Initialisation for spwb() function:
## Package 'medfate' [ver. 4.1.0]
# Soil
examplesoil <- soil(defaultSoilParams(n = 4))
# Load example plot plant data
data(exampleforest)
# Prepare input for 'Sureau' transpiration mode
control <- defaultControl("Sureau")
# Create input for spwb
x <- forest2spwbInput(exampleforest,examplesoil,SpParamsMED, control)Create Sureau network (similar) for each of the three plant cohort in
x. This returns a list with three elements:
cn <- initSureauNetworks(x)
length(cn)## [1] 3You can inspect the structure of the network for the first object using:
network <- cn[[1]]
str(network)## List of 40
## $ params :List of 27
## ..$ TPhase_gmin : num 37.5
## ..$ Q10_1_gmin : num 1.2
## ..$ Q10_2_gmin : num 4.8
## ..$ Gsw_AC_slope : num 6.24
## ..$ gCrown0 : num 150
## ..$ fTRBToLeaf : num 0.8
## ..$ C_SApoInit : num 2e-05
## ..$ C_LApoInit : num 1e-05
## ..$ k_SLApoInit : num 8
## ..$ k_CSApoInit : num 1.34
## ..$ k_RCApoInit : num [1:4] 2.3828 0.48335 0.04257 0.00742
## ..$ slope_gs : num 30
## ..$ P50_gs : num -1.2
## ..$ gmin20 : num 3.09
## ..$ gsMax : num 285
## ..$ gmin_S : num 3.09
## ..$ gsNight : num 14.2
## ..$ VCleaf_P50 : num -1.2
## ..$ VCleaf_slope : num 115
## ..$ VCstem_P50 : num -4.46
## ..$ VCstem_slope : num 45.9
## ..$ VCroot_P50 : num -0.88
## ..$ VCroot_slope : num 103
## ..$ PiFullTurgor_Leaf: num -1.59
## ..$ epsilonSym_Leaf : num 8.92
## ..$ PiFullTurgor_Stem: num -2.01
## ..$ epsilonSym_Stem : num 13.3
## $ LAI : num 0.849
## $ Psi_LApo : num -0.033
## $ Psi_LSym : num -0.033
## $ Psi_RCApo : num -0.033
## $ Psi_SApo : num -0.033
## $ Psi_SSym : num -0.033
## $ Psi_SApo_cav : num 0
## $ Psi_LApo_cav : num 0
## $ PsiSoil : num [1:4] -0.033 -0.033 -0.033 -0.033
## $ PLC_Stem : num 0
## $ PLC_Leaf : num 0
## $ C_SApo : num 2e-05
## $ C_LApo : num 1e-05
## $ C_SSym : num 1239
## $ C_LSym : num 1798
## $ k_SLApo : num 8
## $ k_CSApo : num 1.34
## $ k_SSym : num 0.26
## $ k_LSym : num 8
## $ k_RSApo : num [1:4] 0.8575 0.35519 0.04126 0.00738
## $ k_SoilToStem : num [1:4] 0.85629 0.3537 0.0411 0.00736
## $ k_Soil : num [1:4] 607.38 84.32 10.67 3.49
## $ k_Plant : num 0.747
## $ Q_SApo_sat_mmol_perLeafArea: num 316823
## $ Q_LApo_sat_mmol_perLeafArea: num 10298
## $ Q_SSym_sat_mmol_perLeafArea: num 26192
## $ Q_LSym_sat_mmol_perLeafArea: num 18916
## $ Einst : num 0
## $ Elim : num 0
## $ Elim_SL : num NA
## $ Elim_SH : num NA
## $ Emin_L : num 0
## $ Emin_L_SL : num NA
## $ Emin_L_SH : num NA
## $ Emin_S : num 0
## $ Diag_nwhile_cavit : int NA
## $ Diag_deltaRegulMax : int NA
## $ Diag_deltaPLCMax : int NA
## $ Diag_timeStepInSeconds : int NAsemi_implicit_integration()
If we modify the values of Elim, Emin_L or
Emin_S, then a call to
semi_implicit_integration() should update the water
potentials according to these flows. The water potentials prior to the
call are:
network$Psi_LApo## [1] -0.033
network$Psi_LSym## [1] -0.033
network$Psi_SApo## [1] -0.033
network$Psi_SSym## [1] -0.033We now set the options and time step size:
opt <- c("Lsym" = 1.0, "Ssym" = 1.0,
"Eord" = 1.0, "Lcav" = 1.0, "Scav" = 1.0,
"CLapo" = 1.0, "CTapo" = 1.0)
# Number of small steps per hour sub-steps
nsmalltimesteps <- c(2, 4, 8, 16)
# Seconds of the small time step (four sub-steps per hour)
dt <- 3600.0 / nsmalltimesteps[2] We also specify the flows and call
semi_implicit_integration():
network$Elim <- 0.1
network$Emin_L <- 0.01
network$Emin_S <- 0.01
semi_implicit_integration(network, dt, opt)The function modifies the network object, whose water
potentials are now:
network$Psi_LApo## [1] -0.033
network$Psi_LSym## [1] -0.04649922
network$Psi_SApo## [1] -0.033
network$Psi_SSym## [1] -0.03962152