vezy / dynacof Goto Github PK

Create a variable that keeps track of the total number of fruits on the coffee each days.

For now, lifespan is used as a ratio over the total dry mass for each organ. It should be used to remove organ mass that was created lifespan_organ days before "i".
This is what we do:

  S$Sim$Mact_CR_Tree[i]=
    S$Sim$CM_CR_Tree[previous_i(i,1)]/S$Parameters$lifespanCR_Tree

This is what we should do:

  S$Sim$Mact_CR_Tree[i]=
    S$Sim$NPP_CR_Tree[previous_i(i,S$Parameters$lifespanCR_Tree)]*
         after(i,S$Parameters$lifespanCR_Tree)

With after() a function to avoid a positive value of NPP if i is before any mortality:

after= function(x,ref){
  index= x-ref
  index[index<=0]= 0
  index[index>0]=1
  return(index)
}

This technique will remove only the old dry mass instead of a constant ratio of the dry mass.

I'm trying to understand how to run DynACof with parameters for shade trees.

The example code supplied uses Tree = NULL, which if I understand correctly assumes that there are no shade trees.

I tried loading the sample data available from the DynACof_inputs github, but when I run the code

sim= DynACof(Inpath = dynacof_data, FileName = list(Site = "site.R", Meteo ="meteorology.txt", Soil = "soil.R",Coffee = "coffee.R", Tree = "tree.R"))

as suggested, I keep getting the error:

Error in Tree() : object 'Metamodels' not found

The tree.R file from DynACof_inputs seems to define Metamodels = Metamodels, but as far as I can tell the function or object does not exist. In contrast, Allometries seems to be a function that loads as part of the DynACof library.

Is there somewhere to download example files for Metamodels?

(I also posted an issue on the DynACof_inputs, but the Issues here seems slightly more active, so I thought I would try here as well.)

Using this formula:
humedadRelativaTavg: tAvg tempMax: tMax tempMin: tMin
"RH = 100 - 5 (T - Td) Td= temp dewpoint : point de rosée.
RH = (Td - T + 20) * 5
Td = 0.38 Tmax - 0.018 Tmax^2 + 1.4 Tmin - 5"

TairCanopy_Tree is very much equal to Tair. Investigate why (either H is very low, either conductance is too high)

Intercrevapor, the evaporation from the leaves -i.e. the precipitation intercepted by leaves and re-evaporated- is computed using the net radiation computed in the meteorology with Allen et al. (1998) equations. This should be replaced by an Rn computed by the model.
The difficulty is that Rn can only be computed knowing Intercrevapor, so an iteration process is needed. We could maybe find another equation to avoid that because it will increase the computation time that is already long.

Sometimes coffee resprouts are pruned just before harvest in the model. This is nonsense as coffees always are pruned after harvest to avoid fruit loss.

Many variables should only be computed (and kept) with 2 digits only. Find an efficient way to do that:

• Search if there is a way to limit the digits allowed in the main list
• If not, use round(.,2).

In any case, test the computation time (the first purpose here is to reduce overall computation time).