DOI: 10.5281/zenodo.7256316
title: FishTrapsFoodSec: Nutrient capture and sustainable yield maximized by a gear modification in artisanal fishing traps (v1.0)

description: Nutrient capture and sustainable yield maximized by a gear modification in artisanal fishing traps <strong>Authors:</strong> Bryan P. Galligan, S.J. (bgalligan@jesuits.org) Tim R. McClanahan (tmcclanahan@wcs.org) Austin T. Humphries (humphries@uri.edu) <strong>Data Collectors:</strong> Nancy Birgen (nbirgen@yahoo.com) Michelle Condy (michelle.condy@jcu.edu.au) Mesaidi Fadhili Nseme Ferunzi Ines Gomes (istgomes@gmail.com) Valentine Jepchumba (vlntnjepchumba503@gmail.com) Mwafitina Juma Jesse Kosgei (jkosgei@wcs.org) Harriet Makungu (makunguharriet@yahoo.com) Emmanuel Mbaru (embaru@kmfri.co.ke) Bakari Mchinga (bmchinga@yahoo.com) Ali Musa Asenath Nyachiro (anyachiro@kmfri.co.ke) Douglas Obanyi (douglasmaina@gmail.com) Cavin Omondi (omondikev13@gmail.com) Evyonne Ongoro (ongoroyvonne@gmail.com) Maureen Otieno (motieno@wcs.org) Ahmed Omar Saidi (addieomar2021@gmail.com) Amir Shekiondo (amosheki@gmail.com) Ali Shilingi Ramadhan Tungu Nina Wambiji (nwambiji@yahoo.com) John Wanyoike (karungoj@yahoo.com) Janet Warui (janetwarui@gmail.com) <strong>Recommended Citation:</strong> Galligan, B. P., Birgen, N., Condy, M., Fadhili, M., Ferrunzi, N., Gomes, I., Jepchumba, V., Juma, M., Kosgei, J., Makungu, H., Mbaru, E., Mchinga, B., Musa, A., Nyachiro, A., Obanyi, D., Omondi, C., Ongoro, E., Otieno, M., Saidi, A. O., Shekiondo, A., Shilingi, A., Tungu, R., Wambiji, N., Wanyoike, J., Warui, J., Humphries, A. T., & McClanahan, T. R. (2022). FishTrapsFoodSec: Nutrient capture and sustainable yield maximized by a gear modification in artisanal fishing traps. Zenodo. <strong>License:</strong> This project is licensed under the terms of the MIT license. <strong>Overview</strong> This repository is the data management and analysis workflow of a research project investigating the ecosystem and food security benefits and tradeoffs of adding escape gaps to traditional African fish traps. It includes 10 years of landings data from artisanal trap fishers operating in the inshore waters of Kenya and Tanzania. <strong>Instructions</strong> For data access only: The processed data files are described later in this document. The same section contains file paths at which these data can be found. Please note that some parameters in these files are not original, but are drawn from other sources (refer to metadata). Where this is the case, please cite the original data source as well as this archived dataset. To reproduce the analysis: R scripts should be run in numeric order, beginning with <code>01_CleanData_FishTrapsFoodSec.R</code>. Each script has two corresponding folders in the repository, one called <code>temp</code> and one called <code>out</code>. The <code>temp</code> folder contains temporary output files that are not needed for further analysis or reference. The <code>out</code> folder contains output files that will be used by subsequent scripts, kept for future reference, or formatted as data tables for publication. The R script <code>02_FishLife_FishTrapsFoodSec.R</code> retrieves estimated life history parameters for all species in the catch using Jim Thorson's <code>FishLife</code> package (Thorson, 2020; Thorson et al., 2017). <strong>You must restart R twice while running this script</strong>, once after running the first line, which installs an older version of <code>rfishbase</code>, and once at the end of the script, which re-installs the newest version of <code>rfishbase</code>. This is necessary because <code>FishLife</code>is only compatible with earlier versions of <code>rfishbase</code>. These instructions are commented in the script itself. <strong>Built With</strong> R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" RStudio "Spotted Wakerobin" Release (7872775e, 2022-07-22) for macOS The following R packages: <code>AICcmodavg (v2.3-1)</code> <code>corrplot (v0.92)</code> <code>data.table (v1.14.2)</code> <code>DHARMa (v0.4.6)</code> <code>dplyr (v1.0.9)</code> <code>factoextra (v1.0.7)</code> <code>FactoMineR (v2.6)</code> <code>FishLife (v2.0.1)</code> <code>ggeffects (v1.1.3)</code> <code>ggplot2 (v3.3.6)</code> <code>ggpubr (v0.4.0)</code> <code>glmmTMB (v1.1.4)</code> <code>magrittr (v2.0.3)</code> <code>mFD (v1.0.1)</code> <code>mgcv (v1.8-40)</code> <code>moments (v0.14.1)</code> <code>plotrix (v3.8-2)</code> <code>readr (v2.1.2)</code> <code>readxl (v1.4.1)</code> <code>rfishbase (v4.0.0)</code> <code>rstatix (v0.7.0)</code> <code>strex (v1.4.3)</code> <code>stringr (v1.4.1)</code> <code>taxize (v0.9.100)</code> <code>tidymv (v3.3.2)</code> <code>tidyr (v1.2.0)</code> <strong>Repository Files</strong> File/Folder Enclosed File Type Notes 00_RawData Folder Contains raw data CombinedTrapData_2010_2019_Anonymized.csv Spreadsheet WCS landings data FunctionalGroupKey_DietBased_Condy2015.xlsx Spreadsheet A key developed for previous WCS studies assigning select species to diet-based functional groups Traits_MbaruEtAl2020.xls Spreadsheet A list of species with categorizations by functional trait, developed by Mbaru et al. (2020). ValueByFamily.csv Spreadsheet A list of fish families and their corresponding values in Kenya Shillings developed for previous WCS studies. 01_CleanData_FishTrapsFoodSec.R R Script Cleans the data and saves an edited and more compact version. Produces three normalized output spreadsheets as found in <code>01_CleanData_Out</code>. 01_CleanData_Out Folder Contains output files from eponymous R script CatchData_GatedTraps_Galligan.csv Spreadsheet Contains landings data; each row is an individual fish SpeciesData_GatedTraps_Galligan.csv Spreadsheet Data for each species in the catch TripData_GatedTraps_Galligan.csv Spreadsheet Contains landings data; each row is one fishing trip 01_CleanData_Temp Folder Contains temporary output files from eponymous R script SuspiciousPrices.csv Spreadsheet A list of price data from the original WCS spreadsheet that seemed suspicious. These prices have all been replaced. TrapData_Cleaned.csv Spreadsheet A cleaned copy of the original WCS data sheet. Unique_Species.csv Spreadsheet A list of species found in the WCS landings data 02_FishLife_FishTrapsFoodSec.R R Script Obtains estimates of life history parameters for all species using Jim Thorson's <code>FishLife</code> package. 02_FishLife_Out Folder Contains output files from eponymous R script CatchData_GatedTraps_Galligan.csv Spreadsheet Updates catch data to include life history parameters SpeciesData_GatedTraps_Galligan.csv Spreadsheet Updates species data to include life history parameters TripData_GatedTraps_Galligan.csv Spreadsheet Updates trip data to include life history parameters 02_FishLife_Temp Folder Empty 03_FunctionalDiversity_FishTrapsFoodSec.R R Script Workflow for the <code>mFD</code> package, which computes multidimensional functional diversity indices 03_FunctionalDiversity_Out Folder Contains output files from eponymous R script FunctionalSpacesQuality.png Figure Results of PCoA analysis determining the quality of functional spaces PositionSpeciesFunctionalAxes.png Figure Plots functional entities along pairs of functional axes TraitsAndPCoAAxes.png Figure Plots relationships between traits and PCoA axes TripData_GatedTraps_Galligan.csv Spreadsheet Updates trip data with functional diversity measures 03_FunctionalDiversity_Temp Folder Empty 04_DataExploration_FishTrapsFoodSec.R R Script Explores data following procedures of Zuur et al. (2010) 04_DataExploration_Out Folder Empty TripDataForAnalysis_GatedTraps_Galligan.csv Spreadsheet TripData cleaned for analysis. Unreasonable values have been removed. 04_DataExploration_Temp Folder Empty 05_PrincipalComponents_FishTrapsFoodSec.R R Script Runs and reports on FAMD and PCA analyses. 05_PrincipalComponents_Out Folder Contains output files from eponymous R script. AllBiplots.jpeg Figure All important biplots - to be used in the article. Fig3_FoodSecBiplot.jpeg Figure Biplot of food security PCA dimensions (not actually Fig. 3) Fig5_ConservationBiplots.jpeg Figure Biplots of conservation PCA dimensions (not actually Fig. 5) TripData_ForModeling.csv Spreadsheet Estimates from PCA and food security dimensions to be modeled using linear regression in script 6. 05_PrincipalComponents_Temp Folder Empty 06_AdditionalAnalysis_FishTrapsFoodSec.R R Script Performs follow-up analyses after the PCA 06_AdditionalAnalysis_Out Folder Contains output files from eponymous R script CPUEDensity_FishTrapsFoodSec.jpeg Figure Density plot of CPUE for gated and traditional traps CPUE_LLopt_GAMM.jpeg Figure Linear regression and scatter plot of CPUE for both trap types as response to L/Lopt CPUETransformedDensity_FishTrapsFoodSec.jpeg Figure Density plot of square root transformed CPUE for gated and traditional traps CatchStability.csv Spreadsheet Skewness and kurtosis for non-transformed CPUE for gated and traditional traps CatchStability_SqrtTransformed.csv Spreadsheet Skewness and kurtosis for square root transformed CPUE for gated and traditional traps Fig4_FoodSecModels.jpeg Figure Food security linear regression results dot and whisker plot (not actually Fig. 4) &lt;