sole: Sole Eggs in the Bristol Channel

In gamair: Data for 'GAMs: An Introduction with R'

Description

Data on Sole Egg densities in the Bristol Channel (West Coast of England, UK.) The data are from 5 research cruises undertaken for the purpose of measuring Sole egg densities. Samples were taken at each of a number of sampling stations, by hauling a net vertically through the water column. Sole eggs were counted and assigned to one of four developmental stages.

Usage

data(sole)

Format

A data frame with 7 columns and 1575 rows. The columns are:

la

latitude of sampling station

lo

longitude of sampling station

t

time of sampling station: actually time of midpoint of the cruise on which this sample was taken. Measured in Julian days (days since January 1st).

eggs

egg density per square metre of sea surface.

stage

to which of 4 stages the sample relates.

a.0

lower age limit for the stage (i.e. age of youngest possible egg in this sample).

a.1

upper age limit of this stage (i.e. age of oldest possible egg in sample).

Source

Dixon (2003)

References

Dixon, C.E. (2003) Multi-dimensional modelling of physiologically and temporally structured populations. PhD thesis. University of St Andrews

Horwood, J. (1993) The Bristol Channel Sole (solea solea (L.)): A fisheries case study. Advances in Marine Biology 29, 215-367

Horwood, J. and M. Greer Walker (1990) Determinacy of fecundity in Sole (solea solea) from the Bristol Channel. Journal of the Marine Biology Association of the United Kingdom. 70, 803-813.

Wood (2006, 2017) Generalized Additive Models: An Introduction with R. CRC

Examples

  require(gamair)
  data(sole);data(coast)
  par(mfrow=c(2,3))
  sample.t <- unique(sole$t)
  stage <- 1
  for (i in 1:5)
  { egg<-sole[sole$stage==stage&sole$t==sample.t[i],] 
    plot(egg$lo,egg$la,xlab="lo",ylab="la",main=paste("day",sample.t[i]),cex=egg$eggs/4,
    xlim=range(sole$lo),ylim=range(sole$la),cex.axis=1.5,cex.lab=1.5,cex.main=1.5)
    points(egg$lo,egg$la,pch=".",col=2)
    lines(coast)
  }
  ## boundary definition list and knots suitable for soap film smoothing
  bnd <- list(list(lo=c(-6.74,-5.72,-5.7 ,-5.52,-5.37,-5.21,-5.09,-5.02,
          -4.92,-4.76,-4.64,-4.56,-4.53,-4.3,-4.16,-3.8 ,-3.8,-5.04,-6.76,
	  -6.74),
          la=c(50.01,50.02,50.13,50.21,50.24,50.32,50.41,50.54,50.59,50.64,
	  50.74,50.86,51.01,51  ,51.2,51.22,51.61,51.7,51.7,50.01)))

  knt <- list(lo=c(-4.643,-5.172,-5.638,-6.159,-6.665,-6.158,-5.656,-5.149,
  -4.652,-4.154,-3.901,-4.146,-4.381,-4.9,-5.149,-5.37,-5.866,-6.36,-6.635,
  -6.12,-5.626,-5.117,-4.622,-4.695,-4.875,-5.102,-5.609,-5.652,-5.141,
  -5.354,-5.843,-6.35,-6.628,-6.127,-5.63,-5.154,-5.356,-5.652,-5.853,
  -6.123),
   la=c(51.626,51.61,51.639,51.638,51.376,51.377,51.373,51.374,51.374,
   51.376,51.379,51.226,51.129,51.194,51.083,51.147,51.129,51.151,50.901,
   50.891,50.959,50.958,50.942,50.728,50.676,50.818,50.825,50.684,50.693,
   50.568,50.564,50.626,50.397,50.451,50.443,50.457,50.325,50.193,50.322,
   50.177))

   points(knt$lo,knt$la,pch=19,col=2,cex=.6)
   lines(bnd[[1]]$lo,bnd[[1]]$la,col=2)

Example output

gamair documentation built on Aug. 23, 2019, 5:03 p.m.