`R/MSE_Plotting.R`

`Pplot2.Rd`

A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield

```
Pplot2(
MSEobj,
YVar = c("F_FMSY", "SSB_SSBMSY"),
MPs = NA,
sims = NULL,
traj = c("all", "quant", "both"),
quants = c(0.1, 0.9),
incquant = TRUE,
quantcol = "lightgray",
RefYield = c("lto", "curr"),
LastYr = TRUE,
ref.lines = c(0.5, 1, 1.5),
maxMP = 6,
alpha = 60,
cex.axis = 1,
cex.lab = 1,
YLab = NULL,
incMP = TRUE,
MPcex = 1,
MPcol = "black",
incLeg = TRUE,
cex.leg = 1.5,
legPos = "topleft",
yline = NULL,
xline = NULL,
parOR = FALSE,
xaxis = TRUE,
yaxis = TRUE,
oneIt = TRUE,
...
)
```

- MSEobj
An object of class MSE

- YVar
What to plot on the y-axis? Options are:

`c('SSB_SSB0', 'SSB_SSBMSY', 'F_FMSY', 'Yield')`

- MPs
Optional subset by MP

- sims
Optional subset by simulation

- traj
Plot all projections (

`all`

), only quantiles (`quant`

), or both projections and median (`both`

)- quants
Numeric vector of length 2 specifying the quantiles (e.g., 10th and 90th. Median is always included)

- incquant
Logical. Include the quantiles or only plot median?

- quantcol
Colour of the quantile polygon

- RefYield
Should yield be relative to long-term optimum (

`lto`

) or last historical year (`curr`

)- LastYr
Logical. Include the last historical year in the yield projections?

- ref.lines
Numeric vector of y-values for horizontal reference lines. Set to NULL to remove lines.

- maxMP
Maximum number of MPs to plot

- alpha
Alpha for transparency of lines

- cex.axis
Size of axis text

- cex.lab
Size of axis label

- YLab
Optional label for y-axis

- incMP
Logical. Include name of MP?

- MPcex
Size of MP label

- MPcol
Optional character vector of colors for MP labels

- incLeg
Logical. Include a legend?

- cex.leg
Size of legend text

- legPos
Legend position

- yline
Optional horizontal lines

- xline
Optional vertical lines

- parOR
Logical to over-ride the par parameters

- xaxis
Logical. Should x-axis labels be displayed?

- yaxis
Logical. Should y-axis labels be displayed?

- oneIt
Logical. Should one iteration be plotted on the quantile plot?

- ...
Additional arguments to be passed to plotting functions