Published October 27, 2022 | Version v1.0
Dataset Open

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

Authors:

Data Collectors:

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

References

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

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