R/getKeyRes.R

In HelenKettle/microPop: Modelling Microbial Populations

#' Finds the name of the key resource for each path for each MFG
#' @param microbeNames Vector of strings which contains the names of the microbial groups in the system e.g. c('Bacteroides','Acetogens')
#' @param numPaths Named vector. Number of paths for each microbial group. Names are microbeNames
#' @return list of vectors where the names are microbeNames
#' @export
getKeyRes = function(microbeNames, numPaths) {
    
    key = list()
    
    for (gname in microbeNames) {
        
        data = get(gname)
        
        vec = seq(1, numPaths[gname]) * NA
        names(vec) = paste("path", seq(1, numPaths[gname]), sep = "")
        
        for (p in 1:numPaths[gname]) {
            
            if (p == 1) {
                kvar = "keyResource"
                Rvar = "Rtype"
            } else {
                kvar = paste("keyResource.", p, sep = "")
                Rvar = paste("Rtype.", p, sep = "")
            }
            
            if (any(colnames(data) == "units") | any(colnames(data) == "Units")) {
                vec[p] = data[kvar, ][[2]]
            } else {
                vec[p] = data[kvar, ][[1]]
            }
            
            if (any(data[Rvar, ] == "Se") | any(data[Rvar, ] == "Sb") | any(data[Rvar, 
                ] == "Sm")) {
                # if (!vec[p]%in%colnames(data)){stop(paste('MICROPOP ERROR: The key resource
                # for',gname,'on path',p,'is not one of its resources'))}
            } else {
                if (!is.na(vec[p])) {
                  print(vec[p])
                  print(paste("MICROPOP NOTE TO USER: The key resource for", gname, 
                    "on path", p, "is not used"))
                }
            }
            
        }  #path loop
        
        key = append(key, list(vec))
    }
    
    names(key) = microbeNames
    
    return(key)
}