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(v1.2.0.9035) as.mo() speed improvement

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dr. M.S. (Matthijs) Berends
2020-07-22 10:24:23 +02:00
parent 6ab468362d
commit 09fba38ea6
37 changed files with 174 additions and 441 deletions
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data-raw/microorganisms.translation.rds
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1
data-raw/microorganisms.txt
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@ -11207,6 +11207,7 @@
"F_CANDD_KAZU" "Candida kazuoi" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "(unknown family)" "Candida" "kazuoi" "" "species" "Nakase et al., 2007" "3d20db459296758ec4a5beb7a56e3a44" "CoL" 2
"F_CANDD_KRSN" "Candida keroseneae" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "(unknown family)" "Candida" "keroseneae" "" "species" "Buddie et al., 2011" "83b3ea8ab59f4c455de8a30e5b4d6a28" "CoL" 2
"F_CANDD_KH-T" "Candida khao-thaluensis" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "(unknown family)" "Candida" "khao-thaluensis" "" "species" "Groenew et al., 2011" "3767929e75dd19022c79bde32143733f" "CoL" 2
"F_CANDD_KRUS" "Candida krusei" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "(unknown family)" "Candida" "krusei" "" "species" "" "manually added" 2 "444877006"
"F_CANDD_KUOI" "Candida kuoi" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "(unknown family)" "Candida" "kuoi" "" "species" "Kurtzman, 2012" "2ddb2646cbee79c1aaaa725927e2e4c6" "CoL" 2
"F_CANDD_LBDR" "Candida labiduridarum" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "(unknown family)" "Candida" "labiduridarum" "" "species" "Suh et al., 2008" "79db540254156bc73399caaca772652e" "CoL" 2
"F_CANDD_LCT-" "Candida lactis-condensi" "Fungi" "Ascomycota" "Saccharomycetes" "Saccharomycetales" "(unknown family)" "Candida" "lactis-condensi" "" "species" "Mey et al., 1978" "9f04e19bd4cba3af175dbebad0f84bf0" "CoL" 2

12
data-raw/reproduction_of_microorganisms.R
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@ -667,7 +667,16 @@ MOs <- MOs %>%
ref = NA_character_,
species_id = "",
source = "manually added"),
# Blastocystis hominis does not exist (it means 'got a Bastocystis from humans', PMID 15634993)
# Candida krusei
MOs %>%
filter(genus == "Candida", species == "glabrata") %>% .[1,] %>%
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_KRUS", mo),
species = "krusei" ,
fullname = "Candida krusei",
ref = NA_character_,
species_id = "",
source = "manually added"),
# Blastocystis hominis does not exist (it means 'got a Blastocystis from humans', PMID 15634993)
# but let's be nice to the clinical people in microbiology
MOs %>%
filter(fullname == "Blastocystis") %>%
@ -897,6 +906,7 @@ rsi_translation$mo <- as.mo(rsi_translation$mo)
microorganisms.codes$mo <- as.mo(microorganisms.codes$mo)
class(microorganisms.codes$mo) <- c("mo", "character")
microorganisms.translation <- microorganisms.translation %>%
# (to do: add last package version to column pkg_version)
left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
by = c("mo_new" = "fullname")) %>%
mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>%