Changelog

Source: NEWS.md

ypr 0.6.0.9000

• Same as previous version.

ypr 0.6.0

CRAN release: 2022-08-29

• Rk is now the egg to tR survival if between 0 and 1.

ypr 0.5.2

CRAN release: 2021-07-03

• Internal changes only.

ypr 0.5.1

CRAN release: 2020-07-10

• House-keeping.

ypr 0.5.0

CRAN release: 2020-03-18

• Pass yield parameters Ly, harvest and biomass to ypr_report().
• Removed suggests dependency on checkr.

ypr 0.4.0

CRAN release: 2020-01-13

Major Features

Population Parameters

Replaced parameters

• M (annual instantaneous natural mortality rate)
• Mb (annual instantaneous natural mortality rate (as a function of length) scaling exponent)
• A0 (initial post age tR density independent mortality probability)

with

• n (annual natural mortality rate from age tR to length Ln)
• nL (annual natural mortality rate from length Ln)
• Ln (length at which the natural mortality rate switches from n to nA)

And

• Added parameters k2, Linf2 and L2 to allow for biphasic growth.
• Set Lp value to be 1000 as opposed to Linf.
• Set Ls and Lv arguments to be 50 as opposed to Linf/2.
• Allow L2, Ln, Ls and Lv to also take ages (as negative values).

Population(s)

• Added expand = TRUE argument to ypr_populations() to allow control over all combinations.
• Added ypr_populations_expand() to create all combinations of parameters.
• Added ypr_populations_update() (as well as update.ypr_population() and update.ypr_populations()).
• ypr_populations no longer requires names.
• Added ypr_population_names() to allow user to generate names.
• Added as_ypr_populations.data.frame().
• Added data.frame.ypr_population() and data.frame.ypr_populations().
• Added ypr_age_at_length() to get ages at specific lengths for a given population.
• Added ypr_length_at_age() to get lengths at specific ages for a given population.

Population Reports

• Added description = "" argument to ypr_report() to allow user to describe report.
• ypr_report() now starts with table of parameter values with parameter descriptions.
• Added view = FALSE argument to ypr_report() to allow user to view report in browser.
• Added ask = TRUE argument to ypr_report() to ask before overwriting or creating a file.
• Deprecated requirement to provide file extension in ypr_report().
• Soft deprecated ypr_schedule() for ypr_tabulate_schedule().

Plots

• Added plot of biomass and eggs to report.
• Added percent = FALSE argument to ypr_plot_fish()

Tables

• Added ypr_tabulate_biomass() to easily calculate total biomass and eggs.
• Renamed column HandlingMortality to HandlingMortalities in ypr_tabulate_fish() and ypr_plot_fish().
• Renamed column Spawning to Spawners in ypr_tabulate_fish() and ypr_plot_fish().

Bug Fixes

• Improved handling of unsustainable populations (no longer negative fish numbers).

ypr 0.3.1

CRAN release: 2019-04-26

• ypr_populations() now generates names
• Fixed Quesnel Lake Trout and Rainbow Trout mix up

ypr 0.3.0

CRAN release: 2018-11-26

• Now uses q instead of Ea and Eb for effort
• Parameter Rk now has to be greater than >= 1

ypr 0.2.0

• Added ypr_exploitation() to convert capture probabilities to exploitation probabilities.
• Added ypr_report() to generate Rmd file for population.
• Can now pass Rk as egg to recruit survival (at low density).
• Set default value of Wa to be 0.01.
• Added ypr_populations() to generate all combinations of parameters.
• Made ypr_tabulate_sr(), ypr_tabulate_yield(), ypr_tabulate_yields(), ypr_plot_yield() generic with definitions for ypr_population and ypr_populations objects.
• Added scaling parameter A0 for initial interval mortality of recruits.
• Added scaling parameters Ea and Eb to allow plots of yield per effort.
• Added Age, Length, Weight and Effort to ypr_tabulate_yield() and added ypr_tabulate_yields()
• Added y arg to ypr_plot_yield() to allow plotting of mean age, length, weight, effort or yield per effort by exploitation or capture probability.
• Added ypr_plot_histogram() to plot frequency distributions of catch, spawners and in lake by age, length or weight bins.
• Added ypr_tabulate_parameters() to get table of parameters, values and descriptions and ypr_detabulate_parameters() to convert back to a population object.
• Added ypr_tabulate_sr() to get table of eggs and recruits at unfished, actual and optimal rates.
• Added print.ypr_population().

ypr 0.1.0

• Added Mb to scale mortality by length and BH to distinguish between Beverton-Holt and Ricker curves and es for probability of a mature fish spawning and Sm for spawning mortality probability and Sp for spawning power and vulnerability power Vp and slot limit non-complicance parameter Nc and scaling parameter R0.
• Added ypr_population_update() to update population parameters.
• Added ypr_yield_tabulate() to tabulate actual and optimal yields.
• Added ypr_sr() to get stock recruitment parameters and ypr_plot_sr() to plot.
• Added ypr_inst2inter() and ypr_inter2instant() to convert mortality rates.
• Switched nu for M and R0 for Rmax.
• Switched yield parameters harvest and biomass to FALSE by default.
• Renamed a to Wa and b to Wb and eta to Hm and mu to pi and Rt to tR.
• Removed Capture (as covered by single value) and TotalMortality from schedule and added Spawning.

ypr 0.0.1

• Initial Release