Description Usage Arguments Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 | ## S3 method for class '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,
open = TRUE,
dev = FALSE,
...
)
## S3 method for class '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 class '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 class '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 class '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 class '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 class '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,
...
)
|
x |
An object of class |
Object |
An object of class |
Stock |
An object of class |
nsamp |
The number of random samples to show in the plot |
nsim |
The number of simulations (only used for objects not of class |
nyears |
The number of historical years (only used for objects not of class |
proyears |
The number of projection years (only used for objects not of class |
output_file |
Name of the output html file (without file extension) |
output_dir |
Output directory. Defaults to |
quiet |
An option to suppress printing of the pandoc command line |
tabs |
Include tabs in the HTML file? |
title |
Optional title for the markdown report |
date |
Optional date for the markdown report |
plotPars |
A named list with options for plots:
|
open |
Logical. Open the html file? |
dev |
Logical. For development use only. |
... |
Not used |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | ## Not run:
# Plot Stock Object:
Stock <- DLMtool::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 <- DLMtool::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 <- DLMtool::Imprecise_Unbiased
plot(Obs)
# Plot Imp Object
Imp <- DLMtool::Overages
plot(Imp)
# Plot Hist Object
OM <- DLMtool::testOM
Hist <- runMSE(OM, Hist=TRUE)
plot(Hist)
# Plot OM Object
plot(OM)
## End(Not run)
|
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