Package 'openMSE'

At-Age Time Series Variables

Description

At-Age Time Series Variables

Usage

At_Age_TS_Variables

Format

An object of class data.frame with 6 rows and 3 columns.

---

Run an example MSE

Description

Run an example MSE using three data-limited management procedures from DLMtool and one stock assessment model from SAMtool.

Usage

demo()

Details

The MSE is run and three example performance metrics plots are produced: a trade-off plot, a projection plot, and a Kobe plot.

An MSE about is invisibly returned, and can be explored further (e.g., summary(MSE)).

Value

Invisibly returns an MSE object, and produces example plots of performance metrics.

Examples

MSE <- demo()

---

Create a data.frame with estimated values from a SAMtool assessment method used in an MSE

Description

Create a data.frame with estimated values from a SAMtool assessment method used in an MSE

Usage

get_Assess_Estimates(x, model = "Model 1")

## S3 method for class 'MSE'
get_Assess_Estimates(x, model = "Model 1")

## S3 method for class 'list'
get_Assess_Estimates(x, model = NULL)

## S3 method for class 'MMSE'
get_Assess_Estimates(x, model = NULL)

Arguments

x	An object of class MSE or a list of MSE objects, where MSE includes management procedures that use SAMtool stock assessment functions that return estimated values in MSE@PPD.
model	An optional name for the model. If x is a list of objects, model will be taken from names(x). If names(x) is NULL, model will be given sequential numerical values (e.g., ⁠Model 1⁠, ⁠Model 2⁠, ...)

Value

A data.frame with columns:

Year_assess	The year the assessment was run in the MSE
Year_est	The year corresponding with the estimated value
Variable	The estimated variable
Value	The estimated value
MP	The name of the management procedure
Simulation	The simulation number
Model	The name of model

---

Create a data.frame with at-age schedules by simulation and year

Description

Note that the Selectivity and Retention curves in these plots are from the operating model. If an MP changes the selectivity/retention, this is not shown in these plots.

Usage

get_at_Age(x, model = "Model 1", ...)

## S3 method for class 'Hist'
get_at_Age(x, model = "Model 1", ...)

## S3 method for class 'list'
get_at_Age(x, model = "Model 1", ...)

## S3 method for class 'MSE'
get_at_Age(x, model = "Model 1", ...)

## S3 method for class 'multiHist'
get_at_Age(x, model = "Model 1", ...)

## S3 method for class 'MMSE'
get_at_Age(x, model = "Model 1", ...)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
model	An optional name for the model. If x is a list of objects, model will be taken from names(x). If names(x) is NULL, model will be given sequential numerical values (e.g., ⁠Model 1⁠, ⁠Model 2⁠, ...)
...	additional arguments

Value

A data.frame

---

Create a data.frame with time-series information by simulation and year

Description

Create a data.frame with time-series information by simulation and year

Usage

get_at_age_ts(
  x,
  variable = "Spawning Biomass",
  model = "Model 1",
  scale = NULL
)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
variable	A character string with a valid name for a time-series variable. Use valid_ts_variables() for valid variable names.
model	An optional name for the model. If x is a list of objects, model will be taken from names(x). If names(x) is NULL, model will be given sequential numerical values (e.g., ⁠Model 1⁠, ⁠Model 2⁠, ...)
scale	An optional function with a single numeric argument that returns transformed or scaled numeric values. See lb2kg and kg2lb for example. Can be a list of functions for list objects (NA for no transformation)

---

Create a data.frame with at-length selectivity and retention schedules by simulation and year

Description

Note that the Selectivity and Retention curves in these plots are from the operating model. If an MP changes the selectivity/retention, this is not shown in these plots.

Usage

get_at_Length(x, model = "Model 1", ...)

## S3 method for class 'multiHist'
get_at_Length(x, model = "Model 1", ...)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
model	An optional name for the model. If x is a list of objects, model will be taken from names(x). If names(x) is NULL, model will be given sequential numerical values (e.g., ⁠Model 1⁠, ⁠Model 2⁠, ...)
...	additional arguments

Value

A data.frame

---

Get Life History Parameters

Description

Extracts the life-history parameters: Linf, K, L50, and ageM

Usage

get_LifeHistory(x, model = "Model 1", ...)

## S3 method for class 'Hist'
get_LifeHistory(x, model = "Model 1", ...)

## S3 method for class 'list'
get_LifeHistory(x, model = "Model 1", ...)

## S3 method for class 'MSE'
get_LifeHistory(x, model = "Model 1", ...)

## S3 method for class 'MMSE'
get_LifeHistory(x, model = "Model 1", ...)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
model	An optional name for the model. If x is a list of objects, model will be taken from names(x). If names(x) is NULL, model will be given sequential numerical values (e.g., ⁠Model 1⁠, ⁠Model 2⁠, ...)
...	additiona arguments (not used)

Value

A data.frame

---

Extract the meta-data from a Hist or MSE object

Description

Extract the meta-data from a Hist or MSE object

Usage

get_Metadata(x)

## S3 method for class 'Hist'
get_Metadata(x)

## S3 method for class 'MSE'
get_Metadata(x)

## S3 method for class 'list'
get_Metadata(x)

## S3 method for class 'MMSE'
get_Metadata(x)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects

Details

If x is a list of objects, each object must have identical structure, i.e., same number of simulations, same number of age-classes, historical and projection years, management procedures, etc

Value

A named list with elements:

nsim	The number of simulations
nage	The number of age classes
Ages	The age classes
nyear	The number of historical years
Hist.Years	A data.frame with the historical years in the Year column
proyears	The number of projection years
Pro.Years	A data.frame with the projection years in the Year column
All.Years	A data.frame with the historical and the projection years in the Year column
nMPs	The number of MPs (if x is an object of class MSE)
MPs	The MPs (if x is an object of class MSE)

---

Create a data.frame with time-series information by simulation and year

Description

Create a data.frame with time-series information by simulation and year

Usage

get_ts(x, variable = "Spawning Biomass", model = "Model 1", scale = NULL)

valid_ts_variables()

valid_at_age_ts_variables()

## S3 method for class 'Hist'
get_ts(x, variable = "Spawning Biomass", model = "Model 1", scale = NULL)

## S3 method for class 'MSE'
get_ts(x, variable = "Spawning Biomass", model = "Model 1", scale = NULL)

## S3 method for class 'list'
get_ts(x, variable = "Spawning Biomass", model = "Model 1", scale = NULL)

## S3 method for class 'multiHist'
get_ts(x, variable = "Spawning Biomass", model = "Model 1", scale = NULL)

## S3 method for class 'MMSE'
get_ts(x, variable = "Spawning Biomass", model = "Model 1", scale = NULL)

get_Biomass(x, model = "Model 1", ...)

get_Landings(x, model = "Model 1", ...)

get_Removals(x, model = "Model 1", ...)

get_Recruits(x, model = "Model 1", ...)

get_SSB(x, model = "Model 1", ...)

get_SB_SBMSY(x, model = "Model 1", ...)

get_F(x, model = "Model 1", ...)

get_Biomass_at_Age(x, model = "Model 1", ...)

get_Number_at_Age(x, model = "Model 1", ...)

get_SSB_at_Age(x, model = "Model 1", ...)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
variable	A character string with a valid name for a time-series variable. Use valid_ts_variables() for valid variable names.
model	An optional name for the model. If x is a list of objects, model will be taken from names(x). If names(x) is NULL, model will be given sequential numerical values (e.g., ⁠Model 1⁠, ⁠Model 2⁠, ...)
scale	An optional function with a single numeric argument that returns transformed or scaled numeric values. See lb2kg and kg2lb for example. Can be a list of functions for list objects (NA for no transformation)
...	named arguments passed to get_ts

---

Create a data.frame with Historical and Projection years

Description

Create a data.frame with Historical and Projection years

Usage

get_Years(x)

## S3 method for class 'MSE'
get_Years(x)

## S3 method for class 'MMSE'
get_Years(x)

## S3 method for class 'Hist'
get_Years(x)

## S3 method for class 'multiHist'
get_Years(x)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects

Value

A data.frame with years and period (Historical or Projection)

---

Convert numeric values to a different scale

Description

Convert numeric values to a different scale

Usage

lb2kg(x)

lb2mt(x)

kg2lb(x)

kg2_1000lb(x)

kg2mt(x)

inch2mm(x)

inch2cm(x)

mm2inch(x)

cm2inch(x)

divide_1000(x)

divide_100(x)

divide_10(x)

multiply_1000(x)

multiply_100(x)

multiply_10(x)

Arguments

x	A vector of numeric values

Value

The vector of numeric values converted to the appropriate scale

Functions

• lb2kg(): Convert from pounds to kilograms

• lb2mt(): Convert from pounds to metric tons

• kg2lb(): Convert from kilograms to pounds

• kg2_1000lb(): Convert from kilograms to 1000 pounds

• kg2mt(): Convert from kilograms to metric tons

• inch2mm(): Convert from inches to millimeters

• inch2cm(): Convert from inches to centimeters

• mm2inch(): Convert from millimeters to inches

• cm2inch(): Convert from centimeters to inches

• divide_1000(): Divide values by 1000

• divide_100(): Divide values by 100

• divide_10(): Divide values by 10

• multiply_1000(): Multiply values by 1000

• multiply_100(): Multiply values by 100

• multiply_10(): Multiply values by 10

Examples

lb2kg(1:10)
kg2lb(1:10)

---

Plot at-Age schedules

Description

Plots Length, Weight, Maturity, Natural-Mortality, Selectivity, and Retention-at-Age schedules.

Usage

plot_at_Age(
  x,
  quantiles = c(0.025, 0.975),
  scale = NULL,
  variable = "Length",
  xlab = "Age (Year)",
  ylab = NULL,
  title = "",
  years = NULL,
  alpha = 0.1,
  lwd = 1,
  use_theme = NULL,
  colpalette = "Dark2",
  print = TRUE
)

plot_Length(x, ...)

plot_Weight(x, ...)

plot_Maturity(x, ...)

plot_N.Mortality(x, ...)

plot_Select(x, ...)

plot_Retention(x, ...)

plot_Select_Maturity(x, ...)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
quantiles	Lower and upper quantiles to calculate. Numeric vector of length 2.
scale	An optional function with a single numeric argument that returns transformed or scaled numeric values. See lb2kg and kg2lb for example. Can be a list of functions for list objects (NA for no transformation)
variable	String. One of 'Length', 'Weight', 'N.Mortality','Maturity', 'Select', 'Retention'
xlab	X-axis label (default 'Age (Year)')
ylab	Y-axes label
title	Optional title
years	Optional numeric vector specifying the years to plot. Default is the first and last historical year, and the last projection year
alpha	Transparency parameter
lwd	Line width
use_theme	Optional ggplot theme
colpalette	Color palette from RColorBrewer
print	Logical. Print the plot?
...	Named arguments passed to plot_at_Age

Details

Note that the Selectivity and Retention curves in these plots are from the operating model. If an MP changes the selectivity/retention, this is not shown in these plots.

Value

A named list with:

p	The ggplot object
df	Data.frame with the summary statistics (median and quantiles)

Functions

• plot_Length(): Plot Length-at-Age

• plot_Weight(): Plot Weight-at-Age

• plot_Maturity(): Plot Maturity-at-Age

• plot_N.Mortality(): Plot N.Mortality-at-Age

• plot_Select(): Plot Selectivity-at-Age

• plot_Retention(): Plot Retention -at-Age

• plot_Select_Maturity(): Plot Selectivity-, Retention-, and Maturity-at-Age

---

Plots the median and quantiles of a time-series

Description

Plots the median and quantiles of a time-series

Usage

plot_TS(
  x,
  xlab = "Year",
  ylab = "Spawning Biomass",
  title = "",
  quantiles = c(0.025, 0.975),
  scale = NULL,
  alpha = 0.1,
  lwd = 1,
  use_theme = NULL,
  colpalette = "Dark2",
  facet = TRUE,
  inc.Legend = !facet,
  inc.Hist = FALSE,
  print = TRUE,
  get_function = get_SSB,
  years = NULL,
  ...
)

plot_SSB(x, ...)

plot_Biomass(x, ylab = "Biomass", ...)

plot_Landings(x, ylab = "Landings", ...)

plot_Removals(x, ylab = "Removals", ...)

plot_Recruits(x, ylab = "Recruits", ...)

plot_F(x, ylab = "Fishing Mortality (F)", ...)

plot_LifeHistory(
  x,
  xlab = "Year",
  ylab = "Median (quantiles)",
  title = "",
  quantiles = c(0.025, 0.975),
  scale = NULL,
  alpha = 0.1,
  lwd = 1,
  use_theme = NULL,
  colpalette = "Dark2",
  facet = TRUE,
  inc.Legend = !facet,
  inc.Hist = FALSE,
  print = TRUE
)

Arguments

x	An object of class Hist, MSE, or a list of Hist or MSE objects
xlab	X-axis label (default 'Year')
ylab	Y-axes label
title	Optional title
quantiles	Lower and upper quantiles to calculate. Numeric vector of length 2.
scale	An optional function with a single numeric argument that returns transformed or scaled numeric values. See lb2kg and kg2lb for example. Can be a list of functions for list objects (NA for no transformation)
alpha	Transparency parameter
lwd	Line width
use_theme	Optional ggplot theme
colpalette	Color palette from RColorBrewer
facet	Logical. Facet the plot?
inc.Legend	Logical. Include legend?
inc.Hist	Logical. For MSE results, include the historical period?
print	Logical. Print the plot?
get_function	get_ function to extract time-series information from x
years	Optional numeric vector specifying the years to plot. Default is all years.
...	Named arguments passed to plot_TS

Value

A named list with:

p	The ggplot object
df	Data.frame with the summary statistics (median and quantiles)

Functions

• plot_SSB(): Plot the Spawning Biomass

• plot_Biomass(): Plot the Total Biomass

• plot_Landings(): Plot the Landings (biomass)

• plot_Removals(): Plot the Removals (biomass)

• plot_Recruits(): Plot the Recruits (numbers)

• plot_F(): Plot the Recruits (numbers)

• plot_LifeHistory(): Plot the Life-History parameters

---

A ggplot2 theme

Description

A simple theme for ggplot2 that loosely resembles nicely themed plots from base graphics.

Usage

theme_default(
  base_size = 11,
  base_family = "",
  text_col = "grey20",
  panel_border_col = "grey70"
)

Arguments

base_size	Base font size.
base_family	Base font family.
text_col	Color for text.
panel_border_col	Color for panel borders.

Examples

p <- ggplot2::ggplot(mtcars) +
  ggplot2::geom_point(ggplot2::aes(x = wt, y = mpg, colour = factor(gear))) +
  ggplot2::facet_wrap(~am)
p + theme_default()

---

Time Series Variables

Description

Time Series Variables

Usage

TS_Variables

Format

An object of class data.frame with 21 rows and 3 columns.

---

Open the openMSE Documentation website

Description

Opens the openMSE Documentation website (requires internet connection)

Usage

userguide()

Value

Nothing is returned. Opens the 'openMSE.com' in the web browser

Examples

userguide()

---