Title:	Yield Per Recruit
Version:	0.6.0
Description:	An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population as described by Walters and Martell (2004) <isbn:0-691-11544-3>. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.
License:	MIT + file LICENSE
URL:	https://github.com/poissonconsulting/ypr
BugReports:	https://github.com/poissonconsulting/ypr/issues
Depends:	R (≥ 3.6)
Imports:	chk, ggplot2, graphics, lifecycle, purrr, stats, tibble, tidyplus, tools, yesno
Suggests:	covr, knitr, readr, rmarkdown, rstudioapi, scales, testthat (≥ 3.0.0), tidyr, usethis, withr
VignetteBuilder:	knitr
ByteCompile:	true
Config/testthat/edition:	3
Encoding:	UTF-8
Language:	en-US
LazyData:	true
RoxygenNote:	7.2.1
NeedsCompilation:	no
Packaged:	2022-08-29 22:15:01 UTC; joe
Author:	Joe Thorley [aut, cre], Ayla Pearson [ctb], Poisson Consulting [cph, fnd]
Maintainer:	Joe Thorley <joe@poissonconsulting.ca>
Repository:	CRAN
Date/Publication:	2022-08-29 22:30:03 UTC

ypr: Yield Per Recruit

Description

An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population as described by Walters and Martell (2004) <isbn:0-691-11544-3>. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.

Author(s)

Maintainer: Joe Thorley joe@poissonconsulting.ca (ORCID)

Other contributors:

• Ayla Pearson (ORCID) [contributor]

• Poisson Consulting [copyright holder, funder]

See Also

Useful links:

• https://github.com/poissonconsulting/ypr

• Report bugs at https://github.com/poissonconsulting/ypr/issues

Adams Lake Bull Trout Population Parameters (2003)

Description

The population parameters for Bull Trout in Adams Lake from Bison et al (2003)

Usage

adams_bt_03

Format

An object of class ypr_population().

References

Bison, R., O’Brien, D., and Martell, S.J.D. 2003. An Analysis of Sustainable Fishing Options for Adams Lake Bull Trout Using Life History and Telemetry Data. BC Ministry of Water Land and Air Protection, Kamloops, B.C.

See Also

Other data: chilliwack_bt_05, kootenay_bt_13, kootenay_rb_13, kootenay_rb, quesnel_bt, quesnel_lt, quesnel_rb

Examples

adams_bt_03
ypr_plot_yield(adams_bt_03)

Coerce to an Ecotypes Object

Description

Coerce to an Ecotypes Object

Usage

as_ypr_ecotypes(x, ...)

## S3 method for class 'data.frame'
as_ypr_ecotypes(x, ...)

## S3 method for class 'ypr_population'
as_ypr_ecotypes(x, ...)

## S3 method for class 'ypr_populations'
as_ypr_ecotypes(x, ...)

## S3 method for class 'ypr_ecotypes'
as_ypr_ecotypes(x, ...)

Arguments

Value

An object of class ypr_ecotypes.

Methods (by class)

• as_ypr_ecotypes(data.frame): Coerce a data.frame to an Ecotypes Object

• as_ypr_ecotypes(ypr_population): Coerce a Population Object to an Ecotypes Object

• as_ypr_ecotypes(ypr_populations): Coerce a Populations Object to an Ecotypes Object

• as_ypr_ecotypes(ypr_ecotypes): Coerce an Ecotypes Object to an Ecotypes Object

See Also

Other ecotypes: ypr_ecotypes()

Examples

as_ypr_ecotypes(as.data.frame(ypr_ecotypes(Ls = c(10, 15, 20))))
as_ypr_ecotypes(ypr_population())
as_ypr_ecotypes(ypr_populations(Ls = c(10, 15, 20)))
as_ypr_ecotypes(ypr_ecotypes(Ls = c(10, 15, 20)))

Coerce to a Population Object

Description

Coerce to a Population Object

Usage

as_ypr_population(x, ...)

## S3 method for class 'data.frame'
as_ypr_population(x, ...)

## S3 method for class 'ypr_population'
as_ypr_population(x, ...)

## S3 method for class 'ypr_populations'
as_ypr_population(x, ...)

## S3 method for class 'ypr_ecotypes'
as_ypr_population(x, ...)

## S3 method for class 'data.frame'
as_ypr_populations(x, ...)

Arguments

Value

An object of class ypr_population.

Methods (by class)

• as_ypr_population(data.frame): Coerce a data.frame to an Population Object

• as_ypr_population(ypr_population): Coerce a Population Object to an Population Object

• as_ypr_population(ypr_populations): Coerce a Populations Object of length 1 to a Population Object

• as_ypr_population(ypr_ecotypes): Coerce a Ecotypes Object of length 1 to a Population Object

Functions

• as_ypr_populations(data.frame): Coerce a data.frame to a Populations Object

Examples

as_ypr_population(as.data.frame(ypr_population()))
as_ypr_population(ypr_populations())
as_ypr_population(ypr_populations())
as_ypr_population(ypr_ecotypes())
as_ypr_populations(as.data.frame(ypr_populations(Rk = c(3, 4))))

Coerce to a Populations Object

Description

Coerce to a Populations Object

Usage

as_ypr_populations(x, ...)

## S3 method for class 'ypr_population'
as_ypr_populations(x, ...)

## S3 method for class 'ypr_populations'
as_ypr_populations(x, ...)

## S3 method for class 'ypr_ecotypes'
as_ypr_populations(x, ...)

Arguments

Value

An object of class ypr_ecotypes.

Methods (by class)

• as_ypr_populations(ypr_population): Coerce a Population Object to an Population Object

• as_ypr_populations(ypr_populations): Coerce a Populations Object of length 1 to a Population Object

• as_ypr_populations(ypr_ecotypes): Coerce a Ecotypes Object of length 1 to a Population Object

See Also

Other populations: chilliwack_bt_05, ypr_plot_yield(), ypr_populations_expand(), ypr_populations(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Examples

as_ypr_populations(ypr_population())
as_ypr_populations(ypr_populations())
as_ypr_populations(ypr_ecotypes())

Check Ecotypes

Description

Checks if an ypr_ecotypes object with valid parameter values.

Usage

check_ecotypes(x, x_name = NULL)

Arguments

Value

An informative error if the test fails or an invisible copy of x.

See Also

Other check: check_populations(), check_population()

Examples

check_ecotypes(ypr_ecotypes())

Check Population

Description

Checks if an ypr_population object with valid parameter values.

Usage

check_population(x, x_name = NULL)

Arguments

Value

An informative error if the test fails or an invisible copy of x.

See Also

Other check: check_ecotypes(), check_populations()

Examples

check_population(ypr_population())

Check Populations

Description

Checks if an ypr_populations object with valid parameter values.

Usage

check_populations(x, x_name = NULL)

Arguments

Value

An informative error if the test fails or an invisible copy of x.

See Also

Other check: check_ecotypes(), check_population()

Examples

check_populations(ypr_populations())

Chilliwack Lake Bull Trout Populations Parameters (2005)

Description

The populations parameters for Bull Trout in Chilliwack Lake from Taylor (2005)

Usage

chilliwack_bt_05

Format

An object of class ypr_populations().

References

Taylor, J.L. 2005. Sustainability of the Chilliwack Lake Char Fishery. Ministry of Water, Land and Air Protection, Surrey, B.C.

See Also

Other populations: as_ypr_populations(), ypr_plot_yield(), ypr_populations_expand(), ypr_populations(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other data: adams_bt_03, kootenay_bt_13, kootenay_rb_13, kootenay_rb, quesnel_bt, quesnel_lt, quesnel_rb

Examples

chilliwack_bt_05
yield <- ypr_tabulate_yield(chilliwack_bt_05, type = "optimal")
yield$pi <- round(yield$pi, 2)
yield <- yield[c("Llo", "Hm", "Rk", "pi")]
yield <- tidyr::spread(yield, Rk, pi)
yield <- yield[order(-yield$Hm), ]
yield
## Not run: 
ypr_plot_yield(chilliwack_bt_05, plot_values = FALSE) +
  ggplot2::facet_grid(Rk ~ Hm) +
  ggplot2::aes(group = Llo, linetype = Llo)

## End(Not run)

Tests if is a Population, Populations or Ecotypes

Description

Tests if is a Population, Populations or Ecotypes

Usage

is.ypr_population(x)

is_ypr_population(x)

is.ypr_populations(x)

is_ypr_populations(x)

is.ypr_ecotypes(x)

is_ypr_ecotypes(x)

Arguments

Functions

• is_ypr_population(): Test if is a Population

• is.ypr_populations(): Test if is a Populations

• is_ypr_populations(): Test if is a Populations

• is.ypr_ecotypes(): Test if is an Ecotypes

• is_ypr_ecotypes(): Test if is an Ecotypes

Examples

is.ypr_population(ypr_population())
is_ypr_population(ypr_population())
is.ypr_populations(ypr_populations())
is_ypr_population(ypr_populations())
is.ypr_ecotypes(ypr_ecotypes())
is_ypr_ecotypes(ypr_ecotypes())

Kootenay Lake Bull Trout Population Parameters (2013)

Description

The population parameters for Bull Trout in Kootenay Lake from Andrusak and Thorley (2013)

Usage

kootenay_bt_13

Format

An object of class ypr_population().

Details

The estimates should not be used for management.

References

Andrusak, G.F., and Thorley, J.L. 2013. Kootenay Lake Exploitation Study: Fishing and Natural Mortality of Large Rainbow Trout and Bull Trout: 2013 Annual Report. A Poisson Consulting Ltd. and Redfish Consulting Ltd. Report, Habitat Conservation Trust Foundation, Victoria, BC.

See Also

Other data: adams_bt_03, chilliwack_bt_05, kootenay_rb_13, kootenay_rb, quesnel_bt, quesnel_lt, quesnel_rb

Examples

kootenay_bt_13
ypr_plot_yield(kootenay_bt_13)

Kootenay Lake Rainbow Trout Population Parameters

Description

The population parameters for Rainbow Trout in Kootenay Lake.

Usage

kootenay_rb

Format

An object of class ypr_population().

Details

The estimates are liable to change and should not be used for management.

References

Thorley, J.L., and Andrusak, G.F. 2017. The fishing and natural mortality of large, piscivorous Bull Trout and Rainbow Trout in Kootenay Lake, British Columbia (2008–2013). PeerJ 5: e2874. doi:10.7717/peerj.2874.

See Also

Other data: adams_bt_03, chilliwack_bt_05, kootenay_bt_13, kootenay_rb_13, quesnel_bt, quesnel_lt, quesnel_rb

Examples

kootenay_rb
ypr_plot_yield(kootenay_rb)

Kootenay Lake Rainbow Trout Population Parameters (2013)

Description

The population parameters for Rainbow Trout in Kootenay Lake from Andrusak and Thorley (2013)

Usage

kootenay_rb_13

Format

An object of class ypr_population().

Details

The estimates should not be used for management.

References

Andrusak, G.F., and Thorley, J.L. 2013. Kootenay Lake Exploitation Study: Fishing and Natural Mortality of Large Rainbow Trout and Bull Trout: 2013 Annual Report. A Poisson Consulting Ltd. and Redfish Consulting Ltd. Report, Habitat Conservation Trust Foundation, Victoria, BC.

See Also

Other data: adams_bt_03, chilliwack_bt_05, kootenay_bt_13, kootenay_rb, quesnel_bt, quesnel_lt, quesnel_rb

Examples

kootenay_rb_13
ypr_plot_yield(kootenay_rb_13)

Parameter Descriptions for ypr Functions

Description

Parameter Descriptions for ypr Functions

Arguments

Plot Population Schedule

Description

Plot Population Schedule

Usage

## S3 method for class 'ypr_population'
plot(x, type = "b", ...)

Arguments

Value

An invisible copy of the original object.

See Also

graphics::plot

Examples

## Not run: 
plot(ypr_population())

## End(Not run)

Quesnel Lake Bull Trout Population Parameters

Description

The population parameters for Bull Trout in Quesnel Lake, BC.

Usage

quesnel_bt

Format

An object of class ypr_population().

Details

The estimates are liable to change and should not be used for management.

See Also

Other data: adams_bt_03, chilliwack_bt_05, kootenay_bt_13, kootenay_rb_13, kootenay_rb, quesnel_lt, quesnel_rb

Examples

quesnel_bt
ypr_plot_yield(quesnel_bt)

Quesnel Lake Lake Trout Population Parameters

Description

The population parameters for Lake Trout in Quesnel Lake, BC.

Usage

quesnel_lt

Format

An object of class ypr_population().

Details

The estimates are liable to change and should not be used for management.

See Also

Other data: adams_bt_03, chilliwack_bt_05, kootenay_bt_13, kootenay_rb_13, kootenay_rb, quesnel_bt, quesnel_rb

Examples

quesnel_lt
ypr_plot_yield(quesnel_lt)

Quesnel Lake Rainbow Trout Population Parameters

Description

The population parameters for Rainbow Trout in Quesnel Lake, BC.

Usage

quesnel_rb

Format

An object of class ypr_population().

Details

The estimates are liable to change and should not be used for management.

See Also

Other data: adams_bt_03, chilliwack_bt_05, kootenay_bt_13, kootenay_rb_13, kootenay_rb, quesnel_bt, quesnel_lt

Examples

quesnel_rb
ypr_plot_yield(quesnel_rb)

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

tibble

as_tibble

Age At Length

Description

Age At Length

Usage

ypr_age_at_length(population, length)

Arguments

Value

A double vector of the lengths.

See Also

Other calculate: ypr_exploitation(), ypr_length_at_age(), ypr_optimize(), ypr_yields(), ypr_yield()

Examples

ypr_age_at_length(ypr_population(), seq(0, 100, by = 10))

Detabulate Population Parameters

Description

Detabulate Population Parameters

Usage

ypr_detabulate_parameters(x)

Arguments

Value

An object of class ypr_population()

See Also

Other tabulate: ypr_report(), ypr_tabulate_biomass(), ypr_tabulate_fish(), ypr_tabulate_parameters(), ypr_tabulate_schedule(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other parameters: ypr_tabulate_parameters()

Examples

ypr_detabulate_parameters(ypr_tabulate_parameters(ypr_population()))

Create Ecotypes Object

Description

Creates an ypr_ecotypes object.

Usage

ypr_ecotypes(..., names = NULL)

Arguments

Value

An ypr_ecotypes() objects

See Also

Other ecotypes: as_ypr_ecotypes()

Examples

ypr_ecotypes(Linf = c(1, 2))
ypr_ecotypes(Linf = c(1, 2), t0 = c(0, 0.5))

Exploitation Probability

Description

Converts capture probabilities into exploitation probabilities based on the release and handling mortality probabilities where the probability of exploitation includes handling mortalities. The calculation assumes that a released fish cannot be recaught in the same year.

Usage

ypr_exploitation(object, pi = ypr_get_par(object))

Arguments

Details

In the case of no release (or 100% handling mortalities) the exploitation probability is identical to the capture probability. Otherwise it is less.

Value

A vector of exploitation probabilities.

See Also

Other calculate: ypr_age_at_length(), ypr_length_at_age(), ypr_optimize(), ypr_yields(), ypr_yield()

Examples

ypr_exploitation(ypr_population(pi = 0.4))
ypr_exploitation(ypr_population(pi = 0.4, rho = 0.6, Hm = 0.2))

Get Parameter Value

Description

Get Parameter Value

Usage

ypr_get_par(object, par = "pi")

Arguments

Value

A numeric or integer scalar or vector of the parameter value.

Examples

ypr_get_par(ypr_population())

Length At Age

Description

Length At Age

Usage

ypr_length_at_age(population, age)

Arguments

Value

A double vector of the lengths.

See Also

Other calculate: ypr_age_at_length(), ypr_exploitation(), ypr_optimize(), ypr_yields(), ypr_yield()

Examples

ypr_length_at_age(ypr_population(), seq(0, 5, by = 0.5))

Population(s) or Ecotype Names

Description

Generates set of unique names based on differences in parameter values.

Usage

ypr_names(x, ...)

## S3 method for class 'ypr_population'
ypr_names(x, ...)

## S3 method for class 'ypr_populations'
ypr_names(x, ...)

## S3 method for class 'ypr_ecotypes'
ypr_names(x, ...)

Arguments

Details

Parameter RPR is ignored because it is irrelevant to population(s) and does not distinguish between ecotypes.

Value

A character vector of the unique parameter based names.

Methods (by class)

• ypr_names(ypr_population): Population Names

• ypr_names(ypr_populations): Populations Names

• ypr_names(ypr_ecotypes): Ecotypes Names

Examples

ypr_names(ypr_population())
ypr_names(ypr_populations())
ypr_names(ypr_populations())

Optimize Capture

Description

Finds the interval annual capture probability (pi) that maximises the yield for a given population.

Usage

ypr_optimize(object, Ly = 0, harvest = TRUE, biomass = FALSE)

Arguments

Value

The interval annual capture probability (pi) that maximises the yield.

See Also

Other calculate: ypr_age_at_length(), ypr_exploitation(), ypr_length_at_age(), ypr_yields(), ypr_yield()

Examples

ypr_optimize(ypr_population())

Plot Biomass

Description

Produces a frequency histogram of the total fish 'Biomass' or 'Eggs' deposition by 'Age' class.

Usage

ypr_plot_biomass(population, y = "Biomass", color = NULL)

Arguments

Value

A ggplot2 object.

See Also

ggplot2::geom_histogram()

Other biomass: ypr_tabulate_biomass()

Other plot: ypr_plot_fish(), ypr_plot_schedule(), ypr_plot_sr(), ypr_plot_yield()

Examples

ypr_plot_biomass(ypr_population(), color = "white")

Plot Fish

Description

Produces a frequency histogram of the number of fish in the 'Survivors', 'Spawners', 'Caught', 'Harvested' or 'Released' categories by 'Length', 'Age' or 'Weight' class.

Usage

ypr_plot_fish(
  population,
  x = "Age",
  y = "Survivors",
  percent = FALSE,
  binwidth = 1L,
  color = NULL
)

Arguments

Value

A ggplot2 object.

See Also

ggplot2::geom_histogram()

Other fish: ypr_tabulate_fish()

Other plot: ypr_plot_biomass(), ypr_plot_schedule(), ypr_plot_sr(), ypr_plot_yield()

Examples

ypr_plot_fish(ypr_population(), color = "white")

Plot Population or Ecotypes Schedule Terms

Description

Produces a bivariate line plot of two schedule terms.

Usage

ypr_plot_schedule(population, x = "Age", y = "Length")

Arguments

Value

A ggplot2 object.

See Also

Other schedule: ypr_tabulate_schedule()

Other plot: ypr_plot_biomass(), ypr_plot_fish(), ypr_plot_sr(), ypr_plot_yield()

Examples

ypr_plot_schedule(ypr_population())

Plot Stock-Recruitment Curve

Description

Plot Stock-Recruitment Curve

Usage

ypr_plot_sr(
  population,
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  plot_values = TRUE
)

Arguments

Value

A ggplot2 object.

See Also

Other sr: ypr_sr(), ypr_tabulate_sr()

Other plot: ypr_plot_biomass(), ypr_plot_fish(), ypr_plot_schedule(), ypr_plot_yield()

Examples

ypr_plot_sr(ypr_population(Rk = 10))
ypr_plot_sr(ypr_population(Rk = 10, BH = 0L))

Plot Yield by Capture

Description

Plots the 'Yield', 'Age', 'Length', 'Weight', 'Effort', or 'YPUE' by the annual interval capture/exploitation probability.

Usage

ypr_plot_yield(object, ...)

## Default S3 method:
ypr_plot_yield(
  object,
  y = "Yield",
  pi = seq(0, 1, length.out = 100),
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  u = harvest,
  plot_values = TRUE,
  ...
)

## S3 method for class 'ypr_populations'
ypr_plot_yield(
  object,
  y = "Yield",
  pi = seq(0, 1, length.out = 100),
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  u = harvest,
  plot_values = TRUE,
  ...
)

Arguments

Value

A ggplot2 object.

Methods (by class)

• ypr_plot_yield(default): Plot Yield by Capture

• ypr_plot_yield(ypr_populations): Plot Yield by Capture

See Also

Other populations: as_ypr_populations(), chilliwack_bt_05, ypr_populations_expand(), ypr_populations(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other yield: ypr_tabulate_yield(), ypr_yields(), ypr_yield()

Other plot: ypr_plot_biomass(), ypr_plot_fish(), ypr_plot_schedule(), ypr_plot_sr()

Examples

## Not run: 
ypr_plot_yield(ypr_populations(
  Rk = c(2.5, 4.6),
  Llo = c(0, 60)
),
plot_values = FALSE
) +
  ggplot2::facet_wrap(~Llo) +
  ggplot2::aes_string(group = "Rk", color = "Rk") +
  ggplot2::scale_color_manual(values = c("black", "blue"))

ypr_plot_yield(ypr_populations(Rk = c(2.5, 4.6), Llo = c(0, 60))) +
  ggplot2::facet_grid(Rk ~ Llo)

## End(Not run)

ypr_plot_yield(ypr_population())

Population Parameters

Description

Generates an object of class ypr_population.

Usage

ypr_population(
  tmax = 20L,
  k = 0.15,
  Linf = 100,
  t0 = 0,
  k2 = 0.15,
  Linf2 = 100,
  L2 = 1000,
  Wb = 3,
  Ls = 50,
  Sp = 100,
  es = 1,
  Sm = 0,
  fb = 1,
  tR = 1L,
  BH = 1L,
  Rk = 3,
  n = 0.2,
  nL = 0.2,
  Ln = 1000,
  Lv = 50,
  Vp = 100,
  Llo = 0,
  Lup = 1000,
  Nc = 0,
  pi = 0.2,
  rho = 0,
  Hm = 0,
  Rmax = 1,
  Wa = 0.01,
  fa = 1,
  q = 0.1,
  RPR = 1
)

Arguments

Value

An object of class ypr_population.

Examples

ypr_population(k = 0.1, Linf = 90)

Population Names

Description

Generates set of unique names based on differences in parameter values.

Usage

ypr_population_names(population)

Arguments

Value

A character vector of the unique parameter based names.

See Also

ypr_names()

Update a Population Object

Description

for ypr_update().

Usage

ypr_population_update(population, ...)

Arguments

Populations

Description

Populations

Usage

ypr_populations(..., expand = TRUE, names = NULL)

Arguments

Value

A list of ypr_population() objects

See Also

Other populations: as_ypr_populations(), chilliwack_bt_05, ypr_plot_yield(), ypr_populations_expand(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Examples

ypr_populations(Rk = c(2.5, 4.6), Hm = c(0.2, 0.05))

Expand Populations

Description

An object of class ypr_population() of all unique combinations of parameter values.

Usage

ypr_populations_expand(populations)

Arguments

Value

An object of class ypr_population.

See Also

Other populations: as_ypr_populations(), chilliwack_bt_05, ypr_plot_yield(), ypr_populations(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Examples

ypr_populations_expand(
  ypr_populations(
    Rk = c(2.5, 4, 2.5),
    Hm = c(0.1, 0.2, 0.1)
  )
)

Report

Description

Creates an Rmd file that can be used to generate a report.

Usage

ypr_report(
  population,
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  title = "Population Report",
  description = "",
  date = Sys.Date(),
  file = "report",
  view = FALSE,
  ask = TRUE
)

Arguments

Value

An invisible character vector of the contents of the file.

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_tabulate_biomass(), ypr_tabulate_fish(), ypr_tabulate_parameters(), ypr_tabulate_schedule(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Examples

## Not run: 
ypr_report(ypr_population(), file = tempfile(), ask = FALSE)

## End(Not run)

Life-History Schedule

Description

DEPRECATED: Replace ypr_schedule() with ypr_tabulate_schedule()

Usage

ypr_schedule(population)

Details

Generates the life-history schedule by age for a population.

Stock-Recruitment Parameters

Description

Returns a single rowed data frame of the SR parameters:

alpha

Survival from egg to age tR at low density

beta

Density-dependence

Rk

Lifetime spawners per spawner at low density

phi

Lifetime eggs deposited per recruit at unfished equilibrium

phiF

Lifetime eggs deposited per recruit at the fished equilibrium

R0

Age tR recruits at the unfished equilibrium

R0F

Age tR recruits at the fished equilibrium

S0

Spawners at the unfished equilibrium

S0F

Spawners at the fished equilibrium

Usage

ypr_sr(object)

Arguments

Value

A data frame of the SR parameters.

See Also

Other sr: ypr_plot_sr(), ypr_tabulate_sr()

Examples

ypr_sr(ypr_population()) # Beverton-Holt
ypr_sr(ypr_population(BH = 0L)) # Ricker

Tabulate Biomass (and Eggs)

Description

Produces a data frame of the 'Weight' and 'Fecundity' and the number of 'Survivors' and 'Spawners' and the total 'Biomass' and 'Eggs' by 'Age' class.

Usage

ypr_tabulate_biomass(population)

Arguments

Value

A data frame

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_report(), ypr_tabulate_fish(), ypr_tabulate_parameters(), ypr_tabulate_schedule(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other biomass: ypr_plot_biomass()

Examples

ypr_tabulate_biomass(ypr_population())

Tabulate Fish Numbers

Description

Produces a data frame of the number of fish in the 'Survivors', 'Spawners', 'Caught', 'Harvested', 'Released' and 'HandlingMortalities' categories by 'Length', 'Age' or 'Weight' class and 'Ecotype' (NA if not applicable)

Usage

ypr_tabulate_fish(population, x = "Age", binwidth = 1L)

Arguments

Value

A data frame

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_report(), ypr_tabulate_biomass(), ypr_tabulate_parameters(), ypr_tabulate_schedule(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other fish: ypr_plot_fish()

Examples

ypr_tabulate_fish(ypr_population())

Tabulate Population Parameters

Description

Tabulate Population Parameters

Usage

ypr_tabulate_parameters(population)

Arguments

Value

A table of population parameters

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_report(), ypr_tabulate_biomass(), ypr_tabulate_fish(), ypr_tabulate_schedule(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other parameters: ypr_detabulate_parameters()

Examples

ypr_tabulate_parameters(ypr_population())

Life-History Schedule

Description

Generates the life-history schedule by age for a population.

Usage

ypr_tabulate_schedule(object, ...)

## S3 method for class 'ypr_population'
ypr_tabulate_schedule(object, ...)

## S3 method for class 'ypr_ecotypes'
ypr_tabulate_schedule(object, ...)

Arguments

Value

A tibble of the life-history schedule by age.

Methods (by class)

• ypr_tabulate_schedule(ypr_population): Tabulate Schedule

• ypr_tabulate_schedule(ypr_ecotypes): Tabulate Schedule

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_report(), ypr_tabulate_biomass(), ypr_tabulate_fish(), ypr_tabulate_parameters(), ypr_tabulate_sr(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other schedule: ypr_plot_schedule()

Examples

ypr_tabulate_schedule(ypr_population())
ypr_tabulate_schedule(ypr_ecotypes(Linf = c(10, 20)))

Tabulate Stock-Recruitment Parameters

Description

Tabulate Stock-Recruitment Parameters

Usage

ypr_tabulate_sr(object, ...)

## Default S3 method:
ypr_tabulate_sr(
  object,
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  all = FALSE,
  ...
)

## S3 method for class 'ypr_populations'
ypr_tabulate_sr(
  object,
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  all = FALSE,
  ...
)

Arguments

Value

A data.frame of stock-recruitment parameters.

Methods (by class)

• ypr_tabulate_sr(default): Tabulate Stock-Recruitment Parameters

• ypr_tabulate_sr(ypr_populations): Tabulate Stock-Recruitment Parameters

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_report(), ypr_tabulate_biomass(), ypr_tabulate_fish(), ypr_tabulate_parameters(), ypr_tabulate_schedule(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other populations: as_ypr_populations(), chilliwack_bt_05, ypr_plot_yield(), ypr_populations_expand(), ypr_populations(), ypr_tabulate_yields(), ypr_tabulate_yield()

Other sr: ypr_plot_sr(), ypr_sr()

Examples

ypr_tabulate_sr(ypr_population()) # Beverton-Holt
ypr_tabulate_sr(ypr_population(BH = 0L)) # Ricker
ypr_tabulate_sr(ypr_populations(Rk = c(2.5, 4.6)))

Tabulate Yield

Description

Tabulate Yield

Usage

ypr_tabulate_yield(object, ...)

## Default S3 method:
ypr_tabulate_yield(
  object,
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  type = "both",
  all = FALSE,
  ...
)

## S3 method for class 'ypr_populations'
ypr_tabulate_yield(
  object,
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  type = "both",
  all = FALSE,
  ...
)

Arguments

Value

A data frame.

Methods (by class)

• ypr_tabulate_yield(default): Tabulate Yield

• ypr_tabulate_yield(ypr_populations): Tabulate Yield

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_report(), ypr_tabulate_biomass(), ypr_tabulate_fish(), ypr_tabulate_parameters(), ypr_tabulate_schedule(), ypr_tabulate_sr(), ypr_tabulate_yields()

Other populations: as_ypr_populations(), chilliwack_bt_05, ypr_plot_yield(), ypr_populations_expand(), ypr_populations(), ypr_tabulate_sr(), ypr_tabulate_yields()

Other yield: ypr_plot_yield(), ypr_yields(), ypr_yield()

Examples

ypr_tabulate_yield(ypr_population())
ypr_tabulate_yield(ypr_populations(Rk = c(3, 5)))

Tabulate Yields

Description

Tabulate Yields

Usage

ypr_tabulate_yields(object, ...)

## Default S3 method:
ypr_tabulate_yields(
  object,
  pi = seq(0, 1, length.out = 100),
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  all = FALSE,
  ...
)

## S3 method for class 'ypr_populations'
ypr_tabulate_yields(
  object,
  pi = seq(0, 1, length.out = 100),
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE,
  all = FALSE,
  ...
)

Arguments

Value

A data frame.

Methods (by class)

• ypr_tabulate_yields(default): Tabulate Yields

• ypr_tabulate_yields(ypr_populations): Tabulate Yields

See Also

Other tabulate: ypr_detabulate_parameters(), ypr_report(), ypr_tabulate_biomass(), ypr_tabulate_fish(), ypr_tabulate_parameters(), ypr_tabulate_schedule(), ypr_tabulate_sr(), ypr_tabulate_yield()

Other populations: as_ypr_populations(), chilliwack_bt_05, ypr_plot_yield(), ypr_populations_expand(), ypr_populations(), ypr_tabulate_sr(), ypr_tabulate_yield()

Examples

ypr_tabulate_yields(ypr_population())
ypr_tabulate_yields(
  ypr_populations(
    Rk = c(3, 5)
  ),
  pi = seq(0, 1, length.out = 10)
)
ypr_tabulate_yields(ypr_ecotypes(Linf = c(10, 20)))

Update a YPR Object Currently just works with scalar parameters for populations and ecotypes.

Description

Update a YPR Object Currently just works with scalar parameters for populations and ecotypes.

Usage

ypr_update(x, ...)

## S3 method for class 'ypr_population'
ypr_update(x, ...)

## S3 method for class 'ypr_populations'
ypr_update(x, ...)

## S3 method for class 'ypr_ecotypes'
ypr_update(x, ...)

Arguments

Methods (by class)

• ypr_update(ypr_population): Update Population Parameters

• ypr_update(ypr_populations): Update Populations Parameters

• ypr_update(ypr_ecotypes): Update Populations Parameters

Examples

ypr_update(ypr_population(), Rk = 2.5)
ypr_update(ypr_populations(Rk = c(2.5, 4)), Rk = 2.5)
ypr_update(ypr_ecotypes(Linf = c(2.5, 4)), k = 1.5)

Yield

Description

Calculates the yield for a population.

Usage

ypr_yield(object, Ly = 0, harvest = TRUE, biomass = FALSE, ...)

Arguments

Details

By default, with Rmax = 1 the number of individuals is the proportion of the recruits at the carrying capacity. If the yield is given in terms of the biomass (kg) then the scaling also depends on the value of Wa (g).

Value

The yield as number of fish or biomass.

See Also

Other yield: ypr_plot_yield(), ypr_tabulate_yield(), ypr_yields()

Other calculate: ypr_age_at_length(), ypr_exploitation(), ypr_length_at_age(), ypr_optimize(), ypr_yields()

Examples

ypr_yield(ypr_population())
ypr_yield(ypr_ecotypes(Linf = c(100, 200)))

Yields

Description

Calculates the yield(s) for a population based on one or more capture rates.

Usage

ypr_yields(
  object,
  pi = seq(0, 1, length.out = 100),
  Ly = 0,
  harvest = TRUE,
  biomass = FALSE
)

Arguments

Value

A numeric vector of the yields.

See Also

Other yield: ypr_plot_yield(), ypr_tabulate_yield(), ypr_yield()

Other calculate: ypr_age_at_length(), ypr_exploitation(), ypr_length_at_age(), ypr_optimize(), ypr_yield()

Examples

pi <- seq(0, 1, length.out = 30)
plot(pi, ypr_yields(ypr_population(), pi), type = "l")