R/getMolarYields.R

In HelenKettle/microPop: Modelling Microbial Populations

getMolarYields = function(microbeNames, numPaths, resData, resNames, molStoi, keyRes, 
    Rtype) {
    
    # molStoi is an array [gname,rname,pname] keyRes is a list of vectors. The
    # elements in the list are the group names The keyRes vectors contain the name
    # (string) of the key resource on each path. They have pathnames (e.g. path1,
    # path2) i.e keyRes$gname['pathname'] Rtype is an array [gname,rname,pname]
    
    molYield = NA * molStoi
    
    for (gname in microbeNames) {
        
        
        pathnames = paste("path", seq(1, numPaths[gname]), sep = "")
        
        for (pname in pathnames) {
            
            key = keyRes[[gname]][pname]
            
            if (!is.na(key)) {
                
                if (key == "Hex" & !key %in% resNames) {
                  # i.e. substitutable resources
                  resType = Rtype[gname, , pname]
                  keyStoi = mean(molStoi[gname, resType == "S", pname], na.rm = TRUE)
                  # print(keyStoi)
                } else {
                  keyStoi = molStoi[gname, key, pname]
                }
                
                molYield[gname, , pname] = molStoi[gname, , pname]/keyStoi
            }
        }
    }
    
    return(molYield)
    
}