Changelog • ypr

ypr 0.6.0.9010

fledge

Bump version to 0.6.0.9009 (#91).

ypr 0.6.0.9009

fledge

Bump version to 0.6.0.9008 (#89).

ypr 0.6.0.9008

fledge

Bump version to 0.6.0.9007 (#87).

ypr 0.6.0.9007

fledge

Bump version to 0.6.0.9006 (#86).

ypr 0.6.0.9006

fledge

Bump version to 0.6.0.9005 (#85).

ypr 0.6.0.9005

fledge

Bump version to 0.6.0.9004 (#84).

ypr 0.6.0.9004

fledge

Bump version to 0.6.0.9003 (#83).

ypr 0.6.0.9003

fledge

Bump version to 0.6.0.9002 (#81).

ypr 0.6.0.9002

fledge

Bump version to 0.6.0.9001 (#80).

ypr 0.6.0.9001

Continuous integration

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).

Documentation

Register poissontemplate usage (@maelle, #71).

Uncategorized

Merge pull request #75 from poissonconsulting/reqName.

replaced requireNamespace() with rlang::check_installed()
Merge pull request #72 from poissonconsulting/before.

ypr 0.6.0.9000

Same as previous version.

ypr 0.6.0

CRAN release: 2022-08-29

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

ypr 0.5.2

CRAN release: 2021-07-03

Internal changes only.

ypr 0.5.1

CRAN release: 2020-07-10

House-keeping.

ypr 0.5.0

CRAN release: 2020-03-18

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

ypr 0.4.0

CRAN release: 2020-01-13

Major Features

Population Parameters

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).

Population(s)

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.

Population Reports

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().

Plots

Added plot of biomass and eggs to report.
Added percent = FALSE argument to ypr_plot_fish()

Tables

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().

Bug Fixes

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

ypr 0.3.1

CRAN release: 2019-04-26

ypr_populations() now generates names
Fixed Quesnel Lake Trout and Rainbow Trout mix up

ypr 0.3.0

CRAN release: 2018-11-26

Now uses q instead of Ea and Eb for effort
Parameter Rk now has to be greater than >= 1

ypr 0.2.0

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().

ypr 0.1.0

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.

ypr 0.0.1

Initial Release