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README

Into the wild: microbiome transplant studies need broader ecological reality

Authors

Christopher J. Greyson-Gaito*1,, Timothy J. Bartley1,2,, Karl Cottenie1,, William Jarvis3,, Amy E.M. Newman1,, Mason R. Stothart4,

Affiliations

*Corresponding author - christopher@greyson-gaito.com

  1. University of Guelph, Department of Integrative Biology, Guelph, ON, Canada
  2. University of Toronto Mississauga, Mississauga, ON, Canada
  3. University of Ottawa, Department of Biology, Ottawa, ON,Canada
  4. University of Calgary, Calgary, AB, Canada

All authors contributed equally

Folder and file structure

  • data
    • EcoRealTable_2019-10-09_Data.csv
  • figs
    • 2019-10-09 CountAnimals.pdf – Figure 2 in manuscript
    • 2019-10-09 Eco-realityComparisons.pdf – Figure 3 in manuscript
    • 2019-10-09 Eco-realityAverageStandardOverTime.pdf – Figure 4 in manuscript
    • 2019-10-09 CumulativeSumArticles.pdf – Supporting Information Figure 1
  • .gitignore – File containing files or folders that git should ignore
  • IntotheWild_Microbiome_Greyson-Gaito_etal_2019.R – R script for analysis and figure creation
  • GreysonGaitoetal_Intothewild_SupportingInformation.pdf – Supporting information (search terms, ordinal data scales, figure)
  • LICENSE – Mozilla Public License 2.0
  • README.md – Important information
  • meta_transplant_microbiome.Rproj – R Project to increase ease of use

Instructions for use

  • Download the whole repository (either by forking and cloning or by downloading a ZIP folder)
  • In RStudio, open the project called meta_transplant_microbiome.Rproj and open the file Intothewild_Microbiome_Greyson-Gaito_etal_2019.R
    • If not using RStudio, open the file Intothewild_Microbiome_Greyson-Gaito_etal_2019.R and edit the path to the data file called EcoRealTable_2019-10-09_Data.csv to whatever path is required on your computer.
  • Run the script in RStudio or however you normally run R scripts.

Supporting Information

See SupportingInformation_Intothewild_GreysonGaitoetal.pdf