This repository contains data and analysis scripts for the manuscript:

Assessing Acropora cervicornis genotype resistance to elevated ammonium and disease

Authors: Ana M. Palacio Castro, Daniele Kroesche, Ian Enochs, Chris Kelble, Ian Smith, Andrew Baker, Stephanie M. Rosales

Journal: Submitted to PlosOne doi:XXX

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Description:

These repository contains all data and code used to study the impact of elevated ammonium and disease on ten A. cervicornis genotypes

Contents:

1.Tank_conditions:

• 1.Experimental_conditons.Rmd: has all the code needed for Figure 1. It sources the data from the Data subfolder and saves statistical summaries and plots in the Outputs subfolder.

2.Mortality:

• 1.Mortatily_Acer.Rmd: has all the code needed for Figure 4 and survivorship analysis. It sources te data from the Data subfolder and saves statistical summaries and plots in the Outputs subfolder.

3.Growth:

• This data and data analysis were not used in the manuscript:**

4.YII:

• 1.IPAM_ImportFunction.R: R function to imports the csv raw IPAM data. Yo do not have to do anything with this file, but the function is called by this file below.
• 2.MergeYIIandID.R: Applies 1.IPAM_ImportFunction.R to the raw data in the IPAM_Raw, adds the sample metadata in the ID_AOI.csv file and creates a long format file with the YII values that is exported to the file Data/YII_tall.csv
• 3.YII_Acer_Nut.Rmd: has all the code needed for Figure 2 and related statistical analisis. It sources the data from the file Data/YII_tall.csv and saves statistical summaries and plots in the Outputs subfolder.

5.Symbiodiniaceae:

• SH_cell_code.Rmd: has all the code needed for Figure 3. It sources the qPCR data from the Data subfolder and the sample metadata from the Metadata.csv file. Statistical summaries and plots are saved in the Outputs subfolder.
• Data: has all the raw data exported from the qPCR machine.

6.Metadata:

• This folder has copies of the metadata files, but are actually not used by any code.

Notes

• All packages.bib files produce a bibliography of the packages used by each .Rmd
• All .html files produce a webpage with code outputs, plots, etc. based on the .Rmd files