jslefche/README.md

## README.md

      
    Raw
  

              README.md
            
          
    Calculation of chlorophyll concentration based on spectrophotometric equations

The function chlA uses the trichromatic equations to convert absorbance values (wavelengths, in nm) to estimates of chlorophyll concentration using the equations from:
Jeffrey, S. W., and G. F. Humphrey. 1975. New spectrophotometric equations for determining chlorophylls a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem Physiol Pflanz BPP:191–194.

The function takes a data.frame with the following values in the column names (corresponding to wavelengths in the equations in Jeffrey & Humphrey): "480", "510", "630", "647", "664", and "750." Additional arguments include extraction container volume (vol) and, optionally, area of extration (area, representing surface area for epiphytic algae).
The function returns the same data.frame with columns appending for chlorophyll-a, -b, and -c, and phaeopigment concentrations.
Examples

# Create fake absorbance data
set.seed(3)

fake.chla.data = data.frame(
  sample = letters[1:20],
  X480nm = sample(seq(0, 0.04, 0.001), 20, replace = TRUE), 
  X510nm = sample(seq(0, 0.02, 0.001), 20, replace = TRUE), 
  X630nm = sample(seq(0, 0.015, 0.001), 20, replace = TRUE), 
  X647nm = sample(seq(0, 0.02, 0.001), 20, replace = TRUE), 
  X664nm = sample(seq(0, 0.08, 0.001), 20, replace = TRUE), 
  X750nm = sample(seq(0, 0.01, 0.001), 20, replace = TRUE)
  )
  
# Run function
chlA(fake.chla.data)

# Run function with different volume
chlA(fake.chla.data, vol = 60)

# Run function but scale to area (in cm2)
chlA(fake.chla.data, area = 20)


## chlA.R
#' `edgarMethod` an R function for estimating algal biomass using the trichromatic equations

#' Author: Jon Lefcheck
#' Last updated: 01 February 2017

#' @param x = a sample-by-wavelength matrix
#' @param volume = the volume (in mL) of the extraction vial
#' @param area = the area of the extraction vial (if reported)
#' @return a `data.frame` containing the original values, and estimated abundances of chlorophyll a, b, c, and phaeopigments

chlA = function(data, vol = 20, area = NULL) {

  # Extract only numeric columns
  data.sub = data[, sapply(data, is.numeric)]

  # Set any negative absorbances to zero
  data.sub[data.sub < 0] = 0

  # Identify which columsn correspond to which absorbances
  WL480 = data.sub[, grepl("480", colnames(data.sub))]
  WL510 = data.sub[, grepl("510", colnames(data.sub))]
  WL630 = data.sub[, grepl("630", colnames(data.sub))]
  WL647 = data.sub[, grepl("647", colnames(data.sub))]
  WL664 = data.sub[, grepl("664", colnames(data.sub))]
  WL750 = data.sub[, grepl("750", colnames(data.sub))]

  # Stop function if missing any absorbances
  if(any(sapply(list(WL480, WL510, WL630, WL647, WL664, WL750), function(x) all(is.na(x))))) {

    # Get missing wavelength
    nm = which(sapply(list(WL480, WL510, WL630, WL647, WL664, WL750), function(x) all(is.na(x))))

    stop(paste("Missing ", c("480", "510", "630", "647", "664", "750")[nm]," nm wavelength!", sep = ""))

  }

  # Use trichromatic equations to convert absorbances into ug mL-1
  chla.data = data.frame(
    chla = 11.85 * (WL664 - WL750) - 1.54 * (WL647 - WL750) - 0.08 * (WL630 - WL750),
    chlb = 21.03 * (WL647 - WL750) - 5.43 * (WL664 - WL750) - 2.66 * (WL630 - WL750),
    chlc = 24.52 * (WL630 - WL750) - 1.67 * (WL664 - WL750) - 7.60 * (WL647 - WL750),
    chlp = 7.60 * ((WL480 - 3 * WL750) - 1.49 * (WL510 - 2 * WL750))
  )

  names(chla.data) = c("chla", "chlb", "chlc", "chlp")

  #Multiply by volume of sample (default is 20 mL) to yield ug biomass
  chla.data = chla.data * 20

  # Standardize to area (if present)
  if(!is.null(area)) chla.data = chla.data / area

  # Return data
  data.frame(data, chla.data)

}
	#' `edgarMethod` an R function for estimating algal biomass using the trichromatic equations

	#' Author: Jon Lefcheck
	#' Last updated: 01 February 2017

	#' @param x = a sample-by-wavelength matrix
	#' @param volume = the volume (in mL) of the extraction vial
	#' @param area = the area of the extraction vial (if reported)
	#' @return a `data.frame` containing the original values, and estimated abundances of chlorophyll a, b, c, and phaeopigments

	chlA = function(data, vol = 20, area = NULL) {

	# Extract only numeric columns
	data.sub = data[, sapply(data, is.numeric)]

	# Set any negative absorbances to zero
	data.sub[data.sub < 0] = 0

	# Identify which columsn correspond to which absorbances
	WL480 = data.sub[, grepl("480", colnames(data.sub))]
	WL510 = data.sub[, grepl("510", colnames(data.sub))]
	WL630 = data.sub[, grepl("630", colnames(data.sub))]
	WL647 = data.sub[, grepl("647", colnames(data.sub))]
	WL664 = data.sub[, grepl("664", colnames(data.sub))]
	WL750 = data.sub[, grepl("750", colnames(data.sub))]

	# Stop function if missing any absorbances
	if(any(sapply(list(WL480, WL510, WL630, WL647, WL664, WL750), function(x) all(is.na(x))))) {

	# Get missing wavelength
	nm = which(sapply(list(WL480, WL510, WL630, WL647, WL664, WL750), function(x) all(is.na(x))))

	stop(paste("Missing ", c("480", "510", "630", "647", "664", "750")[nm]," nm wavelength!", sep = ""))

	}

	# Use trichromatic equations to convert absorbances into ug mL-1
	chla.data = data.frame(
	chla = 11.85 * (WL664 - WL750) - 1.54 * (WL647 - WL750) - 0.08 * (WL630 - WL750),
	chlb = 21.03 * (WL647 - WL750) - 5.43 * (WL664 - WL750) - 2.66 * (WL630 - WL750),
	chlc = 24.52 * (WL630 - WL750) - 1.67 * (WL664 - WL750) - 7.60 * (WL647 - WL750),
	chlp = 7.60 * ((WL480 - 3 * WL750) - 1.49 * (WL510 - 2 * WL750))
	)

	names(chla.data) = c("chla", "chlb", "chlc", "chlp")

	#Multiply by volume of sample (default is 20 mL) to yield ug biomass
	chla.data = chla.data * 20

	# Standardize to area (if present)
	if(!is.null(area)) chla.data = chla.data / area

	# Return data
	data.frame(data, chla.data)

	}