mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 18:01:50 +02:00
(v1.4.0.9017) stringsAsFactors definitions
This commit is contained in:
54
R/mo.R
54
R/mo.R
@ -324,7 +324,8 @@ exec_as.mo <- function(x,
|
||||
format_uncertainty_as_df(uncertainty_level = uncertainty,
|
||||
input = input,
|
||||
result_mo = res_df[1, "mo", drop = TRUE],
|
||||
candidates = as.character(res_df[, "fullname", drop = TRUE])))
|
||||
candidates = as.character(res_df[, "fullname", drop = TRUE])),
|
||||
stringsAsFactors = FALSE)
|
||||
}
|
||||
res[seq_len(min(n, length(res)))]
|
||||
}
|
||||
@ -819,7 +820,8 @@ exec_as.mo <- function(x,
|
||||
uncertainties <- rbind(uncertainties,
|
||||
format_uncertainty_as_df(uncertainty_level = 1,
|
||||
input = x_backup[i],
|
||||
result_mo = lookup(fullname == "Salmonella enterica", "mo", uncertainty = -1)))
|
||||
result_mo = lookup(fullname == "Salmonella enterica", "mo", uncertainty = -1)),
|
||||
stringsAsFactors = FALSE)
|
||||
next
|
||||
}
|
||||
}
|
||||
@ -1022,7 +1024,8 @@ exec_as.mo <- function(x,
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup)))
|
||||
result_mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup)),
|
||||
stringsAsFactors = FALSE)
|
||||
return(x)
|
||||
}
|
||||
|
||||
@ -1043,7 +1046,8 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found)) {
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1071,7 +1075,8 @@ exec_as.mo <- function(x,
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result))
|
||||
result_mo = found_result),
|
||||
stringsAsFactors = FALSE)
|
||||
return(found)
|
||||
}
|
||||
}
|
||||
@ -1095,7 +1100,8 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) {
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1118,7 +1124,8 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) {
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1147,7 +1154,8 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found)) {
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1175,7 +1183,8 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found)) {
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1193,7 +1202,8 @@ exec_as.mo <- function(x,
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result))
|
||||
result_mo = found_result),
|
||||
stringsAsFactors = FALSE)
|
||||
return(found)
|
||||
}
|
||||
if (b.x_trimmed %like_case% "(fungus|fungi)" & !b.x_trimmed %like_case% "fungiphrya") {
|
||||
@ -1203,7 +1213,8 @@ exec_as.mo <- function(x,
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
|
||||
input = a.x_backup,
|
||||
result_mo = found_result))
|
||||
result_mo = found_result),
|
||||
stringsAsFactors = FALSE)
|
||||
return(found)
|
||||
}
|
||||
# (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
|
||||
@ -1228,7 +1239,8 @@ exec_as.mo <- function(x,
|
||||
# uncertainty level 2 only if searched part contains a space (otherwise it will be found with lvl 3)
|
||||
if (x_strip_collapsed %like_case% " ") {
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1261,7 +1273,8 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found)) {
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1287,7 +1300,8 @@ exec_as.mo <- function(x,
|
||||
if (!empty_result(found)) {
|
||||
found_result <- found
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1305,7 +1319,8 @@ exec_as.mo <- function(x,
|
||||
if (!is.na(found) & nchar(g.x_backup_without_spp) >= 6) {
|
||||
found_result <- lookup(mo == found)
|
||||
uncertainties <<- rbind(uncertainties,
|
||||
attr(found, which = "uncertainties", exact = TRUE))
|
||||
attr(found, which = "uncertainties", exact = TRUE),
|
||||
stringsAsFactors = FALSE)
|
||||
found <- lookup(mo == found)
|
||||
return(found)
|
||||
}
|
||||
@ -1498,7 +1513,8 @@ exec_as.mo <- function(x,
|
||||
format_uncertainty_as_df(uncertainty_level = actual_uncertainty,
|
||||
input = actual_input,
|
||||
result_mo = x,
|
||||
candidates = ""))
|
||||
candidates = ""),
|
||||
stringsAsFactors = FALSE)
|
||||
}
|
||||
# this will save the uncertain items as attribute, so they can be bound to `uncertainties` in the uncertain_fn() function
|
||||
x <- structure(x, uncertainties = uncertainties)
|
||||
@ -1520,7 +1536,9 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
|
||||
stringsAsFactors = FALSE)
|
||||
already_set <- getOption("mo_renamed")
|
||||
if (!is.null(already_set)) {
|
||||
options(mo_renamed = rbind(already_set, newly_set))
|
||||
options(mo_renamed = rbind(already_set,
|
||||
newly_set,
|
||||
stringsAsFactors = FALSE))
|
||||
} else {
|
||||
options(mo_renamed = newly_set)
|
||||
}
|
||||
@ -1791,7 +1809,7 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
mo_renamed <- function() {
|
||||
items <- getOption("mo_renamed", default = NULL)
|
||||
if (is.null(items)) {
|
||||
items <- data.frame()
|
||||
items <- data.frame(stringsAsFactors = FALSE)
|
||||
} else {
|
||||
items <- pm_distinct(items, old_name, .keep_all = TRUE)
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user