R/mergeFlow.R

In leppott/baytrends033: Long Term Water Quality Trend Analysis

############################
#' merge flow variable into analysis data frame and update iSpec with variable name
#'
#' @param ct1 analysis data frame
#' @param iSpec iSpec
#' @param gageID "q" + USGS gage ID
#' @param hydro.var averaging windows
#' @param flow.detrended data generated by detrended.flow.  Default = flow.detrended.
#'
#' @keywords internal
#' @export
#' @importFrom stats cor
#'
.mergeFlow <- function(ct1=ct1, iSpec=iSpec, gageID=gageID, hydro.var=hydro.var
                       , flow.detrended=flow.detrended) {
# -----< Change history >--------------------------------------------
# 01May2018: JBH: changed .impute to impute  
# 29Jul2017: JBH: first release

  # merge detrended flow with dependent variable
  tmp <- flow.detrended[[gageID]]
  tmp <- merge(ct1[, c("date",iSpec$dep)],
               tmp[ ,c("date",hydro.var)], by="date", all.x=TRUE)
  tmp[,iSpec$dep] <- if (iSpec$isSurv) impute(tmp[,iSpec$dep]) else tmp[,iSpec$dep]
  # set up data frame to store correlation results
  hydro.var.corr <- data.frame(hydro.var=hydro.var, spearman= NA_real_ ,
                               chosen="-", stringsAsFactors = FALSE)
  # compute spearman correlation
  for (i in 1:nrow(hydro.var.corr)) {
    hydro.var.corr[i,"spearman"] <- cor(y = tmp[,iSpec$dep], x = tmp[,hydro.var[i]],
                                        use = "pairwise.complete.obs", method = "spearman")
  }
  # identify variable yields largest abs. correlation
  hydro.var.corr[which.max(abs(hydro.var.corr[,"spearman"])),"chosen"] <- 'max'
  iSpec$hydro.var.corr   <- hydro.var.corr
  iSpec$hydroTermSel.var <- hydro.var.corr[which.max(abs(hydro.var.corr[,"spearman"])),"hydro.var"]
  # now merge just the needed variable and rename to flw_sal
  tmp <- flow.detrended[[gageID]]
  tmp <- merge(ct1, tmp[ ,c("date",iSpec$hydroTermSel.var )], by="date", all.x=TRUE)
  names(tmp)[names(tmp) == iSpec$hydroTermSel.var] <- 'flw_sal'
  # pack up
  ct1.list <- list(ct1=tmp,iSpec=iSpec)
  return(ct1.list)
}