Phyloseq objects

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