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microorganisms update, added Salmonella groups

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dr. M.S. (Matthijs) Berends
2022-12-16 16:10:43 +01:00
parent 8da2467209
commit 5f3a7694aa
43 changed files with 38933 additions and 105358 deletions
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13
R/mo.R
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@@ -429,10 +429,12 @@ as.mo <- function(x,
# Apply Lancefield ----
if (isTRUE(Lancefield) || Lancefield == "all") {
# (using `%like_case%` to also match subspecies)
# group A - S. pyogenes
out[out == "B_STRPT_PYGN"] <- "B_STRPT_GRPA"
out[out %like_case% "^B_STRPT_PYGN(_|$)"] <- "B_STRPT_GRPA"
# group B - S. agalactiae
out[out == "B_STRPT_AGLC"] <- "B_STRPT_GRPB"
out[out %like_case% "^B_STRPT_AGLC(_|$)"] <- "B_STRPT_GRPB"
# group C - all subspecies within S. dysgalactiae and S. equi (such as S. equi zooepidemicus)
out[out %like_case% "^B_STRPT_(DYSG|EQUI)(_|$)"] <- "B_STRPT_GRPC"
if (Lancefield == "all") {
@@ -441,12 +443,13 @@ as.mo <- function(x,
}
# group F - S. anginosus, incl. S. anginosus anginosus and S. anginosus whileyi
out[out %like_case% "^B_STRPT_ANGN(_|$)"] <- "B_STRPT_GRPF"
# group G - only S. dysgalactiae which is also group C, so ignore it here
# 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)(_|$)"] <- "B_STRPT_GRPG"
# group H - S. sanguinis
out[out == "B_STRPT_SNGN"] <- "B_STRPT_GRPH"
out[out %like_case% "^B_STRPT_SNGN(_|$)"] <- "B_STRPT_GRPH"
# group K - S. salivarius, incl. S. salivarius salivariuss and S. salivarius thermophilus
out[out %like_case% "^B_STRPT_SLVR(_|$)"] <- "B_STRPT_GRPK"
# group L - only S. dysgalactiae which is also group C, so ignore it here
# group L - only S. dysgalactiae which is also group C & G, so ignore it here
}
# All unknowns ----