R: Count of Medically Important Bacteria Species in a Sample
Bact1
R Documentation
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_aurantiusAcinetobacter_baumanniiActinomyces_israeliiAgrobacterium_radiobacterAgrobacterium_tumefaciensAnaplasmaAzorhizobium_caulinodansAzotobacter_vinelandiiBacillus_anthracisBacillus_brevisBacillus_cereusBacillus_fusiformisBacillus_licheniformisBacillus_megateriumBacillus_mycoidesBacillus_stearothermophilusBacillus_subtilisBacteroides_fragilisBacteroides_gingivalisBacteroides_melaninogenicusBartonella_henselaeBartonella_quintanaBordetella_bronchisepticaBordetella_pertussisBorrelia_burgdorferiBrucella_abortusBrucella_melitensisBrucella_suisBurkholderia_cepaciaBurkholderia_malleiBurkholderia_pseudomalleiCalymmatobacterium_granulomatisCampylobacter_coliCampylobacter_fetusCampylobacter_jejuniCampylobacter_pyloriChlamydia_trachomatisChlamydophila_pneumoniaeChlamydophila_psittaciClostridium_botulinumClostridium_difficileClostridium_perfringensClostridium_tetaniCorynebacterium_diphtheriaeCorynebacterium_fusiformeCoxiella_burnetiiEhrlichia_chaffeensisEnterobacter_cloacaeEnterococcus_aviumEnterococcus_duransEnterococcus_faecalisEnterococcus_faeciumEnterococcus_galllinarumEnterococcus_maloratusEscherichia coliFrancisella tularensisFusobacterium_nucleatumGardnerella_vaginalisHaemophilus_ducreyiHaemophilus_influenzaeHaemophilus_parainfluenzaeHaemophilus_pertussisHaemophilus_vaginalisHelicobacter_pyloriKlebsiella_pneumoniaeLactobacillus_BulgaricusLactobacillus_acidophilusLactobacillus_caseiLactococcus_lactisLegionella_pneumophilaListeria_monocytogenesMethanobacterium_extroquensMicrobacterium_multiformeMicrococcus_luteusMoraxella_catarrhalisMycobacteriumMycobacterium_aviumMycobacterium_bovisMycobacterium_diphtheriaeMycobacterium_intracellulareMycobacterium_lepraeMycobacterium_lepraemuriumMycobacterium_phleiMycobacterium_smegmatisMycobacterium_tuberculosisMycoplasma_fermentansMycoplasma_genitaliumMycoplasma_hominisMycoplasma_penetransMycoplasma_pneumoniaeNeisseria_gonorrhoeaeNeisseria_meningitidisPasteurella_multocidaPasteurella_tularensisPeptostreptococcusPorphyromonas_gingivalisPseudomonas_aeruginosaRhizobium_radiobacterRickettsia_prowazekiiRickettsia_psittaciRickettsia_quintanaRickettsia_rickettsiiRickettsia_trachomaeRochalimaeaRochalimaea_henselaeRochalimaea_quintanaRothia_dentocariosaSalmonella_enteritidisSalmonella_typhiSalmonella_typhimuriumSerratia_marcescensShigella_dysenteriaeStaphylococcus_aureusStaphylococcus_epidermidisStenotrophomonas_maltophiliaStreptococcus_agalactiaeStreptococcus_aviumStreptococcus_bovisStreptococcus_cricetusStreptococcus_faceiumStreptococcus_faecalisStreptococcus_ferusStreptococcus_gallinarumStreptococcus_lactisStreptococcus_mitiorStreptococcus_mitisStreptococcus_mutansStreptococcus_oralisStreptococcus_pneumoniaeStreptococcus_pyogenesStreptococcus_rattusStreptococcus_salivariusStreptococcus_sanguisStreptococcus_sobrinusTreponema_denticolaTreponema_pallidumVibrio_choleraeVibrio_commaVibrio_parahaemolyticusVibrio_vulnificusWolbachiaYersinia_enterocoliticaYersinia_pestisYersinia_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")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(DivE)
Loading required package: deSolve
Attaching package: 'deSolve'
The following object is masked from 'package:graphics':
matplot
Loading required package: FME
Loading required package: rootSolve
Loading required package: coda
Loading required package: rgeos
rgeos version: 0.3-19, (SVN revision 524)
GEOS runtime version: 3.5.0-CAPI-1.9.0 r4084
Linking to sp version: 1.2-3
Polygon checking: TRUE
Loading required package: sp
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/DivE/Bact1.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Bact1
> ### Title: Count of Medically Important Bacteria Species in a Sample
> ### Aliases: Bact1 Bact2
> ### Keywords: datasets
>
> ### ** 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")
>
>
>
>
>
> dev.off()
null device
1
>