Statistical analysis of data determining minimal selective concentration of Amoxicillin, doxycycline and enrofloxacin

This repository is containing the datasets with statistical analysis of the paper: "Selection for amoxicillin, doxycycline and enrofloxacin resistant Escherichia coli at concentrations lower tha nthe ECOFF in rich media and in broiler-derived fecal fermenations." The phenotypic analysis Phenotypic amoxicillin R-file: Phenotypic Amox mixed models, CSV-file: Phenotypic data Amox Phenotypic doxycycline R-file: Phenotypic Dox mixed models, CSV-file: Phenotypic data Dox Phenotypic enrofloxacin R-file: Phenotypic Enro mixed models, CSV-file: Phenotypic data Enro The resistome analysis two CSV-files: Resistoom workfile and resistome_reference_file one R-file: Resistome_analysis_antimicrobial_classes Microbiome analysis Alpha- and beta-diversity analysis R-file Biom analysis, CSV-file: metadata2, biom-file: reads_fermentation Microbial abundance analysis R-file: Abundance plot, CSV-file: metadata2. biom-file: reads_fermentation2.biom