P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 13:01:58 +02:00
Code Releases Activity

(v1.7.1.9073) as.rsi() fix for UTIs

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-14 21:47:14 +01:00
parent 5eef01165e
commit bd4bb1d72f
25 changed files with 27787 additions and 27785 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
R/mo.R
View File

@ -485,6 +485,11 @@ exec_as.mo <- function(x,
}
}
# remove spp and species
x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("( spp?.?| ss |subsp.?|subspecies|biovar|serovar|species)", "", x, ignore.case = TRUE, perl = TRUE)
x <- strip_whitespace(x, dyslexia_mode)
x_backup <- x
# from here on case-insensitive
@ -493,11 +498,6 @@ exec_as.mo <- function(x,
x_backup[x %like_case% "^(fungus|fungi)$"] <- "(unknown fungus)" # will otherwise become the kingdom
x_backup[x_backup_untouched == "Fungi"] <- "Fungi" # is literally the kingdom
# remove spp and species
x_backup <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x_backup, perl = TRUE)
x_backup <- gsub("( spp?.?| ss |subsp.?|subspecies|biovar|serovar|species)", "", x_backup, perl = TRUE)
x_backup <- strip_whitespace(x_backup, dyslexia_mode)
# Fill in fullnames and MO codes directly
known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
@ -717,7 +717,7 @@ exec_as.mo <- function(x,
# fewer than 3 chars and not looked for species, add as failure
x[i] <- lookup(mo == "UNKNOWN")
if (initial_search == TRUE) {
failures <- c(failures, x_backup[i])
failures <- c(failures, x_backup_untouched[i])
}
next
}
@ -900,7 +900,7 @@ exec_as.mo <- function(x,
# (at this point the latest reference_df has also been checked)
x[i] <- lookup(mo == "UNKNOWN")
if (initial_search == TRUE) {
failures <- c(failures, x_backup[i])
failures <- c(failures, x_backup_untouched[i])
}
next
}
@ -1425,7 +1425,7 @@ exec_as.mo <- function(x,
# no results found: make them UNKNOWN ----
x[i] <- lookup(mo == "UNKNOWN", uncertainty = -1)
if (initial_search == TRUE) {
failures <- c(failures, x_backup[i])
failures <- c(failures, x_backup_untouched[i])
}
}