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(v0.7.0.9005) ab algorithm update

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dr. M.S. (Matthijs) Berends
2019-06-11 14:18:25 +02:00
parent f6c47c8c88
commit 8f674e19bb
36 changed files with 274 additions and 248 deletions
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14
data-raw/reproduction_of_microorganisms.R
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@ -318,13 +318,13 @@ MOs <- MOs %>%
stringsAsFactors = FALSE),
data.frame(mo = "B_GRAMN",
col_id = NA_integer_,
fullname = "(unknown Gram negatives)",
fullname = "(unknown Gram-negatives)",
kingdom = "Bacteria",
phylum = "(unknown phylum)",
class = "(unknown class)",
order = "(unknown order)",
family = "(unknown family)",
genus = "(unknown Gram negatives)",
genus = "(unknown Gram-negatives)",
species = "(unknown species)",
subspecies = "(unknown subspecies)",
rank = "species",
@ -334,13 +334,13 @@ MOs <- MOs %>%
stringsAsFactors = FALSE),
data.frame(mo = "B_GRAMP",
col_id = NA_integer_,
fullname = "(unknown Gram positives)",
fullname = "(unknown Gram-positives)",
kingdom = "Bacteria",
phylum = "(unknown phylum)",
class = "(unknown class)",
order = "(unknown order)",
family = "(unknown family)",
genus = "(unknown Gram positives)",
genus = "(unknown Gram-positives)",
species = "(unknown species)",
subspecies = "(unknown subspecies)",
rank = "species",
@ -457,7 +457,7 @@ MOs <- MOs %>%
mutate(prevalence = case_when(
class == "Gammaproteobacteria"
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
| mo == "UNKNOWN"
| mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP")
~ 1,
phylum %in% c("Proteobacteria",
"Firmicutes",
@ -494,8 +494,8 @@ saveRDS(MOs, "microorganisms.rds")
saveRDS(MOs.old, "microorganisms.old.rds")
# on the server:
usethis::use_data(microorganisms, overwrite = TRUE)
usethis::use_data(microorganisms.old, overwrite = TRUE)
usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
rm(microorganisms)
rm(microorganisms.old)
# and update the year in R/data.R