Proportional recruitment in Antarctic krill: data and calculations
This repository contains the r-scripts and datasets used to produce the figures and tables reported in Kinzey et al., 2023 (available at https://www.ccamlr.org/en/publications/science_journal/ccamlr-science-volume-24). These include length-frequencies of Antarctic krill in U.S. AMLR summer trawl surveys, the diets of three penguin species (gentoos, adelies, and chinstraps), adelie penguins at the Palmer LTER site (available at https://oceaninformatics.ucsd.edu/datazoo/catalogs/pallter/datasets/89) and observer data collected from the international krill fishery in CCAMLR Subarea 48.1. The r-scripts calculate length-based proportional recruitment (the annual means and standard deviations for each multiyear time series of the proportion of krill smaller than a specified length). The results are illustrated in the 'plots' directory. The plots presented to the Scientific Committee on Antarctic Research Krill Action Group workshop on March 9, 2022 are in the 'plots/SKAG' and 'plots/contours' directories.
To reproduce the results in the 'plots' directory, download '1_manage_scripts.r', and the 'data' and 'r-scripts' directories into a single directory on a local computer. Identify the local working directory in line 2 of the file '1_manage_scripts.r'. Running '1_manage_scripts.r' will call the other nine files in 'r-scripts' to produce the plots.
The 'plots/contours' directory shows the how the distribution of krill lengths varied with month and survey strata in the U. S. AMLR trawls. Here the '1area1leg' subdirectory illustrates the combined distribution of four survey strata and two legs (January and February). The 'measured' plot shows the sample data and the 'scaled' plot shows the sample data scaled up to total catch (a maximum of 200 krill were measured per trawl). The '1area2legs' subdirectory shows the scaled plots for all strata combined but separated by leg. The '4areas1leg' subdirectory shows the distribution separately for each stratum but combined by leg. The '4areas2legs' subdirectory shows the distribution separated by both area and leg.
The 'plots_30mm', 'plots_35mm' and 'plots_40mm' subdirectories show two features of representing the full length distributions shown in the 'contours' subdirectory by a single number and its standard deviation (proportional recruitment). First, the temporal similarity in the peaks and troughs between the different data sources is visible. Second, the differences in proportional recruitment resulting from considering krill to be juveniles when they are less <= three alternative body lengths: 30mm, 35mm, or 40mm is also visible. Other cutoff lengths can also be explored but one of the datasets for Adelie penguin diets in the Palmer LTER, 'Adelie Penguin Diet Composition, Krill.csv', is reported in 5 mm bins. Lengths in the other datasets are reported to the nearest mm.
All the figures in the 'plots' directory can be reproduced by changing the input values of three lines in '1_manage_scripts.r'.
Line 4 of '1_manage_scripts.r' identifies whether the user wants to combine the data from all four spatial strata (enter '1') or consider each stratum separately (enter '4').
Line 5 identifies whether the user wants to combine January and Februrary sampling (enter '1') or consider them separately (enter '2').
Line 6 identifies the length in mm below which krill are considered to be juveniles. These lengths must be either '30', '35', or '40' for the '4_lter_adelie.r' script to work properly (krill lengths are in 5 mm bins in the dataset used by that script).
Literature cited
D. Kinzey, J.T. Hinke, C.S. Reiss and G.M. Watters (2023), Recruitment variability of Antarctic krill in Subarea 48.1 expressed as ‘proportional recruitment’: length threshold effects. CCAMLR Science, Volume 24. 18 pp.
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