This repository contains the code associated with analyses of the density and community composition of Symbiodiniaceae in fish feces.
#Symiodiniaceae cell counts (figure 2).
This code contains everything needed to replicate the analysis for Symbiodiniaceae cell counts. The data can be found attached to the manuscript. DOI:
#Symbiodiniaceae community analysis (figure 3).
This code contains everything needed to replicate the analysis for Symbiodiniaceae community analysis. You will need the following files (that are also in the Fishces_2020 repository:
- Fishces_2019_ITS2_2_profiles.csv #This file contains output from Symportal, but all the individual ITS2 profiles are removed.
- Fishces_ 2019_ITS2_2_profiles_meta.csv #This file contains clade information from the output from Symportal.
- Sample_map.csv #This file contains data on individual samples included in the analysis (e.g. species names and collection zones)
- specode.csv #this file contains a string of names used in one of the figures
- Sym_gen.csv #This file contains Symbiodiniaceae genera names to be used in one of the figures (instead of clade denominations)
#Symbiodiniaceae cell dispersal bootstrap code (figure 4).
This code contains everything needed to replicate the bootstrap analysis used for figure 4. The data can be found attached to the manuscript. DOI: