IonContrib: Ion Matrix Calculation

In leppott/MBSStools: MBSS tool suite for calculations and data manipulation

Ion Matrix Calculation

Description

Calculates conductivity contribution from provided ion concentrations. Uses Kohlrausch's Law. If a total conductivity measurement is not provided the total conductivity is calculated as the sum of all ions present in the data. If the user provides a conductivity measurement then ion contributions are a percentage of that number. In this case "Other" is added as an ion to capture any percentage of total conductivity not represented by the provided ions. Plotting is done outside of this function.

Usage

IonContrib(ion.data, ion.ref = NULL, col.Cond = "")

Arguments

ion.data	Input data. Column names match rows in the ref table
ion.ref	Reference data for ions; Name (matches columns in data), Multiplier, and SortOrder. Default is NULL, uses included ref table.
col.Cond	Column name with conductivity in "data". Default is blank. If blank only ions present are used to calculate total conductivity for samples.

Details

No special libraries are needed for this function.

Value

Returns a data frame with additional fields for "multiplier", "ion conductivity", "total conductivity", "percent contribution" (per ion).

Examples

# Load Data
data.ion <- MBSS.Ion.Data
# Load Reference Table
ref.ion <- MBSS.Ion.Ref
# Calculate Percent Contribution by Ion (data table only)
contrib.ion <- IonContrib(data.ion)
#View(contrib.ion)
# Calculate Percent Contribution by Ion (data table and reference table)
contrib.ion.2 <- IonContrib(data.ion, ref.ion)
#View(contrib.ion.2)
# Calculate Percent Contribution by Ion (data table, reference table, and
# conductivity values)
## add dummy conductivity values for each sample
myCond <- "Cond"
data.ion[,myCond] <- 4000
contrib.ion.3 <- IonContrib(data.ion, ref.ion, myCond)
#View(contrib.ion.3)
# Save Results (use write.table())
# Plot Results
myIons <- c("Chloride (mg/L)", "Bromide (mg/L)", "Nitrate-N (mg/L)",
"Sulfate (mg/L)", "Sodium (mg/L)",
     "Potassium (mg/L)", "Magnesium (mg/L)",  "Calcium (mg/L)" )
myIons.Contrib <- paste0("PctContrib.",myIons)
mySite <- "BELK-101-X"
data.plot <- subset(contrib.ion, contrib.ion[,"Site"]==mySite,
select=c("Site","Cond.Total",myIons.Contrib,myIons))
## Plot, one site (with cond value)
dotchart(as.numeric(as.vector(data.plot[,myIons.Contrib])), labels=myIons,
main=mySite, xlab="Percent Contribution", pch=19, pt.cex=1.2)
mtext(paste0("Conductivity (uS/cm) = ",round(data.plot[,"Cond.Total"],1)))
## Plot all sites using panel.dotplot() in the lattice package
#
## Plot as a horizontal bar plot
# need to change margins to fit labels
par(mai=c(1,2,1,1))
barplot(as.numeric(as.vector(data.plot[,myIons.Contrib])), names.arg=myIons,
main=mySite, xlab="Percent Contribution"
       , axes=TRUE, horiz=TRUE, las=1)
mtext(paste0("Conductivity (uS/cm) = ",round(data.plot[,"Cond.Total"],1)))

leppott/MBSStools documentation built on April 8, 2024, 9:57 p.m.