make_multifig {r4ss}

Create multi-figure plots.

Description

Function created as an alternative to lattice package for multi-figure plots of composition data and fits from Stock Synthesis output.

Usage

make_multifig(
  ptsx,
  ptsy,
  yr,
  linesx = 0,
  linesy = 0,
  ptsSD = 0,
  sampsize = 0,
  effN = 0,
  showsampsize = TRUE,
  showeffN = TRUE,
  sampsize_label = "N=",
  effN_label = "effN=",
  sampsizeround = 1,
  maxrows = 6,
  maxcols = 6,
  rows = 1,
  cols = 1,
  fixdims = TRUE,
  main = "",
  cex.main = 1,
  xlab = "",
  ylab = "",
  size = 1,
  cexZ1 = 1.5,
  bublegend = TRUE,
  maxsize = NULL,
  do.sqrt = TRUE,
  minnbubble = 8,
  allopen = TRUE,
  xbuffer = c(0.1, 0.1),
  ybuffer = c(0, 0.15),
  yupper = NULL,
  ymin0 = TRUE,
  xlas = 0,
  ylas = NULL,
  axis1 = NULL,
  axis2 = NULL,
  axis1labs = NULL,
  linepos = 1,
  type = "o",
  polygons = TRUE,
  bars = FALSE,
  barwidth = "default",
  ptscex = 1,
  ptscol = 1,
  ptscol2 = 1,
  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, 0.8, 0, 0.7), rgb(1, 0, 0, 0.7), rgb(0, 0, 1, 0.7)),
  lty = 1,
  lwd = 2,
  pch = 1,
  nlegends = 3,
  legtext = list("yr", "sampsize", "effN"),
  legx = "default",
  legy = "default",
  legadjx = "default",
  legadjy = "default",
  legsize = c(1.2, 1),
  legfont = c(2, 1),
  venusmars = TRUE,
  sampsizeline = FALSE,
  effNline = FALSE,
  sampsizemean = NULL,
  effNmean = NULL,
  ipage = 0,
  scalebins = FALSE,
  sexvec = NULL,
  multifig_colpolygon = grey(c(0.6, 0.8, 0.7), alpha = 0.7),
  multifig_oma = NULL,
  ...
)

Arguments

ptsx

vector of x values for points or bars

ptsy

vector of y values for points or bars of same length as ptsx

yr

vector of category values (years) of same length as ptsx

linesx

optional vector of x values for lines

linesy

optional vector of y values for lines

ptsSD

optional vector of standard deviations used to plot error bars on top of each point under the assumption of normally distributed error

sampsize

optional sample size vector of same length as ptsx

effN

optional effective sample size vector of same length as ptsx

showsampsize

show sample size values on plot?

showeffN

show effective sample size values on plot?

sampsize_label

label on sampsize

effN_label

label on effN

sampsizeround

rounding level for sample size values

maxrows

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

maxcols

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

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

fixdims

fix the dimensions at maxrows by maxcols or resize based on number of elements in yr input.

main

title of plot

cex.main

character expansion for title

xlab

x-axis label

ylab

y-axis label

size

vector of bubbles sizes if making a bubble plot

cexZ1

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

bublegend

Add legend with example bubble sizes to bubble plots.

maxsize

maximum size of bubbles

do.sqrt

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

minnbubble

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

allopen

should all bubbles be open? see ?bubble3 for more info.

xbuffer

extra space around points on the left and right as fraction of total width of plot

ybuffer

extra space around points on the bottom and top as fraction of total height of plot

yupper

upper limit on ymax (applied before addition of ybuffer)

ymin0

fix minimum y-value at 0?

xlas

label style (las) input for x-axis. Default 0 has horizontal labels, input 2 would provide vertical lables.

ylas

label style (las) input for y-axis. Default NULL has horizontal labels when all labels have fewer than 6 characters and vertical otherwise. Input 0 would force vertical labels, and 1 would force horizontal.

axis1

optional position of bottom axis values

axis2

optional position of left size axis values

axis1labs

optional vector of labels for axis1 (either NULL or needs to match length of axis1)

linepos

should lines be added on top of points (linepos=1) or behind (linepos=2)? A value of linepos = 0 will result in no line.

type

type of line/points used for observed values (see 'type' in ?plot for details) on top of a grey polygon. Default is "o" for overplotting points on lines.

polygons

should polygons be added to the (turning off is required for sex-ratio plot)

bars

should the ptsx/ptsy values be bars instead of points (TRUE/FALSE) NOT CURRENTLY FUNCTIONAL

barwidth

width of bars in barplot, default method chooses based on quick and dirty formula also, current method of plot(...type='h') could be replaced with better approach

ptscex

character expansion factor for points (default=1)

ptscol

color for points/bars

ptscol2

color for negative value points in bubble plots

colvec

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

linescol

color for lines

lty

line type

lwd

line width

pch

point character type

nlegends

number of lines of text to add as legends in each plot

legtext

text in legend, a list of length=nlegends. values may be any of 1. "yr", 2. "sampsize", 3. "effN", or a vector of length = ptsx.

legx

vector of length=nlegends of x-values of legends (default is first one on left, all after on right)

legy

vector of length=nlegends of y-values of legends (default is top for all plots)

legadjx

left/right adjustment of legends around legx

legadjy

left/right adjustment of legends around legy

legsize

font size for legends. default=c(1.2,1.0) (larger for year and normal for others)

legfont

font type for legends, same as "font" under ?par

venusmars

Label females and males with venus and mars symbols?

sampsizeline

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

effNline

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

sampsizemean

mean input sample size value (used when sampsizeline=TRUE)

effNmean

mean effective sample size value (used when effNline=TRUE)

ipage

which page of plots when covering more than will fit within maxrows by maxcols.

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.

sexvec

vector of sex codes if more than one present (otherwise NULL)

multifig_colpolygon

vector of polygon fill colors of length 3 (for females, males, and unsexed fish). Can be input to SS_plots and will be passed to this function via the ... argument.

multifig_oma

vector of outer margins. Can be input to SS_plots and will be passed to this function via the ... argument.

...

additional arguments passed to par.

Author(s)

Ian Taylor

See Also

SS_plots(),SSplotComps()