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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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.