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(v0.7.1.9100) bug_drug speed, MIC levels

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dr. M.S. (Matthijs) Berends
2019-10-08 22:21:33 +02:00
parent 683d226fd3
commit c8f6b97847
22 changed files with 117 additions and 70 deletions
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46
R/mo.R
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@ -412,13 +412,13 @@ exec_as.mo <- function(x,
y <- reference_data_to_use[prevalence == 1][data.table(mo = x), on = "mo", ..property][[1]]
if (any(is.na(y))) {
y[is.na(y)] <- reference_data_to_use[prevalence == 2][data.table(mo = x[is.na(y)]),
on = "mo",
..property][[1]]
on = "mo",
..property][[1]]
}
if (any(is.na(y))) {
y[is.na(y)] <- reference_data_to_use[prevalence == 3][data.table(mo = x[is.na(y)]),
on = "mo",
..property][[1]]
on = "mo",
..property][[1]]
}
x <- y
@ -441,13 +441,13 @@ exec_as.mo <- function(x,
y <- reference_data_to_use[prevalence == 1][data.table(fullname_lower = tolower(x)), on = "fullname_lower", ..property][[1]]
if (any(is.na(y))) {
y[is.na(y)] <- reference_data_to_use[prevalence == 2][data.table(fullname_lower = tolower(x[is.na(y)])),
on = "fullname_lower",
..property][[1]]
on = "fullname_lower",
..property][[1]]
}
if (any(is.na(y))) {
y[is.na(y)] <- reference_data_to_use[prevalence == 3][data.table(fullname_lower = tolower(x[is.na(y)])),
on = "fullname_lower",
..property][[1]]
on = "fullname_lower",
..property][[1]]
}
x <- y
@ -548,7 +548,7 @@ exec_as.mo <- function(x,
x[nchar(x_backup_without_spp) > 10] <- gsub("[+]", paste0("+[", constants, "]?"), x[nchar(x_backup_without_spp) > 10])
}
x <- strip_whitespace(x, dyslexia_mode)
x_trimmed <- x
x_trimmed_species <- paste(x_trimmed, "species")
x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed)
@ -1067,9 +1067,9 @@ exec_as.mo <- function(x,
ref_old = found[1, ref],
ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
mo = microorganismsDT[col_id == found[1, col_id_new], mo])
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
# if (initial_search == TRUE) {
# set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
# }
return(x[i])
}
@ -1099,7 +1099,7 @@ exec_as.mo <- function(x,
message("Running '", d.x_withspaces_start_end, "' and '", e.x_withspaces_start_only, "'")
}
found <- data.old_to_check[fullname_lower %like_case% d.x_withspaces_start_end
| fullname_lower %like_case% e.x_withspaces_start_only]
| fullname_lower %like_case% e.x_withspaces_start_only]
if (NROW(found) > 0 & nchar(g.x_backup_without_spp) >= 6) {
if (property == "ref") {
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
@ -1119,9 +1119,9 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = microorganismsDT[col_id == found[1, col_id_new], mo]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(x, property), 1, force = force_mo_history, disable = disable_mo_history)
}
# if (initial_search == TRUE) {
# set_mo_history(a.x_backup, get_mo_code(x, property), 1, force = force_mo_history, disable = disable_mo_history)
# }
return(x)
}
@ -1520,7 +1520,7 @@ exec_as.mo <- function(x,
# THEN TRY PREVALENT IN HUMAN INFECTIONS ----
x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 2],
data.old_to_check = microorganisms.oldDT[prevalence %in% c(2, 3)], # run all other old MOs the second time,
# otherwise e.g. mo_ref("Chlamydia psittaci") doesn't work correctly
# otherwise e.g. mo_ref("Chlamydia psittaci") doesn't work correctly
a.x_backup = x_backup[i],
b.x_trimmed = x_trimmed[i],
c.x_trimmed_without_group = x_trimmed_without_group[i],
@ -1931,12 +1931,12 @@ print.mo_renamed <- function(x, ...) {
}
for (i in 1:nrow(x)) {
message(blue(paste0("NOTE: ",
italic(x$old_name[i]), ifelse(x$old_ref[i] %in% c("", NA), "",
paste0(" (", gsub("et al.", italic("et al."), x$old_ref[i]), ")")),
" was renamed ",
italic(x$new_name[i]), ifelse(x$new_ref[i] %in% c("", NA), "",
paste0(" (", gsub("et al.", italic("et al."), x$new_ref[i]), ")")),
" [", x$mo[i], "]")))
italic(x$old_name[i]), ifelse(x$old_ref[i] %in% c("", NA), "",
paste0(" (", gsub("et al.", italic("et al."), x$old_ref[i]), ")")),
" was renamed ",
italic(x$new_name[i]), ifelse(x$new_ref[i] %in% c("", NA), "",
paste0(" (", gsub("et al.", italic("et al."), x$new_ref[i]), ")")),
" [", x$mo[i], "]")))
}
}