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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