Define BioCro model test cases
model_test_case.RdBioCro models can be tested using test cases, which are sets of known outputs
that correspond to particular inputs. The model_test_case function
defines such a test case.
Note that model tests are distinct from the module tests
described in module_testing.
Usage
model_test_case(
test_case_name,
model_definition,
drivers,
check_outputs,
directory = '.',
quantities_to_ignore = character(),
row_interval = 24,
digits = 5,
relative_tolerance = 1e-3
)Arguments
- test_case_name
A string describing the test case.
- model_definition
A list defining a model, as described in the documentation for
crop_model_definitions.- drivers
A set of drivers to be passed to
run_biocroalong with themodel_definition.- check_outputs
A logical value indicating whether to compare the simulation output against a stored result.
- directory
A relative or absolute path to a directory containing a stored simulation result. Only used when
check_outputsisTRUE.- quantities_to_ignore
A character vector of any quantities that should not be compared against the stored results. Only used when
check_outputsisTRUE.- row_interval
Determines which rows are saved and compared when using
update_stored_model_results,compare_model_output, orrun_model_test_cases. Only used whencheck_outputsisTRUE.- digits
Passed to
signifto round values when storing saved results. Only used whencheck_outputsisTRUE.- relative_tolerance
A relative tolerance to be used when comparing new values against stored ones. This value will be passed to
all.equalas itstoleranceinput argument. Only used whencheck_outputsisTRUE.
Details
The model_test_case function forms the basis for the BioCro model
testing system. See model_testing for more information.
With the default settings:
Every 24 rows of the simulation output will be stored and compared. When using drivers with an hourly time step, this corresponds to one row for each day.
Values in the stored simulation results will be rounded to five significant digits. This reduces the size of the stored result file.
The value of the relative tolerance was chosen to be the smallest value that enabled the tests to pass on all operating systems.
These default settings have proven useful for the BioCro
miscanthus_x_giganteus, willow, and
soybean models.
Value
A list that defines a model test case, which can be passed to
update_stored_model_results, compare_model_output,
or run_model_test_cases.
Examples
# Define a test case for the miscanthus model
miscanthus_test_case <- model_test_case(
'miscanthus_x_giganteus',
miscanthus_x_giganteus,
get_growing_season_climate(weather$'2005'),
TRUE,
tempdir(),
'soil_evaporation_rate'
)
# The result is a specially formatted list
str(miscanthus_test_case)
#> List of 13
#> $ test_case_name : chr "miscanthus_x_giganteus"
#> $ initial_values :List of 18
#> ..$ cws1 : num 0.32
#> ..$ cws2 : num 0.32
#> ..$ Grain : num 0
#> ..$ Shell : num 0
#> ..$ Leaf : num 7e-04
#> ..$ LeafLitter : num 0
#> ..$ leaf_senescence_index : num 0
#> ..$ Rhizome : num 7
#> ..$ RhizomeLitter : num 0
#> ..$ rhizome_senescence_index: num 0
#> ..$ Root : num 0.007
#> ..$ RootLitter : num 0
#> ..$ root_senescence_index : num 0
#> ..$ soil_water_content : num 0.32
#> ..$ Stem : num 0.007
#> ..$ StemLitter : num 0
#> ..$ stem_senescence_index : num 0
#> ..$ TTc : num 0
#> $ parameters :List of 124
#> ..$ alpha1 : num 0.04
#> ..$ alphab1 : num 0
#> ..$ atmospheric_pressure : num 101325
#> ..$ atmospheric_scattering : num 0.3
#> ..$ atmospheric_transmittance : num 0.6
#> ..$ b0 : num 0.08
#> ..$ b1 : num 3
#> ..$ beta : num 0.93
#> ..$ Catm : num 400
#> ..$ chil : num 1
#> ..$ dry_biomass_per_carbon : num 30
#> ..$ emissivity_sky : num 1
#> ..$ Gs_min : num 0.001
#> ..$ heightf : num 1.33
#> ..$ hydrDist : num 0
#> ..$ iSp : num 1.7
#> ..$ k_diffuse : num 0.1
#> ..$ kGrain1 : num 0
#> ..$ kGrain2 : num 0
#> ..$ kGrain3 : num 0
#> ..$ kGrain4 : num 0
#> ..$ kGrain5 : num 0
#> ..$ kGrain6 : num 0
#> ..$ kLeaf1 : num 0.33
#> ..$ kLeaf2 : num 0.14
#> ..$ kLeaf3 : num 0.01
#> ..$ kLeaf4 : num 0.01
#> ..$ kLeaf5 : num 0.01
#> ..$ kLeaf6 : num 0.01
#> ..$ kparm : num 0.7
#> ..$ kpLN : num 0.2
#> ..$ kRhizome1 : num -8e-04
#> ..$ kRhizome2 : num -5e-04
#> ..$ kRhizome3 : num 0.35
#> ..$ kRhizome4 : num 0.35
#> ..$ kRhizome5 : num 0.35
#> ..$ kRhizome6 : num 0.35
#> ..$ kRoot1 : num 0.3
#> ..$ kRoot2 : num 0.01
#> ..$ kRoot3 : num 0.01
#> ..$ kRoot4 : num 0.01
#> ..$ kRoot5 : num 0.01
#> ..$ kRoot6 : num 0.01
#> ..$ kShell : num 0
#> ..$ kStem1 : num 0.37
#> ..$ kStem2 : num 0.85
#> ..$ kStem3 : num 0.63
#> ..$ kStem4 : num 0.63
#> ..$ kStem5 : num 0.63
#> ..$ kStem6 : num 0.63
#> ..$ lat : num 40
#> ..$ leaf_reflectance_nir : num 0.38
#> ..$ leaf_reflectance_par : num 0.09
#> ..$ leaf_transmittance_nir : num 0.45
#> ..$ leaf_transmittance_par : num 0.04
#> ..$ LeafN : num 2
#> ..$ LeafN_0 : num 2
#> ..$ leafwidth : num 0.04
#> ..$ lnfun : num 0
#> ..$ longitude : num -88
#> ..$ lowerT : num 3
#> ..$ min_gbw_canopy : num 0.005
#> ..$ mrc1 : num 0.02
#> ..$ mrc2 : num 0.03
#> ..$ nalphab0 : num 0.0237
#> ..$ nalphab1 : num 0.000488
#> ..$ net_assimilation_rate_shell: num 0
#> ..$ nileafn : num 85
#> ..$ nkln : num 0.5
#> ..$ nkpLN : num 0.17
#> ..$ nlayers : num 10
#> ..$ nlnb0 : num -5
#> ..$ nlnb1 : num 18
#> ..$ nRdb0 : num -4.59
#> ..$ nRdb1 : num 0.125
#> ..$ nvmaxb0 : num -16.2
#> ..$ nvmaxb1 : num 0.694
#> ..$ par_energy_content : num 0.219
#> ..$ par_energy_fraction : num 0.5
#> ..$ phi1 : num 0.01
#> ..$ phi2 : num 10
#> ..$ Rd : num 0.8
#> ..$ remobilization_fraction : num 0.6
#> ..$ retrans : num 0.9
#> ..$ retrans_rhizome : num 1
#> ..$ rfl : num 0.2
#> ..$ rsdf : num 0.44
#> ..$ rsec : num 0.2
#> ..$ seneLeaf : num 3000
#> ..$ seneRhizome : num 4000
#> ..$ seneRoot : num 4000
#> ..$ seneStem : num 3500
#> ..$ soil_air_entry : num -2.6
#> ..$ soil_b_coefficient : num 5.2
#> ..$ soil_bulk_density : num 1.35
#> ..$ soil_clay_content : num 0.34
#> ..$ soil_clod_size : num 0.04
#> ..$ soil_depth1 : num 0
#> ..$ soil_depth2 : num 2.5
#> .. [list output truncated]
#> $ drivers :'data.frame': 4296 obs. of 9 variables:
#> ..$ year : num [1:4296] 2005 2005 2005 2005 2005 ...
#> ..$ doy : num [1:4296] 123 123 123 123 123 123 123 123 123 123 ...
#> ..$ hour : num [1:4296] 0 1 2 3 4 5 6 7 8 9 ...
#> ..$ time_zone_offset: num [1:4296] -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 ...
#> ..$ precip : num [1:4296] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ rh : num [1:4296] 0.68 0.7 0.71 0.72 0.75 0.79 0.78 0.63 0.49 0.47 ...
#> ..$ solar : num [1:4296] 0 0 0 0 0 36 277 693 1090 1440 ...
#> ..$ temp : num [1:4296] 2.12 1.72 1.61 1.13 0.47 -0.435 0.45 3.55 5.71 6.97 ...
#> ..$ windspeed : num [1:4296] 3.22 2.86 2.7 2.99 2.3 1.46 1.32 1.41 1.53 2.89 ...
#> $ direct_modules :List of 14
#> ..$ : chr "BioCro:format_time"
#> ..$ stomata_water_stress : chr "BioCro:stomata_water_stress_linear"
#> ..$ : chr "BioCro:leaf_water_stress_exponential"
#> ..$ specific_leaf_area : chr "BioCro:sla_linear"
#> ..$ : chr "BioCro:parameter_calculator"
#> ..$ : chr "BioCro:soil_evaporation"
#> ..$ solar_coordinates : chr "BioCro:solar_position_michalsky"
#> ..$ : chr "BioCro:height_from_lai"
#> ..$ : chr "BioCro:canopy_gbw_thornley"
#> ..$ : chr "BioCro:stefan_boltzmann_longwave"
#> ..$ canopy_photosynthesis : chr "BioCro:c4_canopy"
#> ..$ partitioning_coefficients : chr "BioCro:partitioning_coefficient_selector"
#> ..$ partitioning_growth_calculator: chr "BioCro:partitioning_growth_calculator"
#> ..$ : chr "BioCro:carbon_assimilation_to_biomass"
#> $ differential_modules:List of 4
#> ..$ senescence : chr "BioCro:thermal_time_senescence"
#> ..$ : chr "BioCro:partitioning_growth"
#> ..$ thermal_time: chr "BioCro:thermal_time_linear"
#> ..$ soil_profile: chr "BioCro:two_layer_soil_profile"
#> $ ode_solver :List of 5
#> ..$ type : chr "homemade_euler"
#> ..$ output_step_size : num 1
#> ..$ adaptive_rel_error_tol: num 1e-05
#> ..$ adaptive_abs_error_tol: num 1e-05
#> ..$ adaptive_max_steps : num 200
#> $ check_outputs : logi TRUE
#> $ stored_result_file : chr "/tmp/RtmpLEUoCw/miscanthus_x_giganteus_simulation.csv"
#> $ quantities_to_ignore: chr "soil_evaporation_rate"
#> $ row_interval : num 24
#> $ digits : num 5
#> $ relative_tolerance : num 0.001