Description Usage Arguments Author(s) See Also

View source: R/SSplotIndices.R

Plot indices of abundance and associated quantities.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
SSplotIndices(replist, subplots = 1:9, plot = TRUE, print = FALSE,
fleets = "all", fleetnames = "default", smooth = TRUE, add = FALSE,
datplot = FALSE, labels = c("Year", "Index", "Observed index",
"Expected index", "Log index", "Log observed index", "Log expected index",
"Standardized index", "Catchability (Q)", "Time-varying catchability",
"Vulnerable biomass", "Catchability vs. vulnerable biomass"),
col1 = "default", col2 = "default", col3 = "blue", col4 = "red",
pch1 = 21, pch2 = 16, cex = 1, bg = "white", legend = TRUE,
legendloc = "topright", seasnames = NULL, pwidth = 6.5, pheight = 5,
punits = "in", res = 300, ptsize = 10, cex.main = 1, addmain = TRUE,
plotdir = "default", minyr = NULL, maxyr = NULL,
maximum_ymax_ratio = Inf, show_input_uncertainty = TRUE, verbose = TRUE,
...)
``` |

`replist` |
list created by |

`subplots` |
vector controlling which subplots to create |

`plot` |
plot to active plot device? |

`print` |
print to PNG files? |

`fleets` |
optional vector to subset fleets for which plots will be made |

`fleetnames` |
optional replacement for fleenames used in data file |

`smooth` |
add smoothed line to plots of observed vs. expected sample sizes |

`add` |
add to existing plot (not yet implemented) |

`datplot` |
make plot of data only? |

`labels` |
vector of labels for plots (titles and axis labels) |

`col1` |
vector of colors for points in each season for time series plot. Default is red for single season models and a rainbow using the rich.colors.short function for multiple seasons. |

`col2` |
vector of colors for points in each season for obs. vs. exp. plot. Default is blue for single season models and a rainbow using the rich.colors.short function for multiple seasons. |

`col3` |
color of line showing expected index in time series plot. Default is blue. |

`col4` |
color of smoother shown in obs. vs. exp. plots. Default is red. |

`pch1` |
single value or vector of plotting characters (pch parameter) for time-series plots of index fit. Default=21. |

`pch2` |
single value or vector of plotting characters (pch parameter) for sample size plots of index fit. Default=16. |

`cex` |
character expansion factor for points showing observed values. Default=1. |

`bg` |
Background color for points with pch=21. |

`legend` |
add a legend to seasonal colors (only for seasonal models) |

`legendloc` |
add a legend to seasonal colors (default is "topright") |

`seasnames` |
optional vector of names for each season to replace defaults if a legend is used |

`pwidth` |
width of plot |

`pheight` |
height of plot |

`punits` |
units for PNG file |

`res` |
resolution for PNG file |

`ptsize` |
point size for PNG file |

`cex.main` |
character expansion for plot titles |

`addmain` |
switch which allows the plot title to be left off |

`plotdir` |
directory where PNG files will be written. by default it will be the directory where the model was run. |

`minyr` |
First year to show in plot (for zooming in on a subset of values) |

`maxyr` |
Last year to show in plot (for zooming in on a subset of values) |

`maximum_ymax_ratio` |
Maximum allowed value for ymax (specified as ratio of y), which overrides any value of ymax that is greater (default = Inf) |

`show_input_uncertainty` |
switch controlling whether to add thicker uncertainty interval lines indicating the input uncertainty relative to the total uncertainty which may result from estimating a parameter for extra standard deviations |

`verbose` |
report progress to R GUI? |

`...` |
Extra arguments to pass to calls to |

Ian Stewart, Ian Taylor, James Thorson

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