Contributors: Erling Kåre Stenevik1,*, Sondre Hølleland1,4,†, Katja Enberg2, Åge Høines1, Are Salthaug1, Aril Slotte1, Sindre Vatnehol1, Sondre Aanes3
1 Institute of Marine Research, Norway.
2
University of Bergen, Norway.
3 Norwegian Computing
Center, Norway.
4 Norwegian School of Economics, Norway.
* Corresponding author;
[email protected]
†
Responsible for the code. Correspondance related to this to:
[email protected]
This github repository contains all the code used in Stenevik et. al.(2022a). Due to regulations, not all the data is publicly available and some of the results are therefore not possible to reproduce, but we have tried to enable the user to reproduce the main results. The individual herring data (Stenevik et. al. 2022b) is published and can be downloaded either manually from the website (see reference list) or by code provided below. The XSAM time series is available in the supplementary material to the article, while the temperature data is not public.
Density dependent growth, which might influence the effects of fisheries on a population are often ignored when management strategies are evaluated, mainly due to a lack of appropriate models readily available to be implemented. To improve on this, we investigated if somatic growth in Norwegian spring spawning herring (Clupea harengus) depend on cohort density using a formulation of the von Bertalanffy growth function on cohorts from 1921 to 2014 and found a significant negative correlation between estimated asymptotic length and density. This clearly indicates density dependent effects on growth, and we propose a model which can be used to predict size-at-age of Norwegian spring spawning herring as function of herring density (the abundance of two successive cohorts) in future estimation of reference points (FMSY) and short-term predictions of catch advice.
The main data has been put together by Stenevik et al (2022b) and is available at https://doi.org/10.21335/NMDC-496562593. In our R/1_data.R script, the individual herring data is downloaded by running the following code:
if(!("HerringData.csv" %in% list.files(path = "inputdata/") )) {
download.file(url = "https://ftp.nmdc.no/nmdc/IMR/Herring/HerringData.csv",
destfile = "inputdata/HerringData.csv")
}
We are not at liberty to publish the XSAM series here on github, but the
user can download it from the paper supplementary material (Table S3).
If you save it as inputdata/N.txt, the R/1_data.R script will run as
intended without adjustments to the code. We do not have permission to
publish the temperature data, and these are therefore not publicly
available. To have the user be able to run the code for temperature, we
draw independent random Gaussian temperatures with expectation
Sondre Hølleland - holleland
Sindre Vatnehol - sindrevatnehol
The code has been run on the following R version.
## _
## platform x86_64-w64-mingw32
## arch x86_64
## os mingw32
## system x86_64, mingw32
## status
## major 4
## minor 1.2
## year 2021
## month 11
## day 01
## svn rev 81115
## language R
## version.string R version 4.1.2 (2021-11-01)
## nickname Bird Hippie
The code for this project is licensed under the GPL-3.0 License.
Erling Kåre Stenevik (HI), Sondre Hølleland (HI), Katja Enberg (UiB), Åge Høines (HI), Are Salthaug (HI), Aril Slotte (HI), Sindre Vathehol (HI), Sondre Aanes (NR) (2022a) Predicting density dependent somatic growth in Norwegian spring spawning herring. Under review in ICES Journal of Marine Science.
Erling Kåre Stenevik (HI), Sondre Hølleland (HI), Katja Enberg (UiB), Åge Høines (HI), Are Salthaug (HI), Aril Slotte (HI), Sindre Vathehol (HI), Sondre Aanes (NR) (2022b) Individual samples of Norwegian Spring Spawning herring 1935-2019 https://doi.org/10.21335/NMDC-496562593