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

getIndexes

R Documentation

getIndexes

Description

Computes humification index and fluorescence indes from fluorescence data. HIX as defined by Ohno, 2002, Fluorescence inner-filtering correction for determining the humification index of dissolved organic matter. Environ. Sci. Technol. 36: 742-746 doi: 10.1021/es0155276, HIX = sum(I435:I480)/(sum(I300:I345)+sum(I435:I480)) for ex=254 and FI_2005 as defined by Cory and McKnight, 2005, Fluorescence spectroscopy reveals ubiquitous presence of oxidized and reduced quinones in DOM. Environ. Sci. Technol. 39: 8142-8149, doi:10.1021/es0506962 and FI_2001 defined by MCKNIGHT, D. M., E. W. BOYER, P. K. WESTERHOFF, P. T. DORAN, T. KULBE, AND D. T. ANDERSEN. 2001. Spectrofluorometric characterization of DOM for indication of precursor material and aromaticity. Limnol. Oceanogr. 46: 38-48, doi:10.4319/lo.2001.46.1.0038. FI = ex370em470/ex370em520 and freshness index as defined by PARLANTI, E., K. WORZ, L. GEOFFROY, AND M. LAMOTTE. 2000. Dissolved organic matter fluorescence spectroscopy as a tool to estimate biological activity in a coastal zone submitted to anthropogenic inputs. Org. Geochem. 31: 1765-1781, doi:10.1016/S0146-6380(00)00124-8 FreshI = ex310em380/max(ex310 between em470 and em520),

Usage

getIndexes(a, dataSummary, grnum)

Arguments

`a`	an array with 3-D fluorescence results. The 3 dimensions are the excitation wavelength (character), the emission wavelength (character), and the sample names (character).
`dataSummary`	dataframe with summary absorbance and fluoresence data. This function adds columns to the end of this dataframe as additional summary data.
`grnum`	character column name that defines the column with sample names in the dataSummary dataframe. These names are used to merge spectral slope data into the summary dataframe.

Value

dataSummary dataframe with the additional columns containing the humification and fluoresence indices.

Examples

a <- a
dataSummary <- dfsummary 
dataSummary <- dataSummary[,-c(43:46)] #remove columns with fluoresence and humic index
grnum <- "GRnumber"
test1 <- getIndexes(a,dataSummary,grnum)

USGS-R/USGSHydroOpt documentation built on Oct. 18, 2022, 9:50 a.m.