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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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19
man/add_custom_microorganisms.Rd
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@ -58,8 +58,9 @@ mo_name("Enterobacter asburiae/cloacae")
# now add a custom entry - it will be considered by as.mo() and
# all mo_*() functions
add_custom_microorganisms(
data.frame(genus = "Enterobacter",
species = "asburiae/cloacae"
data.frame(
genus = "Enterobacter",
species = "asburiae/cloacae"
)
)
@ -81,8 +82,10 @@ mo_info("Enterobacter asburiae/cloacae")
# the function tries to be forgiving:
add_custom_microorganisms(
data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
SPECIES = "SPECIES")
data.frame(
GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
SPECIES = "SPECIES"
)
)
mo_name("BACTEROIDES / PARABACTEROIDES")
mo_rank("BACTEROIDES / PARABACTEROIDES")
@ -93,9 +96,11 @@ mo_family("Bacteroides/Parabacteroides")
# for groups and complexes, set them as species or subspecies:
add_custom_microorganisms(
data.frame(genus = "Citrobacter",
species = c("freundii", "braakii complex"),
subspecies = c("complex", ""))
data.frame(
genus = "Citrobacter",
species = c("freundii", "braakii complex"),
subspecies = c("complex", "")
)
)
mo_name(c("C. freundii complex", "C. braakii complex"))
mo_species(c("C. freundii complex", "C. braakii complex"))