DivE (version 1.0)

Bact1: Count of Medically Important Bacteria Species in a Sample

Description

This gives a fictitious example of a sample of 7814 bacteria comprising of 144 unique species. Designed as a test dataset for the DivE diversity estimation algorithm.

Usage

data(Bact1)

Format

A data frame with 144 observations on the following 2 variables.

Bacteria

a factor with levels Acetobacter_aurantius Acinetobacter_baumannii Actinomyces_israelii Agrobacterium_radiobacter Agrobacterium_tumefaciens Anaplasma Azorhizobium_caulinodans Azotobacter_vinelandii Bacillus_anthracis Bacillus_brevis Bacillus_cereus Bacillus_fusiformis Bacillus_licheniformis Bacillus_megaterium Bacillus_mycoides Bacillus_stearothermophilus Bacillus_subtilis Bacteroides_fragilis Bacteroides_gingivalis Bacteroides_melaninogenicus Bartonella_henselae Bartonella_quintana Bordetella_bronchiseptica Bordetella_pertussis Borrelia_burgdorferi Brucella_abortus Brucella_melitensis Brucella_suis Burkholderia_cepacia Burkholderia_mallei Burkholderia_pseudomallei Calymmatobacterium_granulomatis Campylobacter_coli Campylobacter_fetus Campylobacter_jejuni Campylobacter_pylori Chlamydia_trachomatis Chlamydophila_pneumoniae Chlamydophila_psittaci Clostridium_botulinum Clostridium_difficile Clostridium_perfringens Clostridium_tetani Corynebacterium_diphtheriae Corynebacterium_fusiforme Coxiella_burnetii Ehrlichia_chaffeensis Enterobacter_cloacae Enterococcus_avium Enterococcus_durans Enterococcus_faecalis Enterococcus_faecium Enterococcus_galllinarum Enterococcus_maloratus Escherichia coli Francisella tularensis Fusobacterium_nucleatum Gardnerella_vaginalis Haemophilus_ducreyi Haemophilus_influenzae Haemophilus_parainfluenzae Haemophilus_pertussis Haemophilus_vaginalis Helicobacter_pylori Klebsiella_pneumoniae Lactobacillus_Bulgaricus Lactobacillus_acidophilus Lactobacillus_casei Lactococcus_lactis Legionella_pneumophila Listeria_monocytogenes Methanobacterium_extroquens Microbacterium_multiforme Micrococcus_luteus Moraxella_catarrhalis Mycobacterium Mycobacterium_avium Mycobacterium_bovis Mycobacterium_diphtheriae Mycobacterium_intracellulare Mycobacterium_leprae Mycobacterium_lepraemurium Mycobacterium_phlei Mycobacterium_smegmatis Mycobacterium_tuberculosis Mycoplasma_fermentans Mycoplasma_genitalium Mycoplasma_hominis Mycoplasma_penetrans Mycoplasma_pneumoniae Neisseria_gonorrhoeae Neisseria_meningitidis Pasteurella_multocida Pasteurella_tularensis Peptostreptococcus Porphyromonas_gingivalis Pseudomonas_aeruginosa Rhizobium_radiobacter Rickettsia_prowazekii Rickettsia_psittaci Rickettsia_quintana Rickettsia_rickettsii Rickettsia_trachomae Rochalimaea Rochalimaea_henselae Rochalimaea_quintana Rothia_dentocariosa Salmonella_enteritidis Salmonella_typhi Salmonella_typhimurium Serratia_marcescens Shigella_dysenteriae Staphylococcus_aureus Staphylococcus_epidermidis Stenotrophomonas_maltophilia Streptococcus_agalactiae Streptococcus_avium Streptococcus_bovis Streptococcus_cricetus Streptococcus_faceium Streptococcus_faecalis Streptococcus_ferus Streptococcus_gallinarum Streptococcus_lactis Streptococcus_mitior Streptococcus_mitis Streptococcus_mutans Streptococcus_oralis Streptococcus_pneumoniae Streptococcus_pyogenes Streptococcus_rattus Streptococcus_salivarius Streptococcus_sanguis Streptococcus_sobrinus Treponema_denticola Treponema_pallidum Vibrio_cholerae Vibrio_comma Vibrio_parahaemolyticus Vibrio_vulnificus Wolbachia Yersinia_enterocolitica Yersinia_pestis Yersinia_pseudotuberculosis

Count

a numeric vector

References

Laydon, D., Melamed, A., Sim, A., Gillet, N. A., Sim, K., Darko, S., Kroll, S., Douek, D. C., Price, D., Bangham, C. R. M., Asquith, B., Quantification of HTLV-1 clonality and TCR diversity, PLOS Comput. Biol. 2014

Examples

data(Bact1)

hist(Bact1[,2], breaks=20, main="Bacterial diversity of a sample",
xlab="Number of bacteria of a given species", ylab="Number of bacterial species")