r4ss - R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.

Last updated 16 days ago

fisheriesfisheries-stock-assessmentstock-synthesis

11.36 score 39 stars 2 dependents 1.0k scripts 479 downloads

rgdal - Bindings for the 'Geospatial' Data Abstraction Library

Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired during October 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience (see <https://r-spatial.org/r/2023/05/15/evolution4.html> and earlier blogs for guidance). Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.

Last updated 2 years ago

gdalprojcpp

8.89 score 11 stars 1 dependents 33k scripts 2.4k downloads

FLCore - Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.

Last updated 17 days ago

fisheriesflrfisheries-modelling

8.80 score 16 stars 23 dependents 948 scripts 49 downloads

stockassessment - State-Space Assessment Model

Fitting SAM...

Last updated 3 days ago

stockassessmentcpp

7.76 score 49 stars 2 dependents 324 scripts

ggplotFL - Using ggplot2 in FLR

Using ggplot2 for FLR. Provides (1) overloaded ggplot methods for various FLR classes, (2) ggplot-based versions of standard plots in the FLCore package, and (3) new geoms for using FLR objects.

Last updated 22 days ago

visualizationggplot2fisheriesflr

7.69 score 4 stars 12 dependents 458 scripts

TAF - Transparent Assessment Framework for Reproducible Research

General framework to organize data, methods, and results used in reproducible scientific analyses. A TAF analysis consists of four scripts (data.R, model.R, output.R, report.R) that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step. Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, the TAF package comes with no dependencies. TAF forms a base layer for the 'icesTAF' package and other scientific applications.

Last updated 3 months ago

6.91 score 3 stars 2 dependents 282 scripts 453 downloads

mse - Tools for Running Management Strategy Evaluations using FLR

A set of functions and methods to enable the development and running of Management Strategy Evaluation (MSE) analyses, using the FLR packages and classes and the a4a methods and algorithms.

Last updated 2 months ago

simulationmsefisheriesflra4a

6.71 score 4 stars 3 dependents 137 scripts

FLBRP - Reference Points for Fisheries Management

Calculates a range of biological reference points based upon yield per recruit and stock recruit based equilibrium calculations. These include F based reference points like F0.1, FMSY and biomass based reference points like BMSY.

Last updated 3 months ago

reference pointsfisheriesflrcpp

6.58 score 2 stars 4 dependents 350 scripts

FLasher - Projection and Forecasting of Fish Populations, Stocks and Fleets

Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.

Last updated 1 months ago

forecastfisheriesflrcpp

6.56 score 2 stars 6 dependents 254 scripts

icesTAF - Functions to Support the ICES Transparent Assessment Framework

Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.

Last updated 2 years ago

6.37 score 5 stars 1 dependents 1.1k scripts 500 downloads

icesSAG - Stock Assessment Graphs Database Web Services

R interface to access the web services of the ICES Stock Assessment Graphs database <https://sg.ices.dk>.

Last updated 4 months ago

6.23 score 11 stars 2 dependents 129 scripts 575 downloads

spict - Stochastic surplus Production model in Continuous-Time (SPiCT)

Fits a surplus production model to fisheries catch and biomass index data.

Last updated 1 years ago

fisheries-managementfisheries-stock-assessmentspictcpp

6.18 score 26 stars 117 scripts

icesDatras - DATRAS Trawl Survey Database Web Services

R interface to access the web services of the ICES (International Council for the Exploration of the Sea) DATRAS trawl survey database <https://datras.ices.dk/WebServices/Webservices.aspx>.

Last updated 20 days ago

5.92 score 12 stars 115 scripts 350 downloads

icesVocab - ICES Vocabularies Database Web Services

R interface to access the Vocabularies REST API of the ICES (International Council for the Exploration of the Sea) Vocabularies database <https://vocab.ices.dk/services/>.

Last updated 20 days ago

5.55 score 6 stars 5 dependents 78 scripts 877 downloads

icesAdvice - Functions Related to ICES Advice

A collection of functions that facilitate computational steps related to advice for fisheries management, according to ICES guidelines. These include methods for calculating reference points and model diagnostics.

Last updated 1 years ago

5.14 score 7 stars 2 dependents 66 scripts 437 downloads

RDBEScore - Functions for the ICES Regional Database and Estimation System (RDBES)

The RDBEScore package provides functions to import and work with fisheries data downloaded from the ICES RDBES database. It also contains functions to perform estimation analysis using the resulting objects.

Last updated 4 months ago

5.06 score 32 scripts

mixfishtools - WGMIXFISH tools for reproducibility

Contains plot templates used in WGMIXFISH-ADVICE and Fisheries Overviews.

Last updated 7 hours ago

4.56 score 2 stars 3 scripts

ss3diags - Stock Synthesis Model Diagnostics for Intergated Stock Assessments

Compilation of diagnostic functions for Stock Synthesis models, which developed for the manuscript "Using Model Diagnostics in Integrated Stock Assessments".

Last updated 8 days ago

stock-synthesis

4.34 score 2 stars 110 scripts

cat3advice - ICES category 3 empirical harvest control rules

A package to apply the the ICES category 3 empirical (model-free) harvest control rules.

Last updated 7 months ago

3.92 score 3 stars 11 scripts

msy - Estimation of Equilibrium Reference Points for Fsisheries

Methods to estimate equilibrium reference points for fisheries data. Currently data must be converted into FLStock objects of the FLR (Fisheries Library in R) style, defined in the R package FLCore.

Last updated 2 years ago

3.91 score 13 stars 42 scripts

icesDatsu - Functions to Interact with the ICES Data Submission Utility (DATSU)

Functions to Interact with the ICES Data Submission Utility (DATSU) <https://datsu.ices.dk/web/index.aspx>.

Last updated 4 months ago

3.78 score 2 stars 2 dependents 2 scripts 586 downloads

icesConnect - Provides User Tokens for Access to ICES Web Services

Provides user tokens for ICES web services that require authentication and authorization. Web services covered by this package are ICES VMS database, the ICES DATSU web services, and the ICES SharePoint site <https://www.ices.dk/data/tools/Pages/WebServices.aspx>.

Last updated 5 months ago

3.78 score 10 dependents 20 scripts 228 downloads

FLSRTMB - FLSR in TMB

Estimates FLR spawner recruitment relationships in TMB

Last updated 2 months ago

stock-recruitfisheriesflrtmbadcpp

3.67 score 1 dependents 26 scripts

icesDatsuQC - Run Quality Checks on Data Prior to Submission to ICES

Run quality checks on data sets using the same checks that are conducted on the ICES Data Submission Utility (DATSU) <https://datsu.ices.dk>.

Last updated 4 months ago

3.48 score 2 stars 1 dependents 572 downloads

FLRef - Reference point computation for advice rules

Blah

Last updated 2 days ago

3.42 score 3 stars 11 scripts

icesFO - Functions to support the creation of ICES Fisheries Overviews

Functions to support the creation of ICES Fisheries Overviews.

Last updated 8 months ago

3.41 score 2 stars 260 scripts

icesSD - Stock Database Web Services

R interface to access the web services of the ICES Stock Database <https://sd.ices.dk>.

Last updated 4 months ago

3.16 score 1 stars 29 scripts 552 downloads

FLFishery - Classes and Methods for Simpler Fleet/Fishery Modelling

A set of classes and methods for modelling of fleet dynamics. Fisheries are groups of vessels sharing an effort time series, with static or changing spatio-temporal patterns in selectivity.

Last updated 2 months ago

fisheriesflr

3.02 score 7 dependents 8 scripts

FLfse - Fisheries Sampling Evaluation In FLR

Fisheries Sampling Evaluation in FLR. A package to interface betwen the SAM stock assessments and FLR, and aid the inclusion of SAM into Management Strategy Evaluation (MSE), including the set up of operating models mimicking SAM.

Last updated 3 years ago

2.71 score 2 stars 51 scripts

icesVMS - Link to the ICES Vessel Monitoring System and Logbook Database Web Services

Links to the ICES Vessel Monitoring System (VMS) and logbook database web services <https://data.ices.dk/vms/webservices> to allow users to download summaries and data products.

Last updated 5 months ago

2.66 score 2 stars 46 scripts 51 downloads

fisheryO - Fisheries Overviews for ICES Advice

Functions that work with International Council for the Exploration of the Sea (ICES) web services and databases to collate, aggregate, and plot Fisheries Overview products.

Last updated 7 years ago

2.45 score 3 stars 19 scripts

icesSharePoint - Helper functions to interact with the ICES sharepoint

Helper functions to interact with the ICES sharepoint used by the International Council for the Exploration of the Sea (ICES).

Last updated 4 years ago

2.33 score 43 scripts

sfdSAR - Functions to calculate Swept area ratio and Surface and subsurface abrasion from VMS data

Functions to calculate Swept area ratio and Surface and subsurface abrasion from VMS data. The data is expected to conform to the ICES WGSFD data call format.

Last updated 1 years ago

2.15 score 2 stars 14 scripts

icesASD - Advice and Scenarios Database Web Services

R interface to access the web services of the ICES Advice and Scenarios database <https://asd.ices.dk/AdviceList>.

Last updated 10 months ago

1.70 score 5 scripts

icesTAFDB - Transparent Assessment Framework (TAF) Database Web Services

R interface to access the web services of the ICES Transparent Assessment Framework (TAF) Database <http://taf.ices.dk>.

Last updated 2 years ago

1.70 score 3 scripts

icesdown - ICES Rmarkdown tools

A collection of rmarkdown and pandoc versions of various ICES templates can be found here.

Last updated 2 years ago

1.70 score 1 scripts

cpmtools - Miscellaneous Functions by 'Colin Millar'

Miscellaneous functions.

Last updated 3 years ago

1.70 score 1 stars

rct3 - Functions to Predict Fish Year-Class Strength from Survey Data

Functions to predict fish year-class strength by calibration regression analysis of multiple recruitment index series.

Last updated 4 years ago

1.70 score 1 scripts 431 downloads