lengthHist: Plots a length frequency histogram from csData
In ldbk/fishPifct: fishPi functions

Description Usage Arguments Details Value Author(s) See Also Examples

Plots histograms of the length frequency data from the hl table of csData objects. Optionally can plot by a grouping variable, and specific factor levels within the grouping variable. The discarded and landed fractions of the catch can be plotted separately or together.

1	lengthHist(x,by="spp",level="all",fraction=c("DIS","LAN"),title=TRUE,...)

`x`	an object of class csData or csDataVal
`by`	the character name of a grouping variable.
`level`	the level within the grouping variable, the default is "all".
`fraction`	the fraction of the catch to plot. DIS for discards, LAN for landings. The default is to plot both if present
`title`	logical. adds a title to the outer margin
`...`	other arguments, particularly those to `hist`.

The possible options for the grouping variable are those within the amalgamated hl table produced by mergecsData and include for time: "year", "month" and "quarter"; for space: "area", and "rect"; for technical: "foCatNat","foCatEu5" and "foCatEu6". Other options include "proj", "trpCode", "commCat" and "sex". The default is to plot by "spp" so, for a single species data set, this will plot all length frequencies.

For plotting selected levels within the grouping variable the names of those levels can be passed as a vector to level, e.g just to plot data from the first quarter then set by ="quarter" and level=1. Grouping variables that are numeric, such as months and quarters, are specified as numerics e.g. level=c(1,3). Grouping variables that are characters are specified as character strings e.g. level=c("OTB_DEM")

The arguments that can be passed as ... includes: col for setting the colour or the bars; border for setting the colour of the borders of the bars; add=TRUE for adding to an existing plot; angle for setting the angle of shading lines; density for setting the density of the shading lines. The argument freq=FASLE will plot a density histogram. If axes=FALSE no axes will be plotted. ylim sets the limits for the y axes (only applicable for frequency plots) and xlab and ylab are for axes labels. Other graphical parameters include main, sub, cex.main, cex.asis, cex.lab e.t.c see hist and par for more details.

The outer margin default title is \"Length distribution of species by grouping variable\". This can be turned off if title=FALSE. The figure titles default to the argument passed as by and, if specified, level. This can be overwritten by a call to main. main="" will result in no figure title.

par(mfrow=c(nrow,ncol)) can be used to adjust the number of plots per page to accommodate the multiple figures generated when the grouping variable has more than one level.

A named list of the grouping variable and levels plotted, each component of which is itself a list of class "histogram" with components breaks, counts, density, intensities, mids xname and equidist. See hist for details.

Alastair Pout a.pout@marlab.ac.uk

agelenPlot which plots lengths against ages.

#data(cod2004cs)
# Plotting the length distribution in the hl table 
#lengthHist(cod2004cs,col=2)

# and now grouped by the commercial category
#lengthHist(cod2004cs,by="commCat",level=1,col=2,density=30,main="")
#for(i in 2:6)lengthHist(cod2004cs,by="commCat",level=i,col=(i+1),density=30,main="",add=TRUE,title=FALSE)

# plotting by quarter
#par(mfrow=c(2,2))
#lengthHist(cod2004cs,by="quarter",col=2,freq=TRUE)
#par(mfrow=c(1,1))