`Rk`

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

- Internal changes only.

- House-keeping.

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

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).

- 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.

- 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()`

.

- Added plot of biomass and eggs to report.
- Added
`percent = FALSE`

argument to`ypr_plot_fish()`

- 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()`

.

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

`ypr_populations()`

now generates names- Fixed Quesnel Lake Trout and Rainbow Trout mix up

- Now uses
`q`

instead of`Ea`

and`Eb`

for effort - Parameter
`Rk`

now has to be greater than >= 1

- 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()`

.

- 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`

.

- Initial Release