The full analysis of the submitted paper: Invasive dreissenid mussels induce shifts in bacterioplankton diversity through selective feeding on high nucleic acid bacteria can be found in the Analysis.Rmd RMarkdown.
Before starting the analysis please unzip 16S.zip (generated using the mothur.batch.taxass script available from here) and download the FCM data for the mussel experiment from here and store them in a directory named data_mussel. The reference FCM data (approx. 1GB) for the cooling water system and Lake Michigan/Muskegon Lake are available from here and here. These data should be stored in a directory called data_reference with subdirectories FCM_CW for the cooling water data and FCM_MI for the Lake Michigan and Muskegon Lake data.
File structure should be
.
├── Analysis.Rmd
├── Analysis.html
├── Analysis.md
├── functions.R
├── /extra_scripts
├── /files
├── /data_reference
│ ├── /FCM_CW
│ └── /FCM_MI
└── /16S
The phenotypic and taxonomic diversities (REF_diversity.csv, Lakes_diversity16S_F.csv and Lakes_diversityFCM_F.csv) were calculated by means of the external scripts in /extra_scripts as the computation can take some time.
Notice: The bootstrap repeats are set rather low (R = 3) to facilitate faster run times. For exactly reproducing the output described in the manuscript please adjust the parameters to those specified in the methods section (R = 100). The output from this markdown file is provided in html format.