Description Usage Arguments Details References Examples
This function plots length frequency (lfq) samples sequentially
arranged in time. An object
of "lfq" class is obatined by applying the lfqRestructure
function. In case growth
parameters are known, von Bertalanffy growth curves can be plotted through the lfq samples.
1 2 3 4 5 6 7 8  ## S3 method for class 'lfq'
plot(x, Fname = "rcounts", par = NULL, agemax = NULL,
rel = FALSE, y = NA, curve.col = 1, hist.sc = 0.5,
hist.col = c("white", "black", "orange", "darkgreen"), image.col = NULL,
region.col = NULL, zlim = NULL, zlimtype = "balanced",
date.axis = "traditional", date.at = seq(as.Date("15000101"),
as.Date("25000101"), by = "months"), date.format = "'%y%b",
xlab = "", ylab = "Length classes", draw = TRUE, ...)

x 
a list of the class "lfq" consisting of following parameters:

Fname 
indicating whether restructured ("rcounts") or original frequencies ("catch") should be displayed (default: "rcounts") 
par 
a list with following growth parameters (default NULL):

agemax 
maximum age of species; default NULL, then estimated from Linf 
rel 
logical; defines if relative numbers per length class should be plotted (relative to the sample size per sampling time, e.g. month). Default: FALSE. 
y 
an optional second list of class "lfq" consisting of same parameters as x. This allows to plot samples from different sources (e.g. different fleets) on top of eachother, classes and dates have to correspond at least partially. Default is NA. 
curve.col 
colour of growth curves (default: 1) 
hist.sc 
defines the scaling factor to use for maximum histogram extent (xaxis direction). The default setting of hist.sc=0.5 will result in a maximum distance equal to half the distance between closest sample dates (i.e. ensures no overlap and full plotting within the plot region). 
hist.col 
vector of 2 values defining coloring to use on negative and positive histogram bars (default: hist.col=c("white", "black", "orange", "darkgreen")) 
image.col 
colour of image, by default (NULL) red and blue colours are used. To remove image coloring, set image.col=NA. 
region.col 
colour of plotting region. Will overwrite image.col (default: region.col=NULL) 
zlim 
the minimum and maximum z values for which colors should be plotted (default : NULL). 
zlimtype 
indicating if zlim should be based on the range of the catch ("range") or based on the maximum absolute value in Fname ("balanced", default). This parameter is only considered if zlim is NULL. 
date.axis 
the style of the x axis. By default the "traditional"
approach is used with years under the months. Alternatively, by using
"modern" the date is plotted in one line according to the chosen
format 
date.at 
the points at which tickmarks are to be drawn. Nonfinite (infinite, NaN or NA) values are omitted. By default it is seq(as.Date("15000101"), as.Date("25000101"), by="months") 
date.format 
format of date (default : "%y%b") 
xlab 
label of x axis (default : "") 
ylab 
label of y axis (default : "Length classes") 
draw 
logical; indicating whether growth curves should be added to lfq plot if parameters are provided (default : TRUE) 
... 
additional options of the plot function 
This function uses lfqFitCurves
when growth
parameters are provided to plot growth curves, this can be turned off with
draw
= FALSE.
Brey, T., Soriano, M., and Pauly, D. 1988. Electronic length frequency analysis: a revised and expanded user's guide to ELEFAN 0, 1 and 2.
Pauly, D. 1981. The relationship between gill surface area and growth performance in fish: a generalization of von Bertalanffy's theory of growth. Meeresforschung. 28:205211
Pauly, D. and N. David, 1981. ELEFAN I, a BASIC program for the objective extraction of growth parameters from lengthfrequency data. Meeresforschung, 28(4):205211
Pauly, D., 1985. On improving operation and use of ELEFAN programs. Part I: Avoiding "drift" of K towards low values. ICLARM Conf. Proc., 1314
Pauly, D., 1987. A review of the ELEFAN system for analysis of lengthfrequency data in fish and aquatic invertebrates. ICLARM Conf. Proc., (13):734
Pauly, D. and G. R. Morgan (Eds.), 1987. Lengthbased methods in fisheries research. (No. 13). WorldFish
Pauly, D. and G. Gaschuetz. 1979. A simple method for fitting oscillating length growth data, with a program for pocket calculators. I.C.E.S. CM 1979/6:24. Demersal Fish Comittee, 26 p.
Pauly, D. 1984. Fish population dynamics in tropical waters: a manual for use with programmable calculators (Vol. 8). WorldFish.
Quenouille, M. H., 1956. Notes on bias in estimation. Biometrika, 43:353360
Somers, I. F., 1988. On a seasonally oscillating growth function. ICLARM Fishbyte 6(1): 811.
Sparre, P., Venema, S.C., 1998. Introduction to tropical fish stock assessment. Part 1. Manual. FAO Fisheries Technical Paper, (306.1, Rev. 2): 407 p.
Tukey, J., 1958. Bias and confidence in not quite large samples. Annals of Mathematical Statistics, 29: 614
Tukey, J., 1986. The future of processes of data analysis. In L. V. Jones (Eds.), The Collected Works of John W. Tukey philosophy and principles of data analysis: 19651986 (Vol. 4, pp. 517549). Monterey, CA, USA: Wadsworth & Brooks/Cole
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31  data(alba)
res < lfqRestructure(alba)
# simple plot or reconstructed frequencies
plot(x = res, Fname = "rcounts")
# add VBGF curves
plot(res, Fname = "rcounts", par = list(Linf = 14, K = 1.1, t_anchor = 0.3))
# add soVBGF curves, adjust hist.sc and xlim
plot(res, Fname = "catch", curve.col=4,
par = list(Linf = 14, K = 1.1, t_anchor = 0.3, C = 0.2, ts = 0.75),
hist.sc = 0.9,
xlim=range(res$dates)+c(30, 0)
)
# adjust image colors
plot(res, Fname = "rcounts", image.col = NA )
plot(res, Fname = "rcounts", image.col = rev(cm.colors(21)) )
plot(res, Fname = "rcounts", image.col = colorRampPalette(c("red","grey90","green"))(21))
# solid plot region color
plot(res, xlim=range(res$dates)+c(60, 60),
hist.sc=0.75, image.col="grey90") # leaves gaps
plot(res, xlim=range(res$dates)+c(60, 60),
hist.sc=0.75, region.col="grey90") # full coverage
# lowlevel plot additions
plot(res)
abline(h=4, lty=2)
mtext("Restructured frequencies (MA=5)", line=0.25, side=3)

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.