1 Work Package 1: Fisheries-dependent (catch) surveys and assessment modeling

1.1 Library for multi-stage estimation

supervisor_account Edvin Fuglebakk (IMR)

calendar_today 2020-11-01

Library for design-based estimation and bootstrap estimation from multi-stage sampling designs. Contains functions for estimation from unequal probability sampling, and example data from the Catchlottery-sampling.

License: LGPL3

URL (software): https://github.com/Sea2Data/CatchLotteryEstimation

Keywords: multi-stage clustered sampling, design-based estimation, Hansen-Hurwitz, Horvitz-Thompson, hierarchical bootstrap, Poisson sampling

1.2 Prototype for RDBES conversion

supervisor_account Edvin Fuglebakk (IMR)

calendar_today 2020-11-01

Prototype for RDBES conversion, preparing data for the RDBES test data call in 2020 (Herring and Blue Whiting). Prepares landings and efforts, and samples from catch lottery and other fisheries-targeted sampling (missiontype 1 and 19).

License: LGPL3

URL (software): https://github.com/edvinf/wkrdb-est-dataconversion

Keywords: RDBES, catch lottery, test data call 2020

1.3 Reporting functions for StoX-Reca

supervisor_account Edvin Fuglebakk (IMR)

calendar_today 2020-11-01

Contains functions and example scripts for generating commonly requested reports from StoX-Reca projects (StoX v2.7).

License: LGPL3

URL (software): https://github.com/Sea2Data/FDAtools/tree/master/stoxReca/reports

Keywords: Rstox, Reca

1.4 Library for Fisheries Dependent Analysis

supervisor_account Edvin Fuglebakk (IMR)

calendar_today 2020-11-01

Library for Fisheries Dependent Analysis. Contains a generic interface to Reca, which facilitate adaptation of Reca to many kinds of data formats, and functions for plotting results. Also contains various support functions for fisheries dependent analysis.

License: LGPL3

URL (software): https://github.com/StoXProject/RstoxFDA

Keywords: Reca, metier-annotation, landings statistics

1.5 Snapshot-extraction

supervisor_account Edvin Fuglebakk (IMR)

calendar_today 2020-11-01

Tool for fetching date-versioned data via NMD-biotic API. E.g. Extract the data as it where on a given date in the past.

License: LGPL3

URL (software): https://github.com/Sea2Data/Dataset-snapshot-extractor

Keywords: snapshot-extraction, NMDbiotic API

1.6 Coastal cod analysis with Reca

supervisor_account Edvin Fuglebakk (IMR)

calendar_today 2020-11-01

Contains script for using Rstox and Reca run catch at age estimate for coastal-cod and NEA cod with stock split estimated from otolith-typing, and area definitions incorporating 12-nm delimiter.

URL (software): https://github.com/Sea2Data/FDAtools/tree/master/stoxReca/coastalCod

Keywords: Reca, coastal cod, Rstox

1.7 Reca support in Rstox

supervisor_account Arne-Johannes Holmin (IMR), Edvin Fuglebakk (IMR)

calendar_today 2020-11-01

Functions for preparing data for Reca and for plotting results and reports

License: LGPL3

URL (software): https://github.com/Sea2Data/Rstox/tree/develop

Keywords: Rstox, Reca

1.8 Easy RECA Package

supervisor_account Ibrahim Umar (IMR), Edvin Fuglebakk (IMR), Hanne W. Rognebakke (NR)

calendar_today 2019-05-07

Reca is a package made for the Institute of Marine Research. The package produces predictions of catch-at-age, i.e. the number of fish caught within each age group, of different fish species. This is a testing version of a universal platform RECA package with OpenBLAS.

URL (software): https://github.com/iambaim/new-reca

Keywords: ECA, IMR, catch-at-age, prediction, fishery dependent, commercial, estimates

1.9 External covariance matrices in SAM

supervisor_account Olav Nikolai Breivik (NR) and Anders Nielsen (DTU-aqua)

calendar_today 2018-04-24

External observation covariance matrices can be utilized in SAM. Link to example: https://github.com/fishfollower/SAM/blob/master/testmore/nscodcovar/script.R

Jupyter notebook: (show) (download)

URL (software): https://github.com/fishfollower/SAM/blob/master/testmore/nscodcovar/script.R