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(v0.7.0.9008) T. vaginalis, rsi_df

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dr. M.S. (Matthijs) Berends
2019-06-13 14:28:46 +02:00
parent 699e87ab4a
commit 254745061c
32 changed files with 382 additions and 259 deletions
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44
data-raw/reproduction_of_microorganisms.R
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@ -444,7 +444,43 @@ MOs <- MOs %>%
fullname = "Beta-haemolytic Streptococcus",
ref = NA_character_,
species_id = "",
source = "manually added")
source = "manually added"),
# Trichomonas vaginalis is missing, same order as Dientamoeba
MOs %>%
filter(fullname == "Dientamoeba") %>%
mutate(mo = gsub("DNTMB", "THMNS", mo),
col_id = NA,
fullname = "Trichomonas",
family = "Trichomonadidae",
genus = "Trichomonas",
source = "manually added",
ref = "Donne, 1836",
species_id = ""),
MOs %>%
filter(fullname == "Dientamoeba fragilis") %>%
mutate(mo = gsub("DNTMB", "THMNS", mo),
mo = gsub("FRA", "VAG", mo),
col_id = NA,
fullname = "Trichomonas vaginalis",
family = "Trichomonadidae",
genus = "Trichomonas",
species = "vaginalis",
source = "manually added",
ref = "Donne, 1836",
species_id = ""),
MOs %>% # add family as such too
filter(fullname == "Monocercomonadidae") %>%
mutate(mo = gsub("MNCRCMND", "TRCHMNDD", mo),
col_id = NA,
fullname = "Trichomonadidae",
family = "Trichomonadidae",
rank = "family",
genus = "",
species = "",
source = "manually added",
ref = "",
species_id = ""),
)
@ -485,8 +521,12 @@ MOs <- MOs %>%
TRUE ~ 3
))
# arrange
MOs <- MOs %>% arrange(fullname)
MOs.old <- MOs.old %>% arrange(fullname)
# save it
MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
MOs <- as.data.frame(MOs, stringsAsFactors = FALSE)
MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
class(MOs$mo) <- "mo"