Note: Earlier references to "stochastic parameters" are now referred as "process error parameters " or "process error for population and fishery processes"
Process Error
Added AGEPRO Keyword parameters for process error for population and fishery processes. (#32)
natural_mortality (natmort)
maturity_fraction (maturity)
fishery_selectivity (fishery)
discard_fraction (discard)
jan_stock_weight_age (stock_weight)
spawning_stock_weight_age (ssb_weight)
mean_population_weight_age (mean_weight)
landed_catch_weight_age (catch_weight)
discard_weight_age (disc_weight)
Implemented AGEPRO input file and experimental JSON input file support for process error parameters. (#12,
Ensure the only "Weight of Age" Process Errors parameters return input_option and time_varying, if it is a valid weight of age option.
Exclude discards and disc_weight if agepro_model doesn't have discards_present
NOTE: Support for Import process data from auxiliary data file location (input_option == 1) is not supported right now.
Added NATMORT, MATURITY, FISHERY, STOCK_WEIGHT, SSB_WEIGHT, MEAN_WEIGHT, and CATCH_WEIGHT to toy example AGEPRO example input data file. Data is based on AGEPRO GUI's example input file Uku Projection Base.
agepro_model instantiate Process Error parameters (and general_params) as active get/set fields
Added projection_years :
Handles the ambiguous use of projection_years interpreted as a single int representing the count of projection years or a vector of sequential values representing a vector of "years".
assert_numeric_substrings : fixed regex numeric string check to include negatives.
Additional Changes
General Parameters
Renamed discards to discards_present
seed defaults to pseudo random number generator
cli tweaks to print out bootstrap fields and variables (keyword_name,inp_keyword)
Recruitment
Raised default num_obervations of Empirical CDF Recruitment to 2
Raised default low_recruits and high_recruits of Two Stage Empirical Recruitmet w/ SSB to 2
Experimental JSON input file. Note: This is a developing file format, and it is unsupported with the AGEPRO calculation engine (#9)
If filepath wasn't passed to write_json, it will now use flle dialog window. (resolves #11)
Added read_json.
subset Emprical Recruitment tables to format as a JSON list in a list object structure
Added Two Stage Empirical Recruitment w/ SSB JSON list object
Fixup formatting of recruit'stype (recruitment model number) (#29)
Removed unused output.R and read_input.R
This removes the rprojroot and usethis dependencies.
Note: Earlier references to "stochastic parameters" are now referred as "process error parameters " or "process error for population and fishery processes"
Process Error
natural_mortality(natmort)maturity_fraction(maturity)fishery_selectivity(fishery)discard_fraction(discard)jan_stock_weight_age(stock_weight)spawning_stock_weight_age(ssb_weight)mean_population_weight_age(mean_weight)landed_catch_weight_age(catch_weight)discard_weight_age(disc_weight)input_optionandtime_varying, if it is a valid weight of age option.discardsanddisc_weightifagepro_modeldoesn't havediscards_presentinput_option == 1) is not supported right now.agepro_modelinstantiate Process Error parameters (andgeneral_params) as active get/set fieldsprojection_years:projection_yearsinterpreted as a single int representing the count of projection years or a vector of sequential values representing a vector of "years".assert_numeric_substrings: fixed regex numeric string check to include negatives.Additional Changes
discardstodiscards_presentseeddefaults to pseudo random number generatorbootstrapfields and variables (keyword_name,inp_keyword)num_obervationsof Empirical CDF Recruitment to 2low_recruitsandhigh_recruitsof Two Stage Empirical Recruitmet w/ SSB to 2write_json, it will now use flle dialog window. (resolves #11)read_json.subsetEmprical Recruitment tables to format as a JSON list in a list object structuretype(recruitment model number) (#29)output.Randread_input.Rrprojrootandusethisdependencies.