vignettes/datasets.Rmd
datasets.Rmd
This data set is in R available as microorganisms
, after
you load the AMR
package.
It was last updated on 3 June 2022 11:18:29 UTC. Find more info about -the structure of this data set here.
+It was last updated on 10 June 2022 11:09:45 UTC. Find more info +about the structure of this data set here.
Direct download links:
AMR
1.8.1.9012AMR
1.8.1.9013as.rsi()
. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.as.rsi()
on certain EUCAST breakpoints for MIC valuesas.integer()
for MIC values, since MIC are not integer values and running table()
on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally as.integer()
on factor
s work)set_mo_source()
, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this packagerandom_*()
function (such as random_mic()
) is now possible by directly calling the package without loading it first: AMR::random_mic(10)
P_TXPL_GOND
) to the microorganisms
data set, together with its genus, family, and orderprevalence
of the microorganisms
data set from 3 to 2 for these genera: Acholeplasma, Alistipes, Alloprevotella, Bergeyella, Borrelia, Brachyspira, Butyricimonas, Cetobacterium, Chlamydia, Chlamydophila, Deinococcus, Dysgonomonas, Elizabethkingia, Empedobacter, Haloarcula, Halobacterium, Halococcus, Myroides, Odoribacter, Ornithobacterium, Parabacteroides, Pedobacter, Phocaeicola, Porphyromonas, Riemerella, Sphingobacterium, Streptobacillus, Tenacibaculum, Terrimonas, Victivallis, Wautersiella, Weeksella
Data Set with 70,760 Microorganisms
Data Set with 70,764 Microorganisms
R/data.R
microorganisms.Rd
A data.frame with 70,760 observations and 16 variables:
mo
ID of microorganism as used by this package
A data.frame with 70,764 observations and 16 variables:
mo
ID of microorganism as used by this package
fullname
Full name, like "Escherichia coli"
kingdom
, phylum
, class
, order
, family
, genus
, species
, subspecies
Taxonomic rank of the microorganism
rank
Text of the taxonomic rank of the microorganism, like "species"
or "genus"
Catalogue of Life: 2019 Annual Checklist as currently implemented in this AMR
package:
Annual Checklist (public online taxonomic database), http://www.catalogueoflife.org
List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this AMR
package:
Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi: 10.1099/ijsem.0.004332
Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; doi: 10.1093/nar/gkt1111
Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi: 10.1099/00207713-47-2-590
List of Prokaryotic names with Standing in Nomenclature (5 October 2021) as currently implemented in this AMR
package:
Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332
Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi:10.1099/ijsem.0.002786
Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; doi:10.1093/nar/gkt1111
Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; doi:10.1099/00207713-47-2-590
US Edition of SNOMED CT from 1 September 2020 as currently implemented in this AMR
package:
Retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009
Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.
-For example, Staphylococcus pettenkoferi was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi: 10.1016/s0732-8893(02)00399-1 -), but it was not before 2007 that a publication in IJSEM followed (doi: 10.1099/ijs.0.64381-0 +
For example, Staphylococcus pettenkoferi was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi:10.1016/s0732-8893(02)00399-1
+), but it was not before 2007 that a publication in IJSEM followed (doi:10.1099/ijs.0.64381-0
). Consequently, the AMR
package returns 2007 for mo_year("S. pettenkoferi")
.
For convenience, some entries were added manually:
11 entries of Streptococcus (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
2 entries of Staphylococcus (coagulase-negative (CoNS) and coagulase-positive (CoPS))
3 entries of Trichomonas (T. vaginalis, and its family and genus)
4 entries of Toxoplasma (T. gondii, and its order, family and genus)
1 entry of Candida (C. krusei), that is not (yet) in the Catalogue of Life
1 entry of Blastocystis (B. hominis), although it officially does not exist (Noel et al. 2005, PMID 15634993)
1 entry of Moraxella (M. catarrhalis), which was formally named Branhamella catarrhalis (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
This data set is available as 'flat file' for use even without R - you can find the file here:
The file in R format (with preserved data structure) can be found here:
This data set is available as 'flat file' for use even without R - you can find the file here: https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt.
+The file in R format (with preserved data structure) can be found here: https://github.com/msberends/AMR/raw/main/data/microorganisms.rda.
+