SSplotComparisons: plot model comparisons

Description

Creates a user-chosen set of plots comparing model output from a summary of multiple models, where the collection was created using the SSsummarize function.

Usage

SSplotComparisons(summaryoutput,subplots=1:14,
  plot=TRUE,print=FALSE,
  models="all",
  endyrvec=NULL,
  indexfleets=NULL,
  indexUncertainty=FALSE,
  indexQlabel = TRUE,
  indexQdigits = 4, 
  indexSEvec="default",
  indexPlotEach=FALSE,         
  labels=c("Year",             
    "Spawning biomass (mt)",   
    "Spawning depletion",      
    "Age-0 recruits (1,000s)", 
    "Recruitment deviations",  
    "Index",                   
    "Log index",               
    "Density"),                
  col="default", shadecol="default",
  pch="default", lty=1, lwd=2,
  spacepoints = 10, staggerpoints = 1, 
  xlim="default", xaxs="r", yaxs="r",
  type="o", uncertainty=TRUE, shadealpha=0.1,
  legend=TRUE, legendlabels="default", legendloc="topright",
  btarg=0.4, minbthresh=0.25,
  pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
  plotdir=NULL,
  densitynames=c("SPB_Virgin",
                 "SPB_2011",
                 "Bratio_2011",
                 "SR_R0",
                 "SR_LN(R0)",
                 "TotYield_MSY"),
  densityxlabs=c("B0 (mt)",
                 "Spawning Biomass in 2011 (mt)",
                 "depletion in 2011",
                 "log(R0)",
                 "MSY (mt)"),
  densityscalex=1,
  densityscaley=1,
  fix0=TRUE,
  new=TRUE,
  verbose=TRUE,
  mcmcVec="default")

Arguments

summaryoutput

list created by SSsummarize

subplots

Vector of subplots to be created.

plot

plot to active plot device?

send plots to PNG files in directory specified by plotdir

models

optional subset of the models described in summaryoutput. Either "all" or a vector of numbers indicating columns in summary tables.

endyrvec

optional single year or vector of years representing the final year of values to show for each model

indexfleets

vector of fleets for each model for which to compare indices of abundance. Only necessary if any model has more than one index.

indexUncertainty

show uncertainty intervals on index data? Default=FALSE because if models have any extra standard deviations added, these intervals may differ across models.

indexQlabel

add catchability to legend in plot of index fits (TRUE/FALSE)?

indexQdigits

number of significant digits for catchability in legend (if indexQlabel=TRUE)

indexSEvec

optional replacement for the SE values in summaryoutput$indices to deal with the issue of differing uncertainty by models described above.

indexPlotEach

TRUE plots the observed index for each model with colors, or FALSE just plots observed once in black dots.

labels

vector of labels for plots (titles and axis labels)

col

optional vector of colors to be used for lines. Input 'default' makes use of rich.colors.short function.

shadecol

optional vector of colors to be used for shading uncertainty intervals. Input 'default' makes use of rich.colors.short function with alpha transparency.

pch

optional vector of plot character values

lty

optional vector of line types

lwd

optional vector of line widths

spacepoints

number of years between points shown on top of lines (for long timeseries, points every year get mashed together)

staggerpoints

number of years to stagger the first point (if spacepoints > 1) for each line (so that adjacent lines have points in different years)

xlim

optional x limits

xaxs

choice of xaxs parameter (see ?par for more info)

yaxs

choice of yaxs parameter (see ?par for more info)

type

type parameter passed to points (default 'o' overplots points on top of lines)

uncertainty

show plots with uncertainty intervals

shadealpha

transparency parameter used to make default shadecol values (see ?rgb for more info)

legend

add a legend?

legendlabels

optional vector of labels to include in legend. Default is 'model1','model2',etc.

legendloc

location of legend. See ?legend for more info.

btarg

target biomass value at which to show a line (set to 0 to remove)

minbthresh

minimum biomass threshhold at which to show a line (set to 0 to remove)

pwidth

width of plot written to PNG file

pheight

height of plot written to PNG file

punits

units for PNG file

res

resolution for PNG file

ptsize

ptsize for PNG file

cex.main

character expansion for plot titles

plotdir

directory where PNG or PDF files will be written. By default it will be the directory where the model was run.

densitynames

vector of names of parameters or derived quantities contained in summaryoutput$pars$Label or summaryoutput$quants$Label for which to make density plots

densityxlabs

vector of x-axis labels to use in the density plots (must be equal in length to densitynames)

densityscalex

scalar for upper x-limit in density plots (values below 1 will cut off the right tail to provide better contrast among narrower distributions

densityscaley

scalar for upper y-limit in density plots (values below 1 will cut off top of highest peaks to provide better contrast among broader distributions

fix0

always include 0 in the density plots?

new

create new empty plot window

verbose

report progress to R GUI?

mcmcVec

vector of TRUE/FALSE values (or single value) indicating whether input values are from MCMC or to use normal distribution around MLE

SSplotComparisons: plot model comparisons

Description

Usage

Arguments

Value

See Also