Package: ageproR 0.9.1

Eric Fletcher

ageproR: R package interface for AGEPRO (Age Structured Projection Model) data

Object-oriented data structures based on the input file format defined in the Age Structured Projection Model Reference Manual. Includes support modules for AGEPRO input file support, and experimental JSON input file format.

Authors:Eric Fletcher [aut, cre], Jon Brodziak [aut]

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 |manual.html✨
card.svg |card.png
ageproR/json (API)
NEWS

# Install 'ageproR' in R:
install.packages('ageproR', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nmfs-ost/agepror/issues

On CRAN:

Conda:

2.60 score 1 stars 2 scripts 42 exports 16 dependencies

Last updated from:7e58d31e5d. Checks:3 ERROR, 6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR130
source / vignettesERROR229
linux-release-x86_64ERROR138
macos-release-arm64OK146
macos-oldrel-arm64OK111
windows-develOK97
windows-releaseOK110
windows-oldrelOK118
wasm-releaseOK108

Exports:agepro_inp_modelagepro_json_modelagepro_modelbeverton_holt_autocorrelated_errorbeverton_holt_curve_modelcase_iddeprecated_recruit_model_9discard_fractiondiscard_weight_ageempirical_cdf_modelempirical_distribution_modelempirical_ssbfishery_selectivityharvest_scenariojan_stock_weight_agelanded_catch_weight_agematurity_fractionmax_boundsmean_population_weight_agemortality_fraction_prior_spawnnatural_mortalitynull_recruit_modeloptions_flagsoptions_outputpercentile_summaryprint_parameter_tableprocess_errorprojection_yearspstar_projectionrebuild_projectionrecruitmentreference_pointsretrospective_adjustmentsricker_curve_autocorrelated_errorricker_curve_modelscaling_factorsshepherd_curve_autocorrelated_errorshepherd_curve_modelspawning_stock_weight_agetwo_stage_empirical_cdftwo_stage_empirical_recruitvalidate_map

Dependencies:backportscheckmateclicollectionsglueherejsonlitelifecyclemagrittrpurrrR6rlangrprojrootrstudioapivctrswithr

Readme and manuals

Help Manual

Help pageTopics
AGEPRO Input File Modelagepro_inp_model
AGEPRO model w/ JSON input file bindingsagepro_json_model
R6 class representing AGEPRO modelagepro_model
Beverton-Holt Curve w/ Autocorrected Lognormal Error (Model #10)beverton_holt_autocorrelated_error
Beverton-Holt w/ Lognormal Error (Model #5)beverton_holt_curve_model
Input information for bootstrap numbers at age filebootstrap
converts output as messagescapture_output_as_message
AGEPRO Case IDcase_id
Validation for BOUNDS active binding in agepro_modelassert_bounds_active_binding check_bounds_active_binding
Validation for CASEID active binding in agepro_modelassert_case_id_active_binding check_case_id_active_binding
Recruitment model number vector count validationassert_model_num_vector_count check_model_num_vector_count
Recruitment Model Number Parameter validationassert_model_num_vector_format check_model_num_vector_format
Validation for PERC active binding in agepro_modelassert_perc_active_binding check_perc_active_binding
Projection year sequence vector validationassert_proj_years_sequence check_proj_years_sequence
Creates a table-like matrix with 'NA' valuescreate_blank_parameter_table
DEPRECATED Recruitment Model #9 (Time-Varying Empirical Recruitment Distribution)deprecated_recruit_model_9
Discard fraction of numbers at agediscard_fraction
Discard weight at age by fleetdiscard_weight_age
Empirical CDF of Recruitment (Model #14)empirical_cdf_model
Empirical Recruitment Distribution (Model #3)empirical_distribution_model
Empirical Recruitment Model Dataempirical_recruit
Empirical Recruits Per Spawning Biomass Distribution (SSB) (Model #2)empirical_ssb
Fishery Selectivity at age by fleetfishery_selectivity
Input general model parametersgeneral_params
Harvest intensity (of fishing mortality or landings quota) by fleetharvest_scenario
Invalid Path Messageinvalid_path_message
Checks Rstudioapi if Rstudio Desktop is used.is_rstudio_desktop
Stock Weights on January 1st at Agejan_stock_weight_age
Landed Catch weight at age by fleetlanded_catch_weight_age
Maturation fraction at agematurity_fraction
Sets the maximum bounds of Weight(MT) and natural mortalitymax_bounds
Mean (or mid-year) weights at agemean_population_weight_age
Proportion of total mortality occurring prior to spawn in year tmortality_fraction_prior_spawn
Input information for the natural mortality rate (M) at Agenatural_mortality
Null Recruitment UI Fallback Defaultnull_recruit_model
Class container that encapsulates logical flags to enable AGEPRO user-defined optionsoptions_flags options_flag_container
AGEPRO projection output options.options_output
Parametric Recruitment Model w/ correlated lognormal errorparametric_autocorrelated_error
Parametric Recruitment Modelparametric_curve
Percentile summary of the key results of AGEPRO projection outputpercentile_summary
Use cli commands to display AGEPRO table-like valuesprint_parameter_table
Process Errors for Population and Fishery Processesprocess_error
Generalized structure of projection analyses keyword parametersprojection_analyses
Projection Yearsprojection_years
Projection analyses that shows the probability of exceeding overfishing threshold of the target yearpstar_projection
Input information for calculating F to rebuild spawning biomassrebuild_projection
Recruit Modelrecruit_model
AGEPRO Recruitment Parameterrecruitment
Values to output optional agepro model's reference point threshold report.reference_points
Vector of retrospective bias-correction coefficients to adjust to the initial population of numbers of age.retrospective_adjustments
Ricker Curve with Autocorrelated Lognormal Error (Model #11)ricker_curve_autocorrelated_error
Ricker Curve #/ Lognormal Error (Model #6)ricker_curve_model
Scale Factorsscaling_factors
Shepherd Curve with Autocorrelated Lognormal Error (Model #12)shepherd_curve_autocorrelated_error
Shepherd Curve with Lognormal Error (Model #7)shepherd_curve_model
Spawning stock weight at Agespawning_stock_weight_age
Standard Projection Analysesstandard_projection
Two-Stage Empirical Cumulative Distribution Function of Recruitment (Recruit #15)two_stage_empirical_cdf
Two-Stage Empirical Recruitment Basetwo_stage_empirical_recruit
Two-Stage Empirical Recruits Per Spawning Biomass Distribution (Model #4)two_stage_empirical_ssb
Custom mapping function for error handingvalidate_map
Validates the usage of the 'projection years' parameter.validate_proj_years_parameter