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APIS Larval Coregonine

This repository contains data files, analysis scripts, and manuscript figures for manuscript title by ...authors... that has been accepted for publication in ...journal name...

Data Files (not in the repo)

  • data/APIS_Coregonus_2018.xlsx -- Excel file containing the coregonine biological and effort data specific to this project.
  • data/APIS_Zoolankton_2018.xlsx -- Excel file containing the zooplankton biological and effort data specific to this project.
  • data/Superior_Files -- Folder containing the raw zooplankton files created from microscope software, length-weight regression coefficients, and All_Samples.csv, Bytho_Samples.csv, and APIS_Zoop_Summary.csv created in data_prep/Zems_1_Upload.R, data_prep/Zems_2_Upload_Bytho.R, data_prep/Zems_3_Wrangle.R.

Scripts

Length Frequency Analysis

  • Length_Freq.R -- Processes the larval length/yolk data to produce Figure XX in the manuscript.

Yolk-sac Condition - Diet Analysis

  • YolkSac_Diet.R -- Processes the larval length/yolk and diet data to produce Figure XX in the manuscript.

Zooplankton Density and Biomass Visualization

  • Zoop_DensityBiomass_Plots.R -- Produces the zooplankton density, biomass, relative density, and relative biomass figures compiled as Figure XX in the manuscript.

Prey Selectivity Analysis

  • Prey_Selectivity.R -- Processes the larval diet and zooplankton data to calculate Chesson's alpha index and produce Figure XX in the manuscript.

Other Files

  • APISCisco-2018.Rproj -- RStudio project file.
  • .gitignore -- things to ignore when committing or pushing to GitHub.
  • README.md -- This readme file.