SSplotComps: Plot composition data and fits.

Description Usage Arguments Author(s) See Also

View source: R/SSplotComps.R

Description

Plot composition data and fits from Stock Synthesis output. Multi-figure plots depend on make_multifig.

Usage

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SSplotComps(replist, subplots = c(1:21, 24), kind = "LEN", sizemethod = 1,
  aalyear = -1, aalbin = -1, plot = TRUE, print = FALSE,
  fleets = "all", fleetnames = "default", sexes = "all", yupper = 0.4,
  datonly = FALSE, samplesizeplots = TRUE, compresidplots = TRUE,
  bub = FALSE, showyears = TRUE, showsampsize = TRUE, showeffN = TRUE,
  sampsizeline = FALSE, effNline = FALSE, minnbubble = 3,
  pntscalar = NULL, scalebubbles = FALSE, cexZ1 = 1.5, bublegend = TRUE,
  colvec = c(rgb(1, 0, 0, 0.7), rgb(0, 0, 1, 0.7), rgb(0.1, 0.1, 0.1, 0.7)),
  linescol = c(rgb(0, 0.5, 0, 0.7), rgb(0.8, 0, 0, 0.7), rgb(0, 0, 0.8, 0.7)),
  axis1 = NULL, axis2 = NULL, blue = rgb(0, 0, 1, 0.7), red = rgb(1, 0,
  0, 0.7), pwidth = 6.5, pheight = 5, punits = "in", ptsize = 10,
  res = 300, plotdir = "default", cex.main = 1, linepos = 1,
  fitbar = FALSE, do.sqrt = TRUE, smooth = TRUE, cohortlines = c(),
  labels = c("Length (cm)", "Age (yr)", "Year", "Observed sample size",
  "Effective sample size", "Proportion", "cm", "Frequency", "Weight", "Length",
  "(mt)", "(numbers x1000)", "Stdev (Age) (yr)", "Conditional AAL plot, "),
  printmkt = TRUE, printsex = TRUE, maxrows = 6, maxcols = 6,
  maxrows2 = 2, maxcols2 = 4, rows = 1, cols = 1, andre_oma = c(3, 0,
  3, 0), andrerows = 3, fixdims = TRUE, fixdims2 = FALSE,
  maxneff = 5000, verbose = TRUE, scalebins = FALSE, addMeans = TRUE,
  ...)

Arguments

replist

list created by SSoutput

subplots

vector controlling which subplots to create

kind

indicator of type of plot can be "LEN", "SIZE", "AGE", "cond", "GSTAGE", "L[at]A", or "W[at]A".

sizemethod

if kind = "SIZE" then this switch chooses which of the generalized size bin methods will be plotted.

aalyear

Years to plot multi-panel conditional age-at-length fits for all length bins; must be in a "c(YYYY,YYYY)" format. Useful for checking the fit of a dominant year class, critical time period, etc. Default=-1.

aalbin

The length bin for which multi-panel plots of the fit to conditional age-at-length data will be produced for all years. Useful to see if growth curves are ok, or to see the information on year classes move through the conditional data. Default=-1.

plot

plot to active plot device?

print

print to PNG files?

fleets

optional vector to subset fleets for which plots will be made

fleetnames

optional vector of fleet names to put in the labels

sexes

which sexes to show plots for. Default="all" which will include males, females, and unsexed. This option is not fully implemented for all plots.

yupper

upper limit on ymax for polygon/histogram composition plots

datonly

make plots of data without fits as well as data with fits?

samplesizeplots

make sample size plots?

compresidplots

make plots of residuals for fit to composition data?

bub

make bubble plot for numbers at age or size?

showyears

Add labels for years to sample size plots?

showsampsize

add sample sizes to plot

showeffN

add effective sample sizes to plot

sampsizeline

show line for input sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)

effNline

show line for effective sample sizes on top of conditional age-at-length plots (TRUE/FALSE, still in development)

minnbubble

number of unique x values before adding buffer. see ?bubble3 for more info.

pntscalar

This scalar defines the maximum bubble size for bubble plots. This option is still available but a better choice is to use cexZ1 which allow the same scaling throughout all plots.

scalebubbles

scale data-only bubbles by sample size, not just proportion within sample? Default=FALSE.

cexZ1

Character expansion (cex) for point associated with value of 1.

bublegend

Add legend with example bubble sizes to bubble plots.

colvec

Vector of length 3 with colors for females, males, unsexed fish

linescol

Color for lines on top of polygons

axis1

position of bottom axis values

axis2

position of left size axis values

blue

What color to use for males in bubble plots (default is slightly transparent blue)

red

What color to use for females in bubble plots (default is slightly transparent red)

pwidth

default width of plots printed to files in units of punits. Default=7.

pheight

default height width of plots printed to files in units of punits. Default=7.

punits

units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" or "mm". Default="in".

ptsize

point size for plotted text in plots printed to files (see help("png") in R for details). Default=12.

res

resolution of plots printed to files. Default=300

plotdir

directory where PNG files will be written. by default it will be the directory where the model was run.

cex.main

character expansion parameter for plot titles

linepos

should lines be added before points (linepos=1) or after (linepos=2)?

fitbar

show fit to bars instead of points

do.sqrt

scale bubbles based on sqrt of size vector. see ?bubble3 for more info.

smooth

add loess smoother to observed vs. expected index plots and input vs. effective sample size?

cohortlines

optional vector of birth years for cohorts for which to add growth curves to numbers at length bubble plots

labels

vector of labels for plots (titles and axis labels)

printmkt

show market categories in plot titles?

printsex

show gender in plot titles?

maxrows

maximum (or fixed) number or rows of panels in the plot

maxcols

maximum (or fixed) number or columns of panels in the plot

maxrows2

maximum number of rows for conditional age at length plots

maxcols2

maximum number of columns for conditional age at length plots

rows

number or rows to return to as default for next plots to come or for single plots

cols

number or cols to return to as default for next plots to come or for single plots

andre_oma

Outer margins passed to Andre's multi-panel conditional age-at-length plots.

andrerows

Number of rows of Andre's conditional age-at-length plots within each page. Default=3.

fixdims

fix the dimensions at maxrows by maxcols or resize based on number of years of data

fixdims2

fix the dimensions at maxrows by maxcols in aggregate plots or resize based on number of fleets

maxneff

the maximum value to include on plots of input and effective sample size. Occasionally a calculation of effective N blows up to very large numbers, rendering it impossible to observe the relationship for other data. Default=5000.

verbose

return updates of function progress to the R GUI?

scalebins

Rescale expected and observed proportions by dividing by bin width for models where bins have different widths? Caution!: May not work correctly in all cases.

addMeans

Add parameter means in addition to medians for MCMC posterior distributions in which the median and mean differ.

...

additional arguments that will be passed to the plotting.

Author(s)

Ian Taylor

See Also

SS_plots, make_multifig


r4ss documentation built on May 29, 2017, 2:24 p.m.