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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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32
data-raw/reproduction_of_microorganisms.groups.R
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@ -66,7 +66,7 @@ whonet_organisms %>%
group_by(SPECIES_GROUP) %>%
summarise(complex = ORGANISM[ORGANISM %like% " (group|complex)"][1],
organisms = paste0(n(), ": ", paste(sort(unique(ORGANISM)), collapse = ", "))) %>%
filter(!SPECIES_GROUP %in% AMR::microorganisms.codes$code)
filter(!SPECIES_GROUP %in% microorganisms.codes$code)
# create the species group data set ----
microorganisms.groups <- whonet_organisms %>%
@ -98,9 +98,9 @@ microorganisms.groups <- whonet_organisms %>%
# group C - all subspecies within S. dysgalactiae and S. equi (such as S. equi zooepidemicus)
bind_rows(tibble(mo_group = as.mo("Streptococcus Group C"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(DYSG|EQUI)(_|$)")])) %>%
# group F - S. anginosus, incl. S. anginosus anginosus and S. anginosus whileyi
# group F - Milleri group == S. anginosus group, which incl. S. anginosus, S. constellatus, S. intermedius
bind_rows(tibble(mo_group = as.mo("Streptococcus Group F"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_ANGN(_|$)")])) %>%
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(ANGN|CNST|INTR)(_|$)")])) %>%
# group G - S. dysgalactiae and S. canis (though dysgalactiae is also group C and will be matched there)
bind_rows(tibble(mo_group = as.mo("Streptococcus Group G"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(DYSG|CANS)(_|$)")])) %>%
@ -110,6 +110,9 @@ microorganisms.groups <- whonet_organisms %>%
# group K - S. salivarius, incl. S. salivarius salivariuss and S. salivarius thermophilus
bind_rows(tibble(mo_group = as.mo("Streptococcus Group K"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_SLVR(_|$)")])) %>%
# group L - only S. dysgalactiae
bind_rows(tibble(mo_group = as.mo("Streptococcus Group L"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_DYSG(_|$)")])) %>%
# and for EUCAST: Strep group A, B, C, G
bind_rows(tibble(mo_group = as.mo("Streptococcus Group A, B, C, G"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(PYGN|AGLC|DYSG|EQUI|CANS|GRPA|GRPB|GRPC|GRPG)(_|$)")])) %>%
@ -131,8 +134,24 @@ microorganisms.groups <- whonet_organisms %>%
# RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
filter(mo_group != "B_MYCBC_RGM") %>%
bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE))) %>%
# add full names
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE)))
# add subspecies to all species
for (group in unique(microorganisms.groups$mo_group)) {
spp <- microorganisms.groups %>%
filter(mo_group == group & mo_rank(mo, keep_synonyms = TRUE) == "species") %>%
pull(mo) %>%
paste0(collapse = "|") %>%
paste0("^(", ., ")")
mos <- microorganisms %>%
filter(mo %like% spp & rank == "subspecies") %>%
pull(mo)
# add them
microorganisms.groups <- microorganisms.groups %>% bind_rows(tibble(mo_group = group, mo = mos))
}
# add full names, arrange and clean
microorganisms.groups <- microorganisms.groups %>%
mutate(mo_group_name = mo_name(mo_group, keep_synonyms = TRUE, language = NULL),
mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
arrange(mo_group_name, mo_name) %>%
@ -141,6 +160,9 @@ microorganisms.groups <- whonet_organisms %>%
dataset_UTF8_to_ASCII()
mo_uncertainties()
# add subspecies to all species
class(microorganisms.groups$mo_group) <- c("mo", "character")
class(microorganisms.groups$mo) <- c("mo", "character")
usethis::use_data(microorganisms.groups, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)