Package: ebswp 0.0.1.0000

Jim Ianelli

ebswp: Facilitates Model Running for EBS Pollock

Facilitates model running for EBS Pollock.

Authors:Jim Ianelli [aut, cre]

ebswp_0.0.1.0000.tar.gz
ebswp_0.0.1.0000.zip(r-4.7-any)ebswp_0.0.1.0000.zip(r-4.6-any)ebswp_0.0.1.0000.zip(r-4.5-any)
ebswp_0.0.1.0000.tgz(r-4.6-any)ebswp_0.0.1.0000.tgz(r-4.5-any)
ebswp_0.0.1.0000.tar.gz(r-4.7-any)ebswp_0.0.1.0000.tar.gz(r-4.6-any)
ebswp_0.0.1.0000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ebswp/json (API)

# Install 'ebswp' in R:
install.packages('ebswp', repos = c('https://jimianelli.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/afsc-assessments/ebspollock/issues

Pkgdown/docs site:https://afsc-assessments.github.io

On CRAN:

Conda:

3.96 score 2 stars 46 scripts 37 exports 32 dependencies

Last updated from:0420e77369. Checks:7 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develERROR133
source / vignettesOK171
linux-releaseERROR119
macos-releaseERROR131
macos-oldrelERROR124
windows-develERROR82
windows-releaseERROR90
windows-oldrelERROR116
wasm-releaseOK93

Exports:.run_mod.run_mod_windows.run_proj.run_proj_windowsget_resultsget_varsmodel_settingsplot_agefitplot_atsplot_avoplot_btsplot_copeplot_cpueplot_likesplot_mnageplot_Nage_3plot_R_relplot_recruitmentplot_selplot_serplot_srrplot_ssbplot_ssb_relprint_Tier3_tblread_admbread_ctlread_datread_fitread_psvread_represcale_covrun_modelrun_projtab_fittab_refupperCaseFirstwrite_dat

Dependencies:clicpp11dplyrfarvergenericsggplot2ggthemesgluegtablehereisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangrprojrootS7scalesstringistringrtibbletidyselectutf8vctrsviridisLitewithrxtable

EBS pollock model equations
EBS Pollock Model Description | Dynamics | Recruitment | Diagnostics | Parameter estimation | Uncertainty in mean body mass | Tier 1 projections
Rendered fromModel-equations.Rmdusingknitr::rmarkdown

Last update: 2024-07-25
Started: 2024-07-25

Example on how to change and run a model
Example use of ebswp library for setting up a new model | Read in an existing model | For SSB1 | And SSB2 | And obs-error run | Now run them all in parallel
Rendered fromChange_Model_Specs.Rmdusingknitr::rmarkdown

Last update: 2024-07-25
Started: 2024-07-25

Readme and manuals

Help Manual

Help pageTopics
Extract Acoustic Trawl Survey Data.get_ats_df
Get avo data into frame.get_avo_df
Extract bottom trawl survey data from a list of models.get_bts_df
Extract copE data.get_cope_df
Extract CPUE data.get_cpue_df
Extract Likelihood Data Frame.get_like_df
Extract mean age from pollock model run.get_mnage_df
Extract Numbers at age 3.get_Nage_3_df
Extract Recruits (R) from pollock run.get_R_rel_df
Get recruitment data.get_recruitment_df
Extract spawning exploitation rate.get_ser_df
Extract stock recruitment results.get_srr_df
Extract spawning stock biomass (ssb).get_ssb_df
Extract spawning stock biomass (ssb).get_ssb_rel_df
run pollock model.run_mod
run pollock model on windows.run_mod_windows
run projection model DOESN"T WORK...dunno why.run_proj
run projection model for windows.run_proj_windows
Input Data for Model Configurationget_input_data
Fetch Model Results in Parallelget_results
Extract Tier 3 Resultsget_tier3_res
Extract and Compute Several Metrics from Model Outputget_vars
Model Settings Listmodel_settings
Age Composition Data Plotter t(t() This function generates a series of plots visualizing the age composition data from fisheries assessment. It compares observed and predicted data across different years.plot_agefit
Plot Acoustic Trawl Survey Biomass Dataplot_ats
Plot avo dataplot_avo
Plot bottom trawl survey dataplot_bts
Plot copepod somethingplot_cope
Plot predicted CPUEplot_cpue
Plot Likelihood Valuesplot_likes
Plot predicted mean age by gear typeplot_mnage
Plot predicted Numbers at age 3plot_Nage_3
Plot predicted recruitmentplot_R_rel
Plot predicted recruitment and approximate asymptotic error-barsplot_recruitment
Plot selectivityplot_sel
Plot predicted spawning stock biomass (SER)plot_ser
Plot Stock-Recruitment Relationship (SRR)plot_srr
Plot predicted spawning stock biomass (ssb)plot_ssb
Plot predicted spawning stock biomass (ssb)plot_ssb_rel
Generate and Print Tier 3 Summary Tablesprint_Tier3_tbl
Read ADMB output filesread_admb
Read ADMB .ctl fileread_ctl
Read ADMB Data Fileread_dat
Read ADMB .par, .std, and .cor file and return an R object of type 'list' of estimates and correlationsread_fit
Read ADMB .psv fileread_psv
Read ADMB .rep fileread_rep
Rescale a Covariance Matrixrescale_cov
Run Multiple ADMB Models in Parallelrun_model
Run Multiple projection models in Parallelrun_proj
Tabulate fits from models using extended metrics.tab_fit
Tabulate fits from models using extended metrics.tab_ref
Helper function to convert the first character of a string to uppercase.upperCaseFirst
Write Data to Text Filewrite_dat