CanA: Simulates canopy assimilation
In BioCro: Simulation of Biomass Crops

Description Usage Arguments Value Examples

It represents an integration of the photosynthesis function c4photo, canopy evapo/transpiration and the multilayer canopy model sunML.

CanA(lai,doy,hr,solar,temp,rh,windspeed,
     lat=40,nlayers=8,kd=0.7,
     stress=1, chi.l=1, leafwidth=0.04,
     heightFactor = 3,
     photoControl = list(),
     lnControl = list(),
     units = c("kg/m2/hr","Mg/ha/hr"))

`lai`	leaf area index.
`doy`	day of the year, (1–365).
`hr`	hour of the day, (0–23).
`solar`	solar radiation (micro mol m-2 s-1).
`temp`	temperature (Celsius).
`rh`	relative humidity (0–1).
`windspeed`	wind speed (m s-1).
`lat`	latitude.
`nlayers`	number of layers in the simulation of the canopy (max allowed is 50).
`kd`	Ligth extinction coefficient for diffuse light.
`stress`	coefficient controlling the effect of water stress on stomatal conductance and assimilation.
`chi.l`	The ratio of horizontal to vertical projected area of leaves in the canopy segment. A smaller than 1 value represents a more upright canopy and a value higher than 1 is represented by more horizontal leaves.
`leafwidth`	average leaf width.
`heightFactor`	Height Factor. Divide LAI by this number to get the height of a crop.
`photoControl`	list that sets the photosynthesis parameters. See `BioGro`.
`lnControl`	list that sets the leaf nitrogen parameters. LeafN: Initial value of leaf nitrogen (g m-2). kpLN: coefficient of decrease in leaf nitrogen during the growing season. The equation is LN = iLeafN * exp(-kLN * (CumLAI-(LAI/nlayers))). lnFun: controls whether there is a decline in leaf nitrogen with the depth of the canopy. 'none' means no decline, 'linear' means a linear decline controlled by the following two parameters. lnb0: Intercept of the linear decline of vmax in the depth of the canopy. In this function this parameter together with lnb1 will override the vmax value set in photoControl. lnb1: Slope of the linear decline of leaf nitrogen in the depth of the canopy. The equation is 'vmax = leafN_lay * lnb1 + lnb0'.
`units`	Whether to return units in kg/m2/hr or Mg/ha/hr. This is typically run at hourly intervals, that is why the hr is kept, but it could be used with data at finer timesteps and then convert the results.

list

returns a list with several elements

CanopyAssim: hourly canopy assimilation (kg/m2 per hour) or canopy assimilation (Mg/ha per hour)

CanopyTrans: hourly canopy transpiration (kg/m2 per hour) or canopy transpiration (Mg/ha per hour)

CanopyCond: hourly canopy conductance (mmol/m2/s)

TranEpen: hourly canopy transpiration according to Penman (kg m^{-2} per hour) or canopy transpiration according to Penman (Mg ha^{-1} per hour)

TranEpries: hourly canopy transpiration according to Priestly (kg/m2 per hour) canopy transpiration according to Priestly (Mg/ha per hour)

LayMat: hourly by Layer matrix containing details of the calculations by layer (each layer is a row). col1: Direct Irradiance (micro mol/m2/s) col2: Diffuse Irradiance (micro mol/m2/s) col3: Leaf area in the sun (m2/m2) col4: Leaf area in the shade (m2/m2) col5: Transpiration of leaf area in the sun (kg/m2/h) col6: Transpiration of leaf area in the shade (kg/m2/h) col7: Assimilation of leaf area in the sun (micro mol/m2/s) col8: Assimilation of leaf area in the shade (micro mol/m2/s) col9: Difference in temperature between the leaf and the air (i.e. TLeaf - TAir) for leaves in sun (units = C). col10: Difference in temperature between the leaf and the air (i.e. TLeaf - TAir) for leaves in shade (units = C). col11: Stomatal conductance for leaves in the sun col12: Stomatal conductance for leaves in the shade col13: Nitrogen concentration in the leaf (g m^-2) col14: Vmax value as depending on leaf nitrogen col15: Relative humidty (0-1) col16: Wind speed (m/s) col17: Canopy height (m)

 ## Not run: 
  data(doy124)
  tmp <- numeric(24)

  for(i in 1:24){
    lai <- doy124[i,1]
    doy <- doy124[i,3]
    hr  <- doy124[i,4]
    solar <- doy124[i,5]
    temp <- doy124[i,6]
    rh <- doy124[i,7]
    ws <- doy124[i,8]

    tmp[i] <- CanA(lai,doy,hr,solar,temp,rh,ws)$CanopyAssim

  }

  plot(c(0:23),tmp,
            type="l",lwd=2,
            xlab="Hour",
            ylab=expression(paste("Canopy assimilation (kg  ",
            m^-2," ",h^-1,")")))
 
## End(Not run)