Statistical and power calculations animal trial persistant antimicrobials and resistance levels

This repository is containing the datasets with statistical analysis of the paper: "Extended period of selection pressure due to persistancy of antimicrobials in broilers."

Power calculation

Two CSV-files: Power calculation resistant isolates and Power calculation antibiotics

One R-file: Power calculation antimicrobial persistent residues

The phenotypic resistance

R-file: Phenotypic resistance analysis trial, CSV-file: E. coli resistance per treatment

The resistome analysis 

one CSV-files: Resistome workfile 

one R-file: Resistome statistical analysis

Microbiome analysis

Phyloseq object

R-file: Rarfied phyloseq object from biom file, CSV-file: metedata, biom-file: reads_trail  

Alpha- and beta-diversity analysis

R-file: Beta en alpha diversity animal trail, Rdata-file: rarefy.animaltrial

Microbial abundance analysis

R-file: relative abundance animal trial, Rdata-file: rarefy.animaltrial