ISD_bin_plot: Recommended plots of individual size distribution and fit for...

In andrew-edwards/sizeSpectra: Fitting Size Spectra to Ecological Data Using Maximum Likelihood

Recommended plots of individual size distribution and fit for binned data with overlapping bins

Usage

ISD_bin_plot(
  data.year,
  b.MLE,
  b.confMin,
  b.confMax,
  year = NA,
  xlim = NA,
  xmin = NA,
  xmax = NA,
  yScaling = 0.75,
  MLE.round = 2,
  xLabel.small = c(5, 50, 500, 5000),
  yBig.inc = 1000,
  yBig.max = 10,
  ySmall.inc = NA,
  ySmall.tcl = -0.2,
  xLab = expression(paste("Body mass (", italic(x), "), g")),
  yLab = expression(paste("Number of ", values >= italic(x))),
  inset.a = c(0, 0),
  inset.year = c(0, 0.04),
  seg.col = "green",
  rect.col = "grey",
  fit.col = "red",
  fit.lwd = 2,
  conf.lty = 2,
  par.mfrow = c(2, 1),
  par.mai = c(0.4, 0.5, 0.05, 0.3),
  par.cex = 0.7,
  mgp.vals = c(1.6, 0.5, 0),
  IBTS_MEPS_figs = FALSE,
  x.PLB = NA
)

Arguments

data.year	tibble containing columns Year, wmin, wmax, Number, countGTEwmin, lowCount, highCount, for a single year (or instance) to show; Year not used, but no need to remove (it is in the results for the IBTS data). , countGTEwmin is, for a given bin, the total counts greater than that bin's wmin.
b.MLE	maximum likelihood estimate of b (ideally from the MLEbins method)
b.confMin	lower 95\ \item b.confMaxupper 95\ \item yearyear of data to go into legend (use NA if not applicable) \item xlim(soft) limits of x-axis. If NA then automatically uses the minimum wmin and maximum wmax for that data set (so it's good to set it globally when doing multiple years). \item xmin, xmax:values of xmin and xmax to plot the PLB curve \item yScalingScaling of y-minimum of y-axis. Axis can't go to zero on log-log plot, but goes to the proportion yScaling (which is less than 1) of the minimum value of counts greater than the highest wmin value. Do such that can see the right-most bin in all plots. \item MLE.roundnumber of decimal places to show MLE of b on the top plot \item xLabel.smallwhich small tickmarks to label on the x-axis \item yBig.incincrement for labelled big tickmarks on the unlogged y-axis \item yBig.maxmaximum number of desired labelled big tickmarks on the unlogged y-axis \item ySmall.incincrement for small unlabelled tickmarks on the y-axis (if NA then is set to yBig.inc/4) \item ySmall.tcllength of small y-axis tick marks - only for (a) maybe \item xLablabel for x-axis \item yLablabel for y-axis \item inset.ahow far to inset (a) and (b) \item inset.yearhow far to inset the year \item seg.colcolour for horizontal green lines showing range of body sizes for each bin \item rect.colcolour to fill in the rectangles for each bin \item fit.colcolour to plot the MLE curve, and those for the confidence intervals \item fit.lwdline weight for MLE curve \item conf.ltyline type for two curves for the MLE confidence intervals \item par.mfrowvector giving the layout of the figures (number of rows, number of columns) \item par.maimargin size in inches \item par.cexmagnification of plotting text and symbols relative to default \item mgp.valsmargin line for axis title, axis labels and axis line \item IBTS_MEPS_figslogical, TRUE for exactly reproducing the original MEPS Figures 7 and S.5-S.34 (which were done before some improvements to this function) \item x.PLBvector of values to use to plot the fitted PLB curve; if NA then automatically calculated two-panel figure of the recommended plot of binned data and the fitted individual size distribution, like Figures 7 and S.5-S.34 of the MEPS paper. See the vignette MEPS_IBTS_recommend for explicit example. Plots the individual size distribution and the fit from the MLEbins method, with linear and then logarithmic y-axes, in the recommended way that takes into account the bin structure of the data, as in Figures 7 and S.5-S.34 of the MEPS paper. Andrew Edwards

andrew-edwards/sizeSpectra documentation built on June 28, 2023, 7:09 p.m.