waterabs
Light absorption by the water column
Description
The absorption of light by water is highly dependent on the wavelength, this dataset gives the absorption coefficients from 200 to 700 nm.
Usage
data(waterabs)
Format
A data.frame with 2 columns:
- lambda
-
wavelength in nm
- abs
-
absorption coefficient in 1/cm
Source
Data were compiled by Palmeira (2007) from the cited references.
The example section allows to reproduce the left part of figure 2.7 from Palmeira (2007):
References
Palmeira, L. (2007) Analyse et modélisation des dépendances entre
sites voisins dans l'évolution des séquences d'ADN, PhD thesis,
Université Claude Bernard - Lyon I.
Litjens R. A., Quickenden T. I. and Freeman C. G. (1999). Visible and
near-ultraviolet absorption spectrum of liquid water. Applied Optics,
38:1216-1223.
Quickenden T. I. & Irvin J. A. (1980). The ultraviolet absorption spectrum
of liquid water. The Journal of Chemical Physics, 72:4416-4428.
citation("seqinr")
Examples
data(waterabs)
d <- 100*seq(from = 0, to = 150, by = 1) # depth in cm
lambda <- waterabs$lambda # wavelength in nm
abs <- waterabs$absorption # absorption coefficient cm-1
#
# Smooth signal with cubic splines
#
tmp <- spline(lambda, abs, n = 255)
lambda <- tmp$x
abs <- tmp$y
zun <- sapply(abs,function(x) 10^(-x*d))
z <- sapply(nrow(zun):1, function(x) zun[x,])
#
# Set up world coordinates:
#
plot.new()
plot.window(xlim = range(lambda), ylim = range(d), xaxs = "i", yaxs = "i")
#
# Annotate:
#
title(ylab = 'Depth under water surface (m)', xlab = "Wavelength (nm)",
main = "Light absorption by the water column")
axis(2 , at = seq(0, 15000, l = 7),
labels = rev(c("0","25","50","75","100","125","150")), las = 1)
axis(1,at=(3:6)*100,labels= TRUE)
#
# Show me rainbow colors:
#
alpha <- 1
coul=c(rep(rgb(1,1,1, alpha = alpha), 181),
rev(hsv(h=seq(0,5/6,l=320),alpha = alpha)))
rect(seq(200,699), 0, seq(201,700), 15000 , col = coul, border = coul)
#
# Grey scale:
#
ngris <- 5
image(x = lambda, y = d, z = z, col = rgb(1:ngris, 1:ngris, 1:ngris, alpha = 0.7*(ngris:1),
max = ngris),
axes = F, add = TRUE,
breaks = seq(from = min(z), to = max(z), length = ngris + 1))
#
# Contour lines:
#
contour(x = lambda, y = d, z = z, add = TRUE, drawlabels = TRUE,labcex= 0.75,
col='black',
levels = seq(from = min(z), to = max(z), length = ngris + 1))
box()