Phyloseq objects

Phyloseq objects provided<br><br>“Reduced” refers to a data sets reduced (from the full routine biochemical profiling) to the variables that were valid to use and of interest<br><br>“dc” refers to manual contaminant check and removal in the oral and nasal samples (in addition to contaminant removal with “decontam”)<br><br>FECES: <br>ps_all_allo_5_core_reduced_vars: First object for feces samples, absolute count data<br> Used in the alpha diversity script as initial input<br>ps_all_allo_5_core1_reduced: Second object for feces samples, absolute count data, alpha diversity measures calculated and added to sample data<br> Used as initial input for the multivariate script, in the ML script for the boxplots, and in LDA script<br>ps_all_allo_5_core1_reduced_vsd: Third object for feces samples, alpha diversity measures calculated and added to sample data, variance stabilized (vsd) count data<br> Used in the multivariate and ML scripts<br><br>ORAL:<br>ps_all_allo_oral_5_core_dc_reduced_vars: First object for oral samples, absolute count data<br> Used in the alpha diversity script as initial input<br><br>ps_all_allo_oral_5_core_dc1_reduced: Second object for oral samples, absolute count data, alpha diversity measures calculated and added to sample data<br> Used as initial input for the multivariate script, in the ML script for the boxplots, and in LDA script<br>ps_all_allo_oral_5_core_dc1_reduced_vsd: First object for oral samples, absolute count data<br> Used in the multivariate and ML scripts<br><br><br>NASAL: <br><br>ps_all_allo_nasal_5_core_dc_reduced_vars: First object for nasal samples, absolute count data<br> Used in the alpha diversity script as initial input<br><br>ps_all_allo_nasal_5_core_dc1_reduced: Second object for nasal samples, absolute count data, alpha diversity measures calculated and added to sample data<br> Used as initial input for the multivariate script, in the ML script for the boxplots, and in LDA script<br>ps_all_allo_nasal_5_core_dc1_reduced_vsd: First object for nasal samples, absolute count data<br> Used in the multivariate and ML scripts