FishTrapsFoodSec: Nutrient capture and sustainable yield maximized by a gear modification in artisanal fishing traps (v1.0)

Nutrient capture and sustainable yield maximized by a gear modification in artisanal fishing traps

Authors:

Bryan P. Galligan, S.J. ([e-mail])

Tim R. McClanahan ([e-mail])

Austin T. Humphries ([e-mail])

Data Collectors:

Nancy Birgen ([e-mail])

Michelle Condy ([e-mail])

Mesaidi Fadhili

Nseme Ferunzi

Ines Gomes ([e-mail])

Valentine Jepchumba ([e-mail])

Mwafitina Juma

Jesse Kosgei ([e-mail])

Harriet Makungu ([e-mail])

Emmanuel Mbaru ([e-mail])

Bakari Mchinga ([e-mail])

Ali Musa

Asenath Nyachiro ([e-mail])

Douglas Obanyi ([e-mail])

Cavin Omondi ([e-mail])

Evyonne Ongoro ([e-mail])

Maureen Otieno ([e-mail])

Ahmed Omar Saidi ([e-mail])

Amir Shekiondo ([e-mail])

Ali Shilingi

Ramadhan Tungu

Nina Wambiji ([e-mail])

John Wanyoike ([e-mail])

Janet Warui ([e-mail])

Recommended Citation:

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.

License:

This project is licensed under the terms of the MIT license.

Overview

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.

Instructions

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 01_CleanData_FishTrapsFoodSec.R. Each script has two corresponding folders in the repository, one called temp and one called out. The temp folder contains temporary output files that are not needed for further analysis or reference. The out 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 02_FishLife_FishTrapsFoodSec.R retrieves estimated life history parameters for all species in the catch using Jim Thorson's FishLife package (Thorson, 2020; Thorson et al., 2017). You must restart R twice while running this script, once after running the first line, which installs an older version of rfishbase, and once at the end of the script, which re-installs the newest version of rfishbase. This is necessary because FishLifeis only compatible with earlier versions of rfishbase. These instructions are commented in the script itself.

Built With

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:

AICcmodavg (v2.3-1)

corrplot (v0.92)

data.table (v1.14.2)

DHARMa (v0.4.6)

dplyr (v1.0.9)

factoextra (v1.0.7)

FactoMineR (v2.6)

FishLife (v2.0.1)

ggeffects (v1.1.3)

ggplot2 (v3.3.6)

ggpubr (v0.4.0)

glmmTMB (v1.1.4)

magrittr (v2.0.3)

mFD (v1.0.1)

mgcv (v1.8-40)

moments (v0.14.1)

plotrix (v3.8-2)

readr (v2.1.2)

readxl (v1.4.1)

rfishbase (v4.0.0)

rstatix (v0.7.0)

strex (v1.4.3)

stringr (v1.4.1)

taxize (v0.9.100)

tidymv (v3.3.2)

tidyr (v1.2.0)

Repository Files

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 01_CleanData_Out.

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 FishLife 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 mFD 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)

Fig6_ConsModels.jpeg
Figure
Conservation linear regression results dot and whisker plot (not actually Fig. 6)

LengthTrapTypeDensity.jpeg
Figure
Density plots of length by trap type

LmatCalcium.jpeg
Figure
Exploratory plot of calcium concentrations as response to Lmat - linear regression and scatter plot

NutrientConcentrationLLoptGAMMs.jpeg
Figure
GAMMs of nutrient concentrations by trap type as response to L/Lopt by fishing trip

NutrientConcentrationLoptLMs.jpeg
Figure
Linear regressions and scatter plots of nutrient concentrations as response to Lopt by species

NutrientConcentrationsTable.csv
Spreadsheet
Table of nutrient concentrations by trap type with GLMMs to test for significance

NutrientYieldLLoptGAMMs.jpeg
Figure
Nutrient yields by trap type as response to L/Lopt for each trip (GAMMs)

NutrientYieldsTable.csv
Spreadsheet
Comparison of nutrient yields by trap type with RDI and GLMMs to test for significance

06_AdditionalAnalysis_Temp

Folder
Empty

README.md

Markdown
This document

RWorkflow_FishTrapsFoodSec.Rproj

RStudio Project
Sets working directory, source documents, etc. in RStudio

Processed Data

Date of data collection: 2010-2019

Geographic location of data collection: southern coast of Kenya, northern coast of Tanzania

Information about funding sources that supported the collection of the data: data were collected by Wildlife Conservation Society, Mombasa, Kenya

Portions of this data have been used by Condy et al. (2015), Gomes et al. (2014), Mbaru et al. (2020), and Mbaru and McClanahan (2013).

Trip Data

Filepath: 03_FunctionalDiversity_Out/TripData_GatedTraps_Galligan.csv

Number of variables: 67

Number of observations: 2734

Missing data code: NA

Variable List

Variable
Notes

TripID
Alphanumeric identifier for each fishing trip

Date
Sampling date

Country
Sampling location (country)

Site
Sampling location (landing site)

Latitude
Sampling location (decimal degrees)

Longitude
Sampling location (decimal degrees)

Observer
Researcher responsible for data

Fisher
Alphanumeric identifier for each fisher or crew (combination of fishers)

TotalCrew
Size of fishing crew

TrapsOwned
Number of traps owned by this fisher/crew

TrapsFished
Number of traps fished on this trip

TrapLocation
Fishing location

Depth_m
Depth of trap deployment (meters)

SoakTime_Days
Duration of trap deployment (days)

TrapType
Type of trap used on this fishing trip (traditional, gated, or multiple)

GapSize_cm
Size of escape gap on traps used (centimeters or multiple)

B.undulatus
Was Balistapus undulatus present in the catch? (yes/no)

BrowserMass_g
Mass of browsing herbivores in the catch (grams)

BrowserMassRatio
Proportion of browsers in the catch by mass

ScraperMass_g
Mass of scraping herbivores in the catch (grams)

ScraperMassRatio
Proportion of scrapers in the catch by mass

GrazerMass_g
Mass of grazers in the catch (grams)

GrazerMassRatio
Proportion of grazers in the catch by mass

PredatorMass_g
Mass of piscivorous predators in the catch (grams)

PredatorMassRatio
Proportion of piscivorous predators in the catch by mass

TotalCatch_g
Total catch (grams)

LowNoCatch
Was the catch < 1 kg? (LowNoCatch / Catch)

CPUE_kgPerTrap
Catch per unit effort (kilograms per trap)

CPUE_DistFromMean
Catch stability (relative distance of CPUE from mean CPUE for each combination of site and trap type)

TotalValue_KSH
Value of the catch (Kenya Shillings)

ValuePUE
Value per unit effort (Kenya Shillings per trap)

MeanLLmat
Mean ratio of length to length at first maturity

MeanTrophLevel
Mean trophic level

MeanVulnerability
Mean species vulnerability (0-100)

MTC_degC
Mean temperature of the catch (degrees Celsius)

FECount
Functional richness (count of unique functional entities in the catch)

FRic
Functional richness (proportion of hull volume)

FEve
Functional evenness

FDiv
Functional diversity

TotalCa_mg
Total calcium (milligrams)

CaPUE
Calcium per unit effort (milligrams per trap)

CaConc_mgPer100g
Calcium concentration (milligrams per 100 grams)

CaPrice_KSHPermg
Value of calcium (Kenya Shillings per milligram)

TotalFe_mg
Total iron (milligrams)

FePUE
Iron per unit effort (milligrams per trap)

FeConc_mgPer100g
Iron concentration (milligrams per 100 grams)

FePrice_KSHPermg
Value of iron (Kenya Shillings per milligram)

TotalOmega3_g
Total Omega-3 polyunsaturated fatty acids (grams)

Omega3PUE
Omega-3 per unit effort (grams per trap)

Omega3Conc_gPer100g
Omega-3 concentration (grams per 100 grams)

Omega3Price_KSHPerg
Value of omega-3 (Kenya Shillings per gram)

TotalProtein_g
Total protein (grams)

ProteinPUE
Protein per unit effort (grams per trap)

ProteinConc_gPer100g
Protein concentration (grams per 100 grams)

ProteinPrice_KSHPerg
Value of protein (Kenya Shillings per gram)

TotalVA_ug
Total vitamin A (micrograms)

VAPUE
Vitamin A per unit effort (micrograms per trap)

VAConc_ugPer100g
Vitamin A concentration (micrograms per 100 grams)

VAPrice_KSHPerug
Value of vitamin A (Kenya Shillings per microgram)

TotalSe_ug
Total selenium (micrograms)

SePUE
Selenium per unit effort (micrograms per trap)

SeConc_ugPer100g
Selenium concentration (micrograms per 100 grams)

SePrice_KSHPerug
Value of selenium (Kenya Shillings per microgram)

TotalZn_mg
Total zinc (milligrams)

ZnPUE
Zinc per unit effort (milligrams per trap)

ZnConc_ugPer100g
Zinc concentration (milligrams per 100 grams)

ZnPrice_KSHPerug
Value of zinc (Kenya Shillings per milligram)

Catch Data

Filepath: 02_FishLife_Out/CatchData_GatedTraps_Galligan.csv

Number of variables: 11

Number of observations: 25789

Missing data code: NA

Variable List

Variable
Notes

TripID
Alphanumeric identifier for each fishing trip

TrapType
Type of fish trap (gated / traditional)

TrapLocation
Fishing location

SoakTime_Days
Duration of trap deployment (days)

GapSize_cm
Size of escape gap on traps used (centimeters)

Species
Species of fish caught (scientific name)

FD_HC
Is this fish destined for a fish dealer (FD) or household consumption (HC)?

Length_cm
Standard length of fish, from tip of snout to last vertebrae (centimeters)

Depth_m
Depth of trap deployment (meters)

Weight_g
Weight (grams)

LLmat
Ratio of length to length at first maturity (Lmat)

Species Data

Filepath: 02_FishLife_Out/SpeciesData_GatedTraps_Galligan.csv

Number of variables: 44

Number of observations: 215

Missing data code: NA

Variable List

Variable
Notes

Species
Species (scientific name)

Family
Taxonomic family

FishGroups
Coarse fish groupings

EnglishName
Species (common name in English)

KiswahiliName
Species (common name in Kiswahili)

Bycatch
Is this species considered bycatch? (yes/no)

Price_KSHPerkg
Price (Kenya Shillings per kilogram)

FunGr_Diet
Coarse diet-based functional groups (Condy et al., 2015; FishBase)

TrophLevel
Trophic level based on food items (FishBase)

SE_TrophLevel
Standard error of trophic level estimate (FishBase)

Vulnerability
Vulnerability (0-100) (FishBase)

Lmat_cm
Length at first maturity (centimeters) (FishLife)

Lopt_cm
Optimum length (centimeters) (FishLife)

Linf_cm
Asymptotic length (centimeters) (FishLife)

SizeCategory
Functional trait: size (Mbaru et al., 2020)

Diet
Functional trait: diet (Mbaru et al., 2020)

Mobility
Functional trait: mobility (Mbaru et al., 2020)

Active
Functional trait: period of activity (Mbaru et al., 2020)

Schooling
Functional trait: schooling behavior (Mbaru et al., 2020)

Position
Functional trait: position in water column (Mbaru et al., 2020)

TempPrefMin_degC
Minimum temperature preference (degrees Celsius) (FishBase)

TempPrefMean_degC
Mean temperature preference (degrees Celsius) (FishBase)

TempPrefMax_degC
Maximum temperature preference (degrees Celsius) (FishBase)

Calcium_mgPer100g
Calcium concentration (milligrams per 100 grams) (FishBase)

Calcium_L95
Lower 95% credible interval for calcium estimate (FishBase)

Calcium_U95
Upper 95% credible interval for calcium estimate (FishBase)

Iron_mgPer100g
Iron concentration (milligrams per 100 grams) (FishBase)

Iron_L95
Lower 95% credible interval for iron estimate (FishBase)

Iron_U95
Upper 95% credible interval for iron estimate (FishBase)

Omega3_gPer100g
Omega-3 polyunsaturated fatty acid concentration (grams per 100 grams) (FishBase)

Omega3_L95
Lower 95% credible interval for omega-3 estimate (FishBase)

Omega3_U95
Upper 95% credible interval for omega-3 estimate (FishBase)

Protein_gPer100g
Protein concentration (grams per 100 grams) (FishBase)

Protein_L95
Lower 95% credible interval for protein estimate (FishBase)

Protein_U95
Upper 95% credible interval for protein estimate (FishBase)

VitamA_ugPer100g
Vitamin A concentration (micrograms per 100 grams) (FishBase)

VitaminA_L95
Lower 95% credible interval for vitamin A estimate (FishBase)

VitaminA_U95
Upper 95% credible interval for vitamin A estimate (FishBase)

Selenium_ugPer100g
Selenium concentration (micrograms per 100 grams) (FishBase)

Selenium_L95
Lower 95% credible interval for selenium estimate (FishBase)

Selenium_U95
Upper 95% credible interval for selenium estimate (FishBase)

Zinc_ugPer100g
Zinc concentration (micrograms per 100 grams) (FishBase)

Zinc_L95
Lower 95% credible interval for zinc estimate (FishBase)

Zinc_U95
Upper 95% credible interval for zinc estimate (FishBase)

Links

The GitHub repository for this project

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Full Changelog: https://github.com/bryanpgalligan/FishTrapsFoodSec/commits/v1.0