Fetch tags for fledge workflow to avoid unnecessary NEWS entries (#78).
Use larger retry count for lock-threads workflow (#77).
Overwrite from actions-sync (#76).
Merge pull request #75 from poissonconsulting/reqName.
replaced requireNamespace() with rlang::check_installed()
Merge pull request #72 from poissonconsulting/before.
Rk is now the egg to tR survival if between 0 and 1.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
k2, Linf2 and L2 to allow for biphasic growth.Lp value to be 1000 as opposed to Linf.Ls and Lv arguments to be 50 as opposed to Linf/2.L2, Ln, Ls and Lv to also take ages (as negative values).expand = TRUE argument to ypr_populations() to allow control over all combinations.ypr_populations_expand() to create all combinations of parameters.ypr_populations_update() (as well as update.ypr_population() and update.ypr_populations()).ypr_populations no longer requires names.ypr_population_names() to allow user to generate names.as_ypr_populations.data.frame().data.frame.ypr_population() and data.frame.ypr_populations().ypr_age_at_length() to get ages at specific lengths for a given population.ypr_length_at_age() to get lengths at specific ages for a given population.description = "" argument to ypr_report() to allow user to describe report.ypr_report() now starts with table of parameter values with parameter descriptions.view = FALSE argument to ypr_report() to allow user to view report in browser.ask = TRUE argument to ypr_report() to ask before overwriting or creating a file.ypr_report().ypr_schedule() for ypr_tabulate_schedule().percent = FALSE argument to ypr_plot_fish()ypr_tabulate_biomass() to easily calculate total biomass and eggs.HandlingMortality to HandlingMortalities in ypr_tabulate_fish() and ypr_plot_fish().Spawning to Spawners in ypr_tabulate_fish() and ypr_plot_fish().ypr_populations() now generates namesq instead of Ea and Eb for effortRk now has to be greater than >= 1ypr_exploitation() to convert capture probabilities to exploitation probabilities.ypr_report() to generate Rmd file for population.Wa to be 0.01.ypr_populations() to generate all combinations of parameters.ypr_tabulate_sr(), ypr_tabulate_yield(), ypr_tabulate_yields(), ypr_plot_yield() generic with definitions for ypr_population and ypr_populations objects.A0 for initial interval mortality of recruits.Ea and Eb to allow plots of yield per effort.Age, Length, Weight and Effort to ypr_tabulate_yield() and added ypr_tabulate_yields()y arg to ypr_plot_yield() to allow plotting of mean age, length, weight, effort or yield per effort by exploitation or capture probability.ypr_plot_histogram() to plot frequency distributions of catch, spawners and in lake by age, length or weight bins.ypr_tabulate_parameters() to get table of parameters, values and descriptions and ypr_detabulate_parameters() to convert back to a population object.ypr_tabulate_sr() to get table of eggs and recruits at unfished, actual and optimal rates.print.ypr_population().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.ypr_population_update() to update population parameters.ypr_yield_tabulate() to tabulate actual and optimal yields.ypr_sr() to get stock recruitment parameters and ypr_plot_sr() to plot.ypr_inst2inter() and ypr_inter2instant() to convert mortality rates.nu for M and R0 for Rmax.harvest and biomass to FALSE by default.a to Wa and b to Wb and eta to Hm and mu to pi and Rt to tR.Capture (as covered by single value) and TotalMortality from schedule and added Spawning.