fishboot (version 1.0.2)

LinfK_scatterhist: Linf/K scatterplot of bootstrapping results

Description

This function plots a scatterplot of von Bertalanffy growth function parameters \(K\) vs \(L_{inf}\) (“Kimura plot”) with histograms.

Usage

LinfK_scatterhist(
  res,
  Linf.breaks = "Sturges",
  K.breaks = "Sturges",
  gridsize = rep(151, 2),
  H = NULL,
  shading = TRUE,
  shading.cols = NULL,
  dens.contour = TRUE,
  probs = c(25, 50, 75, 95),
  phi.contour = TRUE,
  phi.levels = NULL,
  phi.contour.col = 8,
  phi.contour.lty = 2,
  phi.contour.lwd = 1,
  phi.contour.labcex = 0.75,
  pt.pch = 16,
  pt.col = adjustcolor(1, 0.25),
  pt.cex = 0.5,
  pt.bg = 4,
  xlab = expression(italic("L")[infinity]),
  ylab = expression(italic("K")),
  ...
)

Value

This function returns just the described plot.

Arguments

res

Object of class data.frame, tbl_df, lfqBoot or grotagBoot.

Linf.breaks, K.breaks

Arguments passed to hist function to compute the breakpoints (argument breaks) for Linf and K histograms respectively.

gridsize

numeric 2-length vector specifying the resolution of the grid.

H

Plug-in bandwidth object from Hpi (Default: H = ks::Hpi(res[,c("Linf", "K")]))

shading

logical. Do you want to colour 2D field of density estimates? (Default TRUE)

shading.cols

Colors or color palette used for background shading of 2D field of density estimates. No considered if shading = FALSE.

dens.contour

logical. Do you want to add contour lines? (TRUE by default).

probs

numeric Density probability cutoffs (in by contours. By default probs = c(25, 50, 75, 95) and not considered if dens.contour = FALSE.

phi.contour

logical. Do you want to display phi prime isolines? (FALSE by default)

phi.levels

numeric vector that controls Phi prime values. Omitted if phi.contour = FALSE and if NULL values will be chosen automatically by the contour function.

phi.contour.col, phi.contour.lty, phi.contour.lwd, phi.contour.labcex

Extra arguments used to control the color, line type, line width and labels size of the phi prime contour isolines.

pt.pch, pt.col, pt.cex, pt.bg

Extra arguments to control type, color, size and background color of resampling points.

xlab, ylab

Labels for X and Y axis respectively.

...

Extra arguments passed to main plot function.

Details

Isolines of growth performance (\(Phi’\)) can be plotted, as well as bivariate 95 used for plotting is usually the result of a bootstrapped growth analysis (i.e. a lfqBoot object generated by fishboot functions such as ELEFAN_SA_boot, ELEFAN_GA_boot, grotag_boot, or grolenage_boot).

If NULL, it will be defined as colorRampPalette(c("white", blues9))(1e3).

Examples

data(alba_boot) # lfqBoot object
LinfK_scatterhist(res = alba_boot)

data(bonito_boot) # grotagBoot object
LinfK_scatterhist(res = bonito_boot)