Generate HTML reports with plots of operating model components ("Stock", "Fleet", "Obs", and "Imp"), the historical simulations ("Hist"), or the complete OM ("OM").
The individual component plots of objects of class Stock
and Fleet
can also be generated by
using the generic plot.pars
function. See Examples below.
# S3 method for pars
plot(
x,
Object,
Stock = NULL,
nsamp = 3,
nsim = 200,
nyears = 50,
proyears = 28,
output_file = NULL,
output_dir = getwd(),
quiet = TRUE,
tabs = TRUE,
title = NULL,
date = NULL,
plotPars = NULL,
html = FALSE,
open = TRUE,
dev = FALSE,
...
)
# S3 method for Stock
plot(
x,
nsamp = 3,
nsim = 200,
nyears = 50,
proyears = 28,
output_file = NULL,
output_dir = getwd(),
quiet = TRUE,
tabs = TRUE,
title = NULL,
date = NULL,
plotPars = NULL,
open = TRUE,
dev = FALSE,
...
)
# S3 method for Fleet
plot(
x,
Stock = NULL,
nsamp = 3,
nsim = 200,
nyears = 50,
proyears = 28,
output_file = NULL,
output_dir = getwd(),
quiet = TRUE,
tabs = TRUE,
title = NULL,
date = NULL,
plotPars = NULL,
open = TRUE,
dev = FALSE,
...
)
# S3 method for Obs
plot(
x,
nsamp = 3,
nsim = 200,
nyears = 50,
proyears = 28,
output_file = NULL,
output_dir = getwd(),
quiet = TRUE,
tabs = TRUE,
title = NULL,
date = NULL,
plotPars = NULL,
open = TRUE,
dev = FALSE,
...
)
# S3 method for Imp
plot(
x,
nsamp = 3,
nsim = 200,
nyears = 50,
proyears = 28,
output_file = NULL,
output_dir = getwd(),
quiet = TRUE,
tabs = TRUE,
title = NULL,
date = NULL,
plotPars = NULL,
open = TRUE,
dev = FALSE,
...
)
# S3 method for Hist
plot(
x,
nsamp = 3,
nsim = 200,
nyears = 50,
proyears = 28,
output_file = NULL,
output_dir = getwd(),
quiet = TRUE,
tabs = TRUE,
title = NULL,
date = NULL,
plotPars = NULL,
open = TRUE,
dev = FALSE,
...
)
# S3 method for OM
plot(
x,
nsamp = 3,
nsim = 200,
nyears = 50,
proyears = 28,
output_file = NULL,
output_dir = getwd(),
quiet = TRUE,
tabs = TRUE,
title = NULL,
date = NULL,
plotPars = NULL,
open = TRUE,
dev = FALSE,
...
)
An object of class Stock
, Fleet
, Obs
, Imp
, Hist
, or OM
, OR one
of the following character strings for Object
of class Stock
: "M", "Growth", "Maturity", "Recruitment", "Spatial",
or "Depletion" and for Object
of class Fleet
: "Effort", "Catchability", "MPA",
and "Selectivity".
An object of class Stock
or Fleet
An object of class Stock
required for Fleet
parameters
The number of random samples to show in the plot
The number of simulations (only used for objects not of class OM
)
The number of historical years (only used for objects not of class OM
)
The number of projection years (only used for objects not of class OM
)
Name of the output html file (without file extension)
Output directory. Defaults to getwd()
An option to suppress printing of the pandoc command line
Include tabs in the HTML file?
Optional title for the markdown report
Optional date for the markdown report
A named list with options for plots:
breaks - numeric. Number of breaks in histograms.
col - character. Color of histograms.
axes - logical. Include axes in histogram?
cex.main - numeric. Size of main title in plots.
lwd - numeric. Line width for time-series plots.
Logical. Compile to a HTML report (TRUE) or print plots in R console (FALSE)
Logical. Open the html file?
Logical. For development use only.
Not used
if (FALSE) {
# Plot Stock Object:
Stock <- MSEtool::Albacore
plot(Stock)
# Individual plots:
plot("M", Stock)
plot("Growth", Stock)
plot("Maturity", Stock)
plot("Recruitment", Stock)
plot("Spatial", Stock)
plot("Depletion", Stock)
# Plot Fleet Object
Fleet <- MSEtool::Generic_DecE
plot(Fleet, Stock)
# Individual plots:
plot("Effort", Fleet, Stock)
plot("Catchability", Fleet, Stock)
plot("MPA", Fleet, Stock)
plot("Selectivity", Fleet, Stock)
# Plot Obs Object
Obs <- MSEtool::Imprecise_Unbiased
plot(Obs)
# Plot Imp Object
Imp <- MSEtool::Overages
plot(Imp)
# Plot Hist Object
OM <- MSEtool::testOM
Hist <- Simulate(OM)
plot(Hist)
# Plot OM Object
plot(OM)
}