Function created as an alternative to lattice package for multi-figure plots of composition data and fits from Stock Synthesis output.
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,
...
)vector of x values for points or bars
vector of y values for points or bars of same length as ptsx
vector of category values (years) of same length as ptsx
optional vector of x values for lines
optional vector of y values for lines
optional vector of standard deviations used to plot error bars on top of each point under the assumption of normally distributed error
optional sample size vector of same length as ptsx
optional effective sample size vector of same length as ptsx
show sample size values on plot?
show effective sample size values on plot?
label on sampsize
label on effN
rounding level for sample size values
maximum (or fixed) number or rows of panels in the plot
maximum (or fixed) number or columns of panels in the plot
number or rows to return to as default for next plots to come or for single plots
number or cols to return to as default for next plots to come or for single plots
fix the dimensions at maxrows by maxcols or resize based on
number of elements in yr input.
title of plot
character expansion for title
x-axis label
y-axis label
vector of bubbles sizes if making a bubble plot
Character expansion (cex) for point associated with value of 1.
Add legend with example bubble sizes to bubble plots.
maximum size of bubbles
scale bubbles based on sqrt of size vector. see ?bubble3 for more info.
number of unique x values before adding buffer. see ?bubble3 for more info.
should all bubbles be open? see ?bubble3 for more info.
extra space around points on the left and right as fraction of total width of plot
extra space around points on the bottom and top as fraction of total height of plot
upper limit on ymax (applied before addition of ybuffer)
fix minimum y-value at 0?
label style (las) input for x-axis. Default 0 has horizontal labels, input 2 would provide vertical lables.
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.
optional position of bottom axis values
optional position of left size axis values
optional vector of labels for axis1 (either NULL or needs to match length of axis1)
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 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.
should polygons be added to the (turning off is required for sex-ratio plot)
should the ptsx/ptsy values be bars instead of points (TRUE/FALSE) NOT CURRENTLY FUNCTIONAL
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
character expansion factor for points (default=1)
color for points/bars
color for negative value points in bubble plots
Vector of length 3 with colors for females, males, unsexed fish
color for lines
line type
line width
point character type
number of lines of text to add as legends in each plot
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.
vector of length=nlegends of x-values of legends (default is first one on left, all after on right)
vector of length=nlegends of y-values of legends (default is top for all plots)
left/right adjustment of legends around legx
left/right adjustment of legends around legy
font size for legends. default=c(1.2,1.0) (larger for year and normal for others)
font type for legends, same as "font" under ?par
Label females and males with venus and mars symbols?
show line for input sample sizes on top of conditional age-at-length plots (TRUE/FALSE/scalar, still in development)
show line for effective sample sizes on top of conditional age-at-length plots (TRUE/FALSE/scalar, still in development)
mean input sample size value (used when sampsizeline=TRUE)
mean effective sample size value (used when effNline=TRUE)
which page of plots when covering more than will fit within maxrows by maxcols.
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.
vector of sex codes if more than one present (otherwise NULL)
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.
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.