R/makeParamMatrixS.R

In microPop: Process-Based Modelling of Microbial Populations

#' Gets parameter values for parameters halfSat, yield and maxGrowthRate
#' from the MFGs and puts into a matrix
#' also assigns strain traits
#' since traits are assigned to all strains at once for one param they are
#' stored in Mat[strain,res,path], this is then rearranged to make a matrix
#' for each strain (mat[path,res]).
#' 
#' @param resNames Vector of strings which contains the names of the resources in the system
#' @param microbeNames Vector of strings which contains the names of the microbial groups in the system e.g. c('Bacteroides','Acetogens')
#' @param parameterName Name of parameter
#' @param numPaths Named vector. Number of paths for each microbial group
#' @param numStrains Integer or named vector of integers. Number of strains per group
#' @param strainOptions List of strain options
#' @param oneStrainRandomParams Logical. TRUE for randomized params even if there is only one strain.
#' @return A list called parameterName which contains matrices for all strains (in all groups) with paths on rows and resources on columns
#' @keywords internal

makeParamMatrixS = function(resNames, microbeNames, parameterName, numPaths, numStrains, 
    strainOptions, oneStrainRandomParams) {

    #print(parameterName)
    
    pList = list()
    nam = NULL
    
    for (gname in microbeNames) {
        
        Lr = length(resNames)
        Lp = numPaths[gname]
        if (length(numStrains)>1){
            Ls = numStrains[gname]
        }else{
            Ls = numStrains
        }
        
        # assign strain names to str.names
        if (length(numStrains)==1 & Ls == 1) {
            str.names = gname
        } else {
            str.names = paste(gname, ".", seq(1, Ls), sep = "")
        }
        
        path.names = paste("path", seq(1, Lp), sep = "")
        
        Mat = array(NA, dim = c(Ls, Lr, Lp), dimnames = list(str.names, resNames, 
            path.names))
        
        data = get(gname)  #get dataframe for microbial group
        
        for (path in 1:Lp) {
            
            if (path == 1) {
                var = parameterName
            } else {
                var = paste(parameterName, ".", path, sep = "")
            }
            
            
            if (!var %in% rownames(data)) {
                stop(paste("MICROPOP ERROR: parameter", var, "is not in", gname,
                           "data frame (note code is case sensitive)"))
            }
            
            
            # assign traits
            for (r in 1:Lr) {
                
                rname = resNames[r]
                
                if (rname %in% colnames(data)) {
                  # rname is a resource for group g
                  
                  pval = as.numeric(data[var, rname])
                  
                  if (Ls > 1 | oneStrainRandomParams) {
                    
                    if (parameterName %in% strainOptions$randomParams) {
                      traitVals = assignStrainTraits(Ls, pval, strainOptions, 
                        parameterName, pHtrait = FALSE, gname)
                    } else {
                      traitVals = pval * rep(1, Ls)
                    }
                    
                    Mat[, r, path] = traitVals
                    
                  } else {
                    Mat[1, r, path] = pval
                  }
                  
                } else {
                  # rname is not a resource for group g
                  
                  Mat[, r, path] = NA
                }
                
            }  #r
            
        }  #path
        
        # make matrix for each strain
        for (s in 1:Ls) {
            mat = matrix(NA, nrow = Lp, ncol = Lr, dimnames = list(path.names, resNames))
            for (p in 1:Lp) {
                mat[p, ] = Mat[s, , p]
            }
            if (length(numStrains)==1 & Ls == 1) {
                mat.name = gname
            } else {
                mat.name = paste(gname, ".", s, sep = "")
            }
            nam = append(nam, mat.name)
            pList = append(pList, list(mat))
        }
        
    }
    
    names(pList) = nam

    return(pList)
    
}