#' get stochastically generated pH corners for each strain
#'
#' Returns the values of the pH values of the limit function i.e. where the limit is c(0,1,1,0)
#' Reads these in from the microbe group dataframes
#'
#' @param microbeNames (vector of strings). Names of microbes in the system
#' @param allStrainNames (vector of strings)
#' @param numStrains Integer
#' @param pHcorners vector of 4 scalars definining the pH lim func
#' @param pHLimit (logical) Is microbial growth affected by pH?
#' @param strainOptions list from microPopModel inputs
#'
#' @return (matrix) values of the pH values of the limit function i.e.
#' where the limit is c(0,1,1,0) for each strain
#' @export
getStrainPHcorners = function(microbeNames, allStrainNames, numStrains, pHcorners,
pHLimit, strainOptions) {
mat = matrix(NA, ncol = 4, nrow = length(allStrainNames),
dimnames = list(allStrainNames))
if (pHLimit & "pHtrait" %in% strainOptions$randomParams) {
# assign strain traits
for (g in 1:length(microbeNames)) {
shifts = assignStrainTraits(numStrains, 1, strainOptions,
parName = "pHtrait",
pHtrait = TRUE) - 1
for (i in 1:numStrains) {
mat[((g - 1) * numStrains + i), ] = pHcorners[microbeNames[g], ] +
shifts[i]
}
}
}
return(mat)
}
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