R/logTransFxn.R

In USGS-R/USGSHydroOpt: Tools for optical data analysis

#' getLog10
#'
#' Computes log transform of optical summary data. 
#'
#' @param dataSummary dataframe with summary absorbance and fluoresence data.
#' @param signals character vector of variable names in dataSummary for generating log transforms
#' @param grnum character column name that defines the column with sample names in the dataSummary dataframe.
#' These names are used to merge ratio data into the summary dataframe. 
#' @return dataframe with the log 10 transform of the summary absorbance and fluoresence data.
#' @export
#' @examples
#' dataSummary <- dfsummary
#' signals <- ratioSignals[which(ratioSignals[2]>0),1]
#' grnum<-"GRnumber"
#' test2 <- getLog10(dataSummary,signals,grnum)
getLog10 <- function(dataSummary,signals,grnum){
    
    ratios <- data.frame(dataSummary[,grnum])
    names(ratios) <- grnum
    for(i in 1:(length(signals))){
      if(!any(dataSummary[,signals[i]] < 0,na.rm = TRUE)){
      dataSummary <- cbind(dataSummary,log10(dataSummary[,signals[i]]))
      names(dataSummary)[dim(dataSummary)[2]] <- paste("log",signals[i],sep="")
      }
    }
    
    return(dataSummary)
    
  }