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
yrinput.- main
title of plot
- cex.main
Character expansion for plot titles. The default is
cex.main=1.- 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 labels.
- 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 for plot elements.
- 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.