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add strep groups to ABCG

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dr. M.S. (Matthijs) Berends
2023-07-12 11:41:25 +01:00
parent 66eeeb4b88
commit 7cd9ca274c
7 changed files with 12 additions and 39 deletions
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33
data-raw/reproduction_of_microorganisms.groups.R
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@ -112,7 +112,7 @@ microorganisms.groups <- whonet_organisms %>%
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_SLVR(_|$)")])) %>%
# and for EUCAST: Strep group A, B, C, G
bind_rows(tibble(mo_group = as.mo("Streptococcus Group A, B, C, G"),
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(PYGN|AGLC|DYSG|EQUI|CANS)(_|$)")])) %>%
mo = microorganisms$mo[which(microorganisms$mo %like% "^B_STRPT_(PYGN|AGLC|DYSG|EQUI|CANS|GRPA|GRPB|GRPC|GRPG)(_|$)")])) %>%
# HACEK is:
# - Haemophilus species
# - Aggregatibacter species
@ -133,8 +133,8 @@ microorganisms.groups <- whonet_organisms %>%
bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE))) %>%
# add full names
mutate(mo_group_name = mo_name(mo_group, keep_synonyms = TRUE),
mo_name = mo_name(mo, keep_synonyms = TRUE)) %>%
mutate(mo_group_name = mo_name(mo_group, keep_synonyms = TRUE, language = NULL),
mo_name = mo_name(mo, keep_synonyms = TRUE, language = NULL)) %>%
arrange(mo_group_name, mo_name) %>%
filter(mo_group != mo) %>%
distinct() %>%
@ -146,30 +146,3 @@ class(microorganisms.groups$mo) <- c("mo", "character")
usethis::use_data(microorganisms.groups, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
rm(microorganisms.groups)
devtools::load_all()
#
# microorganisms <- microorganisms %>%
# mutate(mo = as.character(mo)) %>%
# bind_rows(
# microorganisms %>% filter(mo == "B_STRPT_HAEM") %>%
# mutate(mo = as.character(mo),
# mo = "B_STRPT_ABCG",
# fullname = "Streptococcus Group A, B, C, G",
# species = "Group A, B, C, G")) %>%
# arrange(fullname) %>%
# dataset_UTF8_to_ASCII()
#
# microorganisms$rank[which(microorganisms$fullname %like% "^Streptococcus Group")] <- "species group"
# microorganisms$lpsn_parent[which(microorganisms$fullname %like% "^Streptococcus Group")] <- 517118
# microorganisms$gbif_parent[which(microorganisms$fullname %like% "^Streptococcus Group")] <- 3223465
# microorganisms$ref[which(microorganisms$fullname %like% "^Streptococcus Group")] <- "Lancefield, 1933"
# microorganisms$prevalence[which(microorganisms$fullname %like% "^Streptococcus Group")] <- 1.5
# microorganisms$oxygen_tolerance[which(microorganisms$fullname %like% "^Streptococcus Group")] <- "likely facultative anaerobe"
#
class(microorganisms$mo) <- c("mo", "character")
usethis::use_data(microorganisms, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
rm(microorganisms)
devtools::load_all()