each of a small set of + different plant functional type definitions. The PFT definitions are loaded first + and then the output file associated with each PFT is loaded. """ from pyrealm.demography.flora import PlantFunctionalType @@ -87,7 +89,7 @@ def rvalues(): # millimetres, not diameter increase in metres data["delta_d"] = data["delta_d"] / 500 - # The reported P0 in the R tmodel outputs has already had fixed foliar + # NOTE: The reported P0 in the R tmodel outputs has already had fixed foliar # respiration costs removed before calculating anything. The pyrealm # implementation has this as a PFT trait, so in some tests the potential GPP # will need to be proportionally scaled up to make them match, but this is not From a0bbc5c79f89774ee47cdcd016d82bf48b8d0a57 Mon Sep 17 00:00:00 2001 From: David Orme Date: Mon, 16 Sep 2024 11:26:05 +0100 Subject: [PATCH 7/8] Bring original TModel tests up to date with new regression dataset --- tests/regression/tmodel/test_tmodel.py | 114 ++++++++++++------------- 1 file changed, 56 insertions(+), 58 deletions(-) diff --git a/tests/regression/tmodel/test_tmodel.py b/tests/regression/tmodel/test_tmodel.py index cbe95afd..2504399a 100644 --- a/tests/regression/tmodel/test_tmodel.py +++ b/tests/regression/tmodel/test_tmodel.py @@ -3,11 +3,11 @@ Tests the init, grow_ttree and other methods of TModel. """ -import csv from contextlib import nullcontext as does_not_raise from importlib import resources import numpy as np +import pandas as pd import pytest # Fixtures: inputs and expected values from the original implementation in R @@ -22,48 +22,43 @@ def rvalues(): """ from pyrealm.tmodel import TModelTraits - datapath = resources.files("pyrealm_build_data.t_model") / "rtmodel_output.csv" - - with open(str(datapath)) as infile: - rdr = csv.DictReader(infile, quoting=csv.QUOTE_NONNUMERIC) - values = [v for v in rdr] - - name_map = ( - ("dD", "delta_d"), - ("D", "diameter"), - ("H", "height"), - ("fc", "crown_fraction"), - ("Ac", "crown_area"), - ("Wf", "mass_fol"), - ("Ws", "mass_stm"), - ("Wss", "mass_swd"), - ("P0", "potential_gpp"), - ("GPP", "gpp_actual"), - ("Rm1", "resp_swd"), - ("Rm2", "resp_frt"), - ("dWs", "delta_mass_stm"), - ("dWfr", "delta_mass_frt"), + datapath = ( + resources.files("pyrealm_build_data.t_model") / "rtmodel_output_default.csv" ) - # copy values under R names to py names - traits = TModelTraits() + data = pd.read_csv(datapath) + + data = data.rename( + columns={ + "dD": "delta_d", + "D": "diameter", + "H": "height", + "fc": "crown_fraction", + "Ac": "crown_area", + "Wf": "mass_fol", + "Ws": "mass_stm", + "Wss": "mass_swd", + "P0": "potential_gpp", + "GPP": "gpp_actual", + "Rm1": "resp_swd", + "Rm2": "resp_frt", + "dWs": "delta_mass_stm", + "dWfr": "delta_mass_frt", + } + ) - for row in values: - for rnm, pynm in name_map: - # Fix some scaling differences: - if pynm == "delta_d": - # The R tmodel implementation rescales reported delta_d as - # a radial increase in millimetres, not diameter increase in metres - row[pynm] = row[rnm] / 500 - elif pynm == "gpp_actual": - # The R tmodel implementation slices off foliar respiration costs from - # GPP before doing anything - the pyrealm.tmodel implementation keeps - # this cost within the tree calculation - row[pynm] = row[rnm] / (1 - traits.resp_f) - else: - row[pynm] = row[rnm] + # Fix some scaling differences: + # The R tmodel implementation rescales reported delta_d as a radial increase in + # millimetres, not diameter increase in metres + data["delta_d"] = data["delta_d"] / 500 + + # The R tmodel implementation slices off foliar respiration costs from + # GPP before doing anything - the pyrealm.tmodel implementation keeps + # this cost within the tree calculation + traits = TModelTraits() + data["gpp_actual"] = data["gpp_actual"] / (1 - traits.resp_f) - return values + return data @pytest.mark.parametrize(argnames="row", argvalues=np.arange(0, 100, 10)) @@ -73,10 +68,11 @@ def test_tmodel_init(rvalues, row): from pyrealm.constants.tmodel_const import TModelTraits from pyrealm.tmodel import TTree - ttree = TTree(traits=TModelTraits, diameters=rvalues[row]["diameter"]) + row = rvalues.iloc[row] + ttree = TTree(traits=TModelTraits, diameters=row["diameter"]) for geom_est in ("height", "crown_area", "mass_fol", "mass_stm", "mass_swd"): - assert np.allclose(getattr(ttree, geom_est), rvalues[row][geom_est]) + assert np.allclose(getattr(ttree, geom_est), row[geom_est]) @pytest.mark.parametrize(argnames="row", argvalues=np.arange(0, 100, 10)) @@ -87,10 +83,11 @@ def test_tmodel_reset_diameters(rvalues, row): from pyrealm.tmodel import TTree ttree = TTree(diameters=0.001, traits=TModelTraits()) - ttree.reset_diameters(rvalues[row]["diameter"]) + row = rvalues.iloc[row] + ttree.reset_diameters(row["diameter"]) for geom_est in ("height", "crown_area", "mass_fol", "mass_stm", "mass_swd"): - assert np.allclose(getattr(ttree, geom_est), rvalues[row][geom_est]) + assert np.allclose(getattr(ttree, geom_est), row[geom_est]) def test_tmodel_init_array(rvalues): @@ -99,11 +96,11 @@ def test_tmodel_init_array(rvalues): from pyrealm.constants.tmodel_const import TModelTraits from pyrealm.tmodel import TTree - diams = np.array([rw["diameter"] for rw in rvalues]) + diams = np.array(rvalues["diameter"]) ttree = TTree(diameters=diams, traits=TModelTraits) for geom_est in ("height", "crown_area", "mass_fol", "mass_stm", "mass_swd"): - vals = [rw[geom_est] for rw in rvalues] + vals = rvalues[geom_est] assert np.allclose(getattr(ttree, geom_est), vals) @@ -150,19 +147,20 @@ def test_tmodel_growth_access(sequence, raises): def test_tmodel_calculate_growth(rvalues, row): """Test calculate_growth with scalars. - Runs a test of the tmodel.TTree against output from the R implementation. - The values in the test come from simulating a 100 year run starting from - a stem diameter of 0.1 and with an annual GPP value of 7. Each row in the - file is the successive growth, but this test just runs some values from the - sequence. + Runs a test of the tmodel.TTree against output from the R implementation. The values + in the test come from simulating a 100 year run starting from a stem diameter of + 0.1. Each row in the file is the successive growth, but this test just runs some + values from the sequence. """ from pyrealm.constants.tmodel_const import TModelTraits from pyrealm.tmodel import TTree # create a tree with the initial diameter given in the row - ttree = TTree(diameters=rvalues[row]["diameter"], traits=TModelTraits()) - ttree.calculate_growth(7) + row = rvalues.iloc[row] + traits = TModelTraits() + ttree = TTree(diameters=row["diameter"], traits=traits) + ttree.calculate_growth(row["potential_gpp"] / (1 - traits.resp_f)) for growth_est in ( "delta_d", @@ -172,7 +170,7 @@ def test_tmodel_calculate_growth(rvalues, row): "delta_mass_stm", "delta_mass_frt", ): - assert np.allclose(getattr(ttree, growth_est), rvalues[row][growth_est]) + assert np.allclose(getattr(ttree, growth_est), row[growth_est]) def test_tmodel_calculate_growth_array(rvalues): @@ -182,9 +180,10 @@ def test_tmodel_calculate_growth_array(rvalues): from pyrealm.tmodel import TTree # create a tree with the initial diameter given in the row - diams = np.array([rw["diameter"] for rw in rvalues]) - ttree = TTree(diameters=diams, traits=TModelTraits) - ttree.calculate_growth(7) + diams = np.array(rvalues["diameter"]) + traits = TModelTraits() + ttree = TTree(diameters=diams, traits=traits) + ttree.calculate_growth(rvalues["potential_gpp"] / (1 - traits.resp_f)) for growth_est in ( "delta_d", @@ -194,8 +193,7 @@ def test_tmodel_calculate_growth_array(rvalues): "delta_mass_stm", "delta_mass_frt", ): - vals = [rw[growth_est] for rw in rvalues] - assert np.allclose(getattr(ttree, growth_est), vals) + assert np.allclose(getattr(ttree, growth_est), rvalues[growth_est]) # @pytest.mark.parametrize( From 1db5cc2ec0e0136cd4e6b8c6cb86fea3d5713f2e Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 18 Sep 2024 09:27:36 +0100 Subject: [PATCH 8/8] Adding refs and clarification of methods differences --- pyrealm/demography/t_model_functions.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/pyrealm/demography/t_model_functions.py b/pyrealm/demography/t_model_functions.py index 6e985e13..1960f08e 100644 --- a/pyrealm/demography/t_model_functions.py +++ b/pyrealm/demography/t_model_functions.py @@ -247,9 +247,11 @@ def calculate_net_primary_productivity( .. math:: P_{net} = y (P - R_m) = y (P - W_{\cdot s} r_s - \zeta \sigma W_f r_r - P r_f) - Note that this differs from Equation 13 of :cite:t:`Li:2014bc`, which removes foliar - respiration from potential GPP. This approach is equivalent but allows the foliar - respiration to vary between plant functional types. + Note that this differs from Equation 13 of :cite:t:`Li:2014bc`, which does not + include a term for foliar respiration. This is because :cite:t:`Li:2014bc` remove + foliar respiration as a fixed proportion of potential GPP as the first step in their + calculations. The approach here is equivalent but allows the foliar respiration to + vary between plant functional types. Args: yld: The yield proportion. @@ -315,7 +317,7 @@ def calculate_growth_increments( Given an estimate of net primary productivity (:math:`P_{net}`), less associated turnover costs (:math:`T`), the remaining productivity can be allocated to growth - and hence estimate resulting increments in: + and hence estimate resulting increments :cite:`Li:2014bc` in: * the stem diameter (:math:`\Delta D`), * the stem mass (:math:`\Delta W_s`), and