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#' 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 or named vector of integers
#' @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
#' @param oneStrainRandomParams logical 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,oneStrainRandomParams) {
# mat = matrix(NA, ncol = 4, nrow = length(allStrainNames),
# dimnames = list(allStrainNames))
mat=NULL
if (pHLimit){
for (g in 1:length(microbeNames)) {
#check if numStrains has a value per group
if (length(numStrains)==1){
Ls=numStrains
}else{
Ls=numStrains[microbeNames[g]]
}
#print(strainOptions)
shifts=rep(0,Ls)
if (Ls>1 | oneStrainRandomParams){
if ("pHtrait" %in% strainOptions$randomParams) {
shifts = assignStrainTraits(Ls, 1, strainOptions,
parName = "pHtrait",
pHtrait = TRUE, microbeNames[g]) - 1
}
}
for (i in 1:Ls) {
mat=rbind(mat,pHcorners[microbeNames[g], ]+shifts[i])
}
}
rownames(mat)=allStrainNames
}
return(mat)
}
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