############################
#' merge salinity into analysis data frame and update iSpec with variable name
#'
#' @param ct1 analysis data frame
#' @param iSpec iSpec
#' @param salinity.detrended data generated by detrended.salinity. Default = detrended.salinity.
#'
#' @keywords internal
#' @export
#' @importFrom stats cor
#'
.mergeSalinity <- function(ct1=ct1, iSpec=iSpec, salinity.detrended=salinity.detrended) {
# -----< Change history >--------------------------------------------
# 29Jul2017: JBH: first release
# grab the salinity data
tmp <- salinity.detrended[[iSpec$stat]]
# pick which salinity series to use (BBP or SAP)
iSpec$hydroTermSel.var <- ifelse(iSpec$layer %in% c("B","BP","BBP"),"BBP","SAP")
# merge data and rename variable to 'flw_sal'
tmp <- merge(ct1, tmp[ ,c("date",iSpec$hydroTermSel.var )], by="date", all.x=TRUE)
names(tmp)[names(tmp) == iSpec$hydroTermSel.var] <- 'flw_sal'
# packup
ct1.list <- list(ct1=tmp,iSpec=iSpec)
return(ct1.list)
}
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