P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-08-28 11:52:13 +02:00
Code Releases Activity

added mo_shortname

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-09-05 10:51:46 +02:00
parent 790bd1622d
commit e39a9a8b05
8 changed files with 88 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
man/mo_property.Rd
View File

@@ -7,6 +7,7 @@
\alias{mo_species}
\alias{mo_subspecies}
\alias{mo_fullname}
\alias{mo_shortname}
\alias{mo_type}
\alias{mo_gramstain}
\alias{mo_aerobic}
@@ -30,6 +31,8 @@ mo_subspecies(x, Becker = FALSE, Lancefield = FALSE)
mo_fullname(x, Becker = FALSE, Lancefield = FALSE)
mo_shortname(x, Becker = FALSE, Lancefield = FALSE)
mo_type(x, language = "en")
mo_gramstain(x, language = "en")
@@ -61,6 +64,7 @@ mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"
mo_subspecies("E. coli") # <NA>
mo_fullname("E. coli") # "Escherichia coli"
mo_shortname("E. coli") # "E. coli"
mo_type("E. coli") # "Bacteria"
mo_gramstain("E. coli") # "Negative rods"
mo_aerobic("E. coli") # TRUE
@@ -77,6 +81,7 @@ mo_gramstain("E. coli", "nl") # "Negatieve staven"
# Abbreviations known in the field
mo_genus("MRSA") # "Staphylococcus"
mo_species("MRSA") # "aureus"
mo_shortname("MRSA") # "S. aureus"
mo_gramstain("MRSA") # "Positive cocci"
mo_genus("VISA") # "Staphylococcus"
@@ -88,12 +93,14 @@ mo_genus("EHEC") # "Escherichia"
mo_species("EHEC") # "coli"
mo_subspecies("EHEC") # "EHEC"
mo_fullname("EHEC") # "Escherichia coli (EHEC)"
mo_shortname("EHEC") # "E. coli"
mo_genus("doylei") # "Campylobacter"
mo_species("doylei") # "jejuni"
mo_fullname("doylei") # "Campylobacter jejuni (doylei)"
mo_fullname("K. pneu rh") # "Klebsiella pneumoniae (rhinoscleromatis)"
mo_shortname("K. pneu rh") # "K. pneumoniae"
# Anaerobic bacteria
@@ -103,12 +110,16 @@ mo_aerobic("B. fragilis") # FALSE
# Becker classification, see ?as.mo
mo_fullname("S. epidermidis") # "Staphylococcus epidermidis"
mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
mo_fullname("S. epidermidis") # "Staphylococcus epidermidis"
mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
mo_shortname("S. epidermidis") # "S. epidermidis"
mo_shortname("S. epidermidis", Becker = TRUE) # "CoNS"
# Lancefield classification, see ?as.mo
mo_fullname("S. pyogenes") # "Streptococcus pyogenes"
mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
mo_fullname("S. pyogenes") # "Streptococcus pyogenes"
mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
mo_shortname("S. pyogenes") # "S. pyogenes"
mo_shortname("S. pyogenes", Lancefield = TRUE) # "GAS"
}
\seealso{
\code{\link{microorganisms}}