Changes in version 0.6.0.9014 Continuous integration - Install binaries from r-universe for dev workflow (#119). Changes in version 0.6.0.9013 Continuous integration - Fix reviewdog and add commenting workflow (#117). Changes in version 0.6.0.9012 Chore - Auto-update from GitHub Actions (#112). Continuous integration - Use workflows for fledge (#115). - Sync (#114). - Use reviewdog for external PRs (#113). - Cleanup and fix macOS (#111). - Format with air, check detritus, better handling of extra-packages (#110). - Enhance permissions for workflow (#108). - Permissions, better tests for missing suggests, lints (#107). - Always use _R_CHECK_FORCE_SUGGESTS_=false (#106). - Correct installation of xml2 (#105). - Sync (#104). Testing - Skip if packages missing (#109). Changes in version 0.6.0.9011 - Merge branch 'main' of github.com:poissonconsulting/ypr. - Have parameter description NA if documentation corrupted. Changes in version 0.6.0.9010 fledge - Bump version to 0.6.0.9009 (#91). Changes in version 0.6.0.9009 fledge - Bump version to 0.6.0.9008 (#89). Changes in version 0.6.0.9008 fledge - Bump version to 0.6.0.9007 (#87). Changes in version 0.6.0.9007 fledge - Bump version to 0.6.0.9006 (#86). Changes in version 0.6.0.9006 fledge - Bump version to 0.6.0.9005 (#85). Changes in version 0.6.0.9005 fledge - Bump version to 0.6.0.9004 (#84). Changes in version 0.6.0.9004 fledge - Bump version to 0.6.0.9003 (#83). Changes in version 0.6.0.9003 fledge - Bump version to 0.6.0.9002 (#81). Changes in version 0.6.0.9002 fledge - Bump version to 0.6.0.9001 (#80). Changes in version 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. Changes in version 0.6.0.9000 - Same as previous version. Changes in version 0.6.0 (2022-08-29) - Rk is now the egg to tR survival if between 0 and 1. Changes in version 0.5.2 (2021-07-03) - Internal changes only. Changes in version 0.5.1 (2020-07-10) - House-keeping. Changes in version 0.5.0 (2020-03-18) - Pass yield parameters Ly, harvest and biomass to ypr_report(). - Removed suggests dependency on checkr. Changes in version 0.4.0 (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). Changes in version 0.3.1 (2019-04-26) - ypr_populations() now generates names - Fixed Quesnel Lake Trout and Rainbow Trout mix up Changes in version 0.3.0 (2018-11-26) - Now uses q instead of Ea and Eb for effort - Parameter Rk now has to be greater than >= 1 Changes in version 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(). Changes in version 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. Changes in version 0.0.1 - Initial Release