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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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3
data-raw/reproduction_of_clinical_breakpoints.R
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@ -297,6 +297,9 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- 2
breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 512
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G now includes all streptococci:
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STRPT" & clinical_breakpoints$ref_tbl %like% "strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
# EUCAST 2022 guideline: S <= 8 and R > 8
# WHONET file: S <= 8 and R >= 16

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()