R: Light absorption by the water column

waterabs {seqinr} | R Documentation

## 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()

[Package seqinr version 3.4-5 Index]