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MO group fixes

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dr. M.S. (Matthijs) Berends
2023-07-12 15:04:48 +01:00
parent 9cf054903b
commit 0c46f61260
28 changed files with 1822 additions and 861 deletions
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6
R/mo.R
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@ -482,13 +482,13 @@ as.mo <- function(x,
# group D - all enterococci
out[out %like_case% "^B_ENTRC(_|$)"] <- "B_STRPT_GRPD"
}
# group F - S. anginosus, incl. S. anginosus anginosus and S. anginosus whileyi
out[out %like_case% "^B_STRPT_ANGN(_|$)"] <- "B_STRPT_GRPF"
# group F - Milleri group == S. anginosus group, which incl. S. anginosus, S. constellatus, S. intermedius
out[out %like_case% "^B_STRPT_(ANGN|CNST|INTR)(_|$)"] <- "B_STRPT_GRPF"
# group G - S. dysgalactiae and S. canis (though dysgalactiae is also group C and will be matched there)
out[out %like_case% "^B_STRPT_(DYSG|CANS)(_|$)"] <- "B_STRPT_GRPG"
# group H - S. sanguinis
out[out %like_case% "^B_STRPT_SNGN(_|$)"] <- "B_STRPT_GRPH"
# group K - S. salivarius, incl. S. salivarius salivariuss and S. salivarius thermophilus
# group K - S. salivarius, incl. S. salivarius salivarius and S. salivarius thermophilus
out[out %like_case% "^B_STRPT_SLVR(_|$)"] <- "B_STRPT_GRPK"
# group L - only S. dysgalactiae which is also group C & G, so ignore it here
}