CropGro(WetDat, day1 = NULL, dayn = NULL, timestep = 1, lat = 40, iRhizome = 7, irtl = 1e-04, canopyControl = list(), seneControl = list(), photoControl = list(), phenoControl = list(), soilControl = list(), nitroControl = list(), SOMpoolsControl = list(), SOMAssignParmsControl = list(), GetCropCentStateVarParmsControl = list(), GetSoilTextureParmsControl = list(), GetBioCroToCropcentParmsControl = list(), GetErosionParmsControl = list(), GetC13ParmsControl = list(), GetLeachingParmsControl = list(), GetSymbNFixationParmsControl = list(), centuryControl = list())
weach function.day1). See details.ha^{-1}).canopyParms function.
Sp (specific leaf area) here the units are ha
Mg^{-1}. If you have data in m^2 of leaf per
kg of dry matter (e.g. 15) then divide by 10 before
inputting this coefficient.
nlayers (number of layers of the canopy) Maximum
50. To increase the number of layers (more than 50) the
C source code needs to be changed slightly.
kd (extinction coefficient for diffuse light)
between 0 and 1.
mResp (maintenance respiration) a vector of length
2 with the first component for leaf and stem and the
second component for rhizome and root.seneParms function.
senLeaf Thermal time at which leaf senescence will
start.
senStem Thermal time at which stem senescence will
start.
senRoot Thermal time at which root senescence will
start.
senRhizome Thermal time at which rhizome
senescence will start.photoParms function.
vmax Vmax passed to the c4photo
function.
alpha alpha parameter passed to the
c4photo function.
kparm kparm parameter passed to the
c4photo function.
theta theta parameter passed to the
c4photo function.
beta beta parameter passed to the
c4photo function.
Rd Rd parameter passed to the
c4photo function.
Catm Catm parameter passed to the
c4photo function.
b0 b0 parameter passed to the
c4photo function.
b1 b1 parameter passed to the
c4photo function.phenoParms function.
tp1-tp6 thermal times which determine the time
elapsed between phenological stages. Between 0 and tp1 is
the juvenile stage. etc.
kLeaf1-6 proportion of the carbon that is
allocated to leaf for phenological stages 1 through 6.
kStem1-6 proportion of the carbon that is
allocated to stem for phenological stages 1 through 6.
kRoot1-6 proportion of the carbon that is
allocated to root for phenological stages 1 through 6.
kRhizome1-6 proportion of the carbon that is
allocated to rhizome for phenological stages 1 through 6.
kGrain1-6 proportion of the carbon that is
allocated to grain for phenological stages 1 through 6.
At the moment only the last stage (i.e. 6 or
post-flowering) is allowed to be larger than zero. An
error will be returned if kGrain1-5 are different from
zero.soilParms function.
FieldC Field capacity. This can be used to
override the defaults possible from the soil types (see
showSoilType).
WiltP Wilting point. This can be used to override
the defaults possible from the soil types (see
showSoilType).
phi1 Parameter which controls the spread of the
logistic function. See wtrstr for more
details.
phi2 Parameter which controls the reduction of the
leaf area growth due to water stress. See
wtrstr for more details.
soilDepth Maximum depth of the soil that the roots
have access to (i.e. rooting depth).
iWatCont Initial water content of the soil the
first day of the growing season. It can be a single value
or a vector for the number of layers specified.
soilType Soil type, default is 6 (a more typical
soil would be 3). To see details use the function
showSoilType.
soilLayer Integer between 1 and 50. The default is
5. If only one soil layer is used the behavior can be
quite different.
soilDepths Intervals for the soil layers.
wsFun one of 'logistic','linear','exp' or 'none'.
Controls the method for the relationship between soil
water content and water stress factor.
scsf stomatal conductance sensitivity factor
(default = 1). This is an empirical coefficient that
needs to be adjusted for different species.
rfl Root factor lambda. A Poisson distribution is
used to simulate the distribution of roots in the soil
profile and this parameter can be used to change the
lambda parameter of the Poisson.
rsec Radiation soil evaporation coefficient.
Empirical coefficient used in the incidence of direct
radiation on soil evaporation.
rsdf Root soil depth factor. Empirical coefficient
used in calculating the depth of roots as a function of
root biomass.nitrolParms function.
iLeafN initial value of leaf nitrogen (g m-2).
kLN coefficient of decrease in leaf nitrogen
during the growing season. The equation is LN = iLeafN *
(Stem + Leaf)^-kLN .
Vmax.b1 slope which determines the effect of leaf
nitrogen on Vmax.
alpha.b1 slope which controls the effect of leaf
nitrogen on alpha.centuryParms function.
SC1-9 Soil carbon pools in the soil. SC1:
Structural surface litter. SC2: Metabolic surface
litter. SC3: Structural root litter. SC4: Metabolic
root litter. SC5: Surface microbe. SC6: Soil microbe.
SC7: Slow carbon. SC8: Passive carbon. SC9: Leached
carbon.
LeafL.Ln Leaf litter lignin content.
StemL.Ln Stem litter lignin content.
RootL.Ln Root litter lignin content.
RhizomeL.Ln Rhizome litter lignin content.
LeafL.N Leaf litter nitrogen content.
StemL.N Stem litter nitrogen content.
RootL.N Root litter nitrogen content.
RhizomeL.N Rhizome litter nitrogen content.
Nfert Nitrogen from a fertilizer source.
iMinN Initial value for the mineral nitrogen pool.
Litter Initial values of litter (leaf, stem, root,
rhizome).
timestep currently either week (default) or day.list structure with components
Simulates dry biomass growth during an entire growing
season. It represents an integration of the photosynthesis
function c4photo, canopy evapo/transpiration
CanA, the multilayer canopy model
sunML and a dry biomass partitioning calendar
and senescence. It also considers, carbon and nitrogen
cycles and water and nitrogen limitations.
## <strong>Not run</strong>: # data(weather05) # # res0 <- BioGro(weather05) # # plot(res0) # # ## Looking at the soil model # # res1 <- BioGro(weather05, soilControl = soilParms(soilLayers = 6)) # plot(res1, plot.kind='SW') ## Without hydraulic distribution # res2 <- BioGro(weather05, soilControl = soilParms(soilLayers = 6, hydrDist=TRUE)) # plot(res2, plot.kind='SW') ## With hydraulic distribution # # # ## Example of user defined soil parameters. # ## The effect of phi2 on yield and soil water content # # ll.0 <- soilParms(FieldC=0.37,WiltP=0.2,phi2=1) # ll.1 <- soilParms(FieldC=0.37,WiltP=0.2,phi2=2) # ll.2 <- soilParms(FieldC=0.37,WiltP=0.2,phi2=3) # ll.3 <- soilParms(FieldC=0.37,WiltP=0.2,phi2=4) # # ans.0 <- BioGro(weather05,soilControl=ll.0) # ans.1 <- BioGro(weather05,soilControl=ll.1) # ans.2 <- BioGro(weather05,soilControl=ll.2) # ans.3 <-BioGro(weather05,soilControl=ll.3) # # xyplot(ans.0$SoilWatCont + # ans.1$SoilWatCont + # ans.2$SoilWatCont + # ans.3$SoilWatCont ~ ans.0$DayofYear, # type='l', # ylab='Soil water Content (fraction)', # xlab='DOY') # # ## Compare LAI # # xyplot(ans.0$LAI + # ans.1$LAI + # ans.2$LAI + # ans.3$LAI ~ ans.0$DayofYear, # type='l', # ylab='Leaf Area Index', # xlab='DOY') # # # # ## <strong>End(Not run)</strong>