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ypr

Introduction

ypr is an R package that implements equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield (Walters and Martell 2004) of a fish population with one or more ecotypes. The yield can be based on the number of fish caught (or harvested) or biomass for all fish or just large (trophy) individuals.

The key life history parameters are

  • The growth coefficient (k) and mean maximum length (Linf) from the Von Bertalanffy growth curve
  • The length at which 50% mature (Ls)
  • The length at which 50% vulnerable to harvest (Lv)
  • The interval annual natural mortality rate (n)
  • The lifetime number of spawners per spawner at low density (Rk)

and in the case of ecotypes

  • The relative proportion of recruits that belong to that ecotype (RPR)

The calculations do not account for stochasticity, predator-prey dynamics, angler responses or density-dependent growth.

Installation

To install the latest release from CRAN

install.packages("ypr")

To install the developmental version from GitHub

# install.packages("remotes")
remotes::install_github("poissonconsulting/ypr")

Demonstration

Schedule

library(ypr)
population <- ypr_population(Rk = 5, Ls = 50, Rmax = 100, rho = 0.6)
ypr_plot_schedule(population, x = "Length", y = "Spawning")

ypr_tabulate_schedule(population)
#> # A tibble: 20 × 11
#>      Age Length Weight Fecundity Spawning NaturalMor…¹ Vulner…² Reten…³ Fishin…⁴
#>    <int>  <dbl>  <dbl>     <dbl>    <dbl>        <dbl>    <dbl>   <dbl>    <dbl>
#>  1     1   13.9   27.0      27.0 3.13e-56          0.2 3.13e-56     0.4 2.50e-57
#>  2     2   25.9  174.      174.  2.91e-29          0.2 2.91e-29     0.4 2.33e-30
#>  3     3   36.2  476.      476.  1.04e-14          0.2 1.04e-14     0.4 8.35e-16
#>  4     4   45.1  918.      918.  3.46e- 5          0.2 3.46e- 5     0.4 2.77e- 6
#>  5     5   52.8 1469.     1469.  9.95e- 1          0.2 9.95e- 1     0.4 7.96e- 2
#>  6     6   59.3 2090.     2090.  1.00e+ 0          0.2 1.00e+ 0     0.4 8.00e- 2
#>  7     7   65.0 2747.     2747.  1.00e+ 0          0.2 1.00e+ 0     0.4 8.00e- 2
#>  8     8   69.9 3412.     3412.  1.00e+ 0          0.2 1.00e+ 0     0.4 8.00e- 2
#>  9     9   74.1 4065.     4065.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 10    10   77.7 4689.     4689.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 11    11   80.8 5274.     5274.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 12    12   83.5 5816.     5816.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 13    13   85.8 6310.     6310.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 14    14   87.8 6758.     6758.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 15    15   89.5 7160.     7160.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 16    16   90.9 7518.     7518.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 17    17   92.2 7836.     7836.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 18    18   93.3 8116.     8116.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 19    19   94.2 8363.     8363.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> 20    20   95.0 8580.     8580.  1   e+ 0          0.2 1   e+ 0     0.4 8   e- 2
#> # … with 2 more variables: Survivorship <dbl>, FishedSurvivorship <dbl>, and
#> #   abbreviated variable names ¹​NaturalMortality, ²​Vulnerability, ³​Retention,
#> #   ⁴​FishingMortality
#> # ℹ Use `colnames()` to see all variable names

Fish

ypr_plot_fish(population, color = "white")
ypr_tabulate_fish(population)
#> # A tibble: 20 × 8
#>      Age Survivors Spawners   Caught Harvested Released HandlingMortal…¹ Ecotype
#>    <dbl>     <dbl>    <dbl>    <dbl>     <dbl>    <dbl>            <dbl> <chr>  
#>  1     1    70.1   2.19e-54 4.39e-55  1.76e-55 2.63e-55                0 <NA>   
#>  2     2    56.1   1.63e-27 3.26e-28  1.30e-28 1.96e-28                0 <NA>   
#>  3     3    44.9   4.68e-13 9.36e-14  3.74e-14 5.62e-14                0 <NA>   
#>  4     4    35.9   1.24e- 3 2.48e- 4  9.93e- 5 1.49e- 4                0 <NA>   
#>  5     5    28.7   2.86e+ 1 5.72e+ 0  2.29e+ 0 3.43e+ 0                0 <NA>   
#>  6     6    21.1   2.11e+ 1 4.23e+ 0  1.69e+ 0 2.54e+ 0                0 <NA>   
#>  7     7    15.6   1.56e+ 1 3.11e+ 0  1.24e+ 0 1.87e+ 0                0 <NA>   
#>  8     8    11.5   1.15e+ 1 2.29e+ 0  9.16e- 1 1.37e+ 0                0 <NA>   
#>  9     9     8.43  8.43e+ 0 1.69e+ 0  6.74e- 1 1.01e+ 0                0 <NA>   
#> 10    10     6.20  6.20e+ 0 1.24e+ 0  4.96e- 1 7.44e- 1                0 <NA>   
#> 11    11     4.57  4.57e+ 0 9.13e- 1  3.65e- 1 5.48e- 1                0 <NA>   
#> 12    12     3.36  3.36e+ 0 6.72e- 1  2.69e- 1 4.03e- 1                0 <NA>   
#> 13    13     2.47  2.47e+ 0 4.95e- 1  1.98e- 1 2.97e- 1                0 <NA>   
#> 14    14     1.82  1.82e+ 0 3.64e- 1  1.46e- 1 2.18e- 1                0 <NA>   
#> 15    15     1.34  1.34e+ 0 2.68e- 1  1.07e- 1 1.61e- 1                0 <NA>   
#> 16    16     0.986 9.86e- 1 1.97e- 1  7.89e- 2 1.18e- 1                0 <NA>   
#> 17    17     0.726 7.26e- 1 1.45e- 1  5.81e- 2 8.71e- 2                0 <NA>   
#> 18    18     0.534 5.34e- 1 1.07e- 1  4.27e- 2 6.41e- 2                0 <NA>   
#> 19    19     0.393 3.93e- 1 7.86e- 2  3.15e- 2 4.72e- 2                0 <NA>   
#> 20    20     0.289 2.89e- 1 5.79e- 2  2.31e- 2 3.47e- 2                0 <NA>   
#> # … with abbreviated variable name ¹​HandlingMortalities

Stock-Recruitment

ypr_plot_sr(population)

ypr_tabulate_sr(population)
#> # A tibble: 3 × 7
#>   Type        pi     u    Eggs Recruits Spawners Fecundity
#>   <chr>    <dbl> <dbl>   <dbl>    <dbl>    <dbl>     <dbl>
#> 1 unfished 0     0     286350.     80      159.      3600.
#> 2 actual   0.2   0.08  167831.     70.1    108.      3112.
#> 3 optimal  0.458 0.183  84129.     54.0     63.7     2641.

Yield

ypr_tabulate_yield(population)
#> # A tibble: 2 × 8
#>   Type       pi     u Yield   Age Length Weight Effort
#>   <chr>   <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl>
#> 1 actual  0.2   0.08   8.63  7.67   65.8  3112.   2.12
#> 2 optimal 0.458 0.183 11.7   6.87   62.6  2641.   5.82
ypr_plot_yield(population)

Information

For more information see the Get Started vignette.

Interaction

To interactively explore the effects of altering individual parameters on the schedule, stock-recruitment and yield see the ypr shiny app.

Creditation

Development of ypr was partially supported by the Habitat Conservation Trust Foundation and the Ministry of Forests, Lands and Natural Resource Operations.

The hex was designed by The Forest.

Contribution

Please report any issues.

Pull requests are always welcome.

Code of Conduct

Please note that the ypr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms

References

Walters, Carl J., and Steven J. D. Martell. 2004. Fisheries Ecology and Management. Princeton, N.J: Princeton University Press.

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Version

Install

install.packages('ypr')

Monthly Downloads

172

Version

0.6.0

License

MIT + file LICENSE

Issues

11

Pull Requests

0

Stars

7

Forks

1

Maintainer

Joe Thorley

Last Published

August 29th, 2022

Functions in ypr (0.6.0)

kootenay_rb

Kootenay Lake Rainbow Trout Population Parameters
ypr_age_at_length

Age At Length
plot.ypr_population

Plot Population Schedule
ypr-package

ypr: Yield Per Recruit
quesnel_bt

Quesnel Lake Bull Trout Population Parameters
reexports

Objects exported from other packages
params

Parameter Descriptions for ypr Functions
ypr_get_par

Get Parameter Value
ypr_optimize

Optimize Capture
ypr_detabulate_parameters

Detabulate Population Parameters
ypr_ecotypes

Create Ecotypes Object
ypr_exploitation

Exploitation Probability
ypr_plot_fish

Plot Fish
kootenay_rb_13

Kootenay Lake Rainbow Trout Population Parameters (2013)
quesnel_lt

Quesnel Lake Lake Trout Population Parameters
quesnel_rb

Quesnel Lake Rainbow Trout Population Parameters
ypr_plot_schedule

Plot Population or Ecotypes Schedule Terms
ypr_names

Population(s) or Ecotype Names
ypr_length_at_age

Length At Age
ypr_plot_biomass

Plot Biomass
ypr_schedule

Life-History Schedule
ypr_sr

Stock-Recruitment Parameters
ypr_report

Report
ypr_population_update

Update a Population Object
ypr_plot_sr

Plot Stock-Recruitment Curve
ypr_populations

Populations
ypr_populations_expand

Expand Populations
ypr_population_names

Population Names
ypr_plot_yield

Plot Yield by Capture
ypr_population

Population Parameters
ypr_yield

Yield
ypr_tabulate_parameters

Tabulate Population Parameters
ypr_tabulate_yields

Tabulate Yields
ypr_yields

Yields
ypr_tabulate_schedule

Life-History Schedule
ypr_tabulate_fish

Tabulate Fish Numbers
ypr_tabulate_sr

Tabulate Stock-Recruitment Parameters
ypr_update

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

Tabulate Yield
ypr_tabulate_biomass

Tabulate Biomass (and Eggs)
is.ypr_population

Tests if is a Population, Populations or Ecotypes
check_ecotypes

Check Ecotypes
as_ypr_ecotypes

Coerce to an Ecotypes Object
chilliwack_bt_05

Chilliwack Lake Bull Trout Populations Parameters (2005)
as_ypr_population

Coerce to a Population Object
check_populations

Check Populations
as_ypr_populations

Coerce to a Populations Object
check_population

Check Population
adams_bt_03

Adams Lake Bull Trout Population Parameters (2003)
kootenay_bt_13

Kootenay Lake Bull Trout Population Parameters (2013)