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Type: Package
Title: R Functions to Model CDOM Spectra
Version: 0.1.0
Date: 2016-02-22
Description: Wrapper functions to model and extract various quantitative information from absorption spectra of chromophoric dissolved organic matter (CDOM).
BugReports: https://github.com/PMassicotte/cdom/issues
URL: https://github.com/PMassicotte/cdom
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Depends: R (≥ 3.0)
LazyData: TRUE
Imports: minpack.lm, ggplot2, tidyr, broom
RoxygenNote: 5.0.1
Suggests: eemR
NeedsCompilation: no
Packaged: 2016-03-04 07:16:53 UTC; persican
Author: Philippe Massicotte [aut, cre]
Maintainer: Philippe Massicotte <pm@bios.au.dk>
Repository: CRAN
Date/Publication: 2016-03-04 08:39:29

Fit an exponential model to CDOM data.

Description

Fit an exponential model to CDOM data.

Usage

cdom_fit_exponential(wl, absorbance, wl0 = 350, startwl, endwl)

Arguments

wl

The wavelength vector.

absorbance

The absorbance vector.

wl0

The reference wavelength (ex.: 350).

startwl

The starting wavelength (ex.: 240).

endwl

The ending wavelength (ex.: 600).

Details

y = a0 + e^{(-S(x - \lambda_0))} + K

Value

A list containing:

params

A data frame with values of fitted parameters.

r2

R2 of the nls model.

data

A data frame with fitted (predicted) values of the model.

The function will return NULL if the model did not converged.

Examples

# Fit an exponential model using the reference wavelength 350 between 190 and 900 nm.

data(spectra)

fit <- cdom_fit_exponential(spectra$wavelength, spectra$spc1, 350, 190, 900)
str(fit)

plot(spectra$wavelength, spectra$spc1)
lines(spectra$wavelength, fit$data$.fitted, col = "red")

Calculate the slope ratio (SR) from an absorption spectra.

Description

Calculate the slope ratio (SR) from an absorption spectra.

Usage

cdom_slope_ratio(wl, absorbance)

Arguments

wl

The wavelength vector.

absorbance

The absorbance vector.

Details

Calculate the slope ratio (SR) as defined by Helms et al. (2008).

SR = \frac{S_{275-295}}{S_{350-400}}

Value

The value of the slope ratio.

References

http://www.aslo.org/lo/toc/vol_53/issue_3/0955.html

Examples

data("spectra")

cdom_slope_ratio(spectra$wavelength, spectra$spc1)


Calculate the spectral curve of CDOM spectra.

Description

Calculate the spectral curve of CDOM spectra has proposed by Loiselle et al. 2009.

Usage

cdom_spectral_curve(wl, absorbance, interval = 21, r2threshold = 0.8)

Arguments

wl

The wavelength vector.

absorbance

The absorbance vector.

interval

The interval used to claculate each slope (default = 21 nm).

r2threshold

The r2 threshold that determines if a slope is "valide". The default value is 0.8 meaning that the determination coefficient of the regression between log-transformed data and wavelength should be >= 0.8.

Value

A dataframe containing the centered wavelength, the calculated slope and the determination coefficient of the linear regression used to claculate the slope.

References

http://doi.wiley.com/10.4319/lo.2009.54.2.0590

Examples

data(spectra)

res <- cdom_spectral_curve(spectra$wavelength, spectra$spc2)
plot(res$wl, res$s, type = "l")

CDOM absorption data.

Description

Simple absorption spectra used to test package's functions.

Usage

data(spectra)

Format

A data frame with 711 rows and 26 variables

Details

Examples

library(ggplot2)
library(tidyr)
data("spectra")

spectra <- gather(spectra, sample, absorption, -wavelength)

ggplot(spectra, aes(x = wavelength, y = absorption, group = sample)) +
 geom_line(size = 0.1)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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