High-Performance Open-Source Archive
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.
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