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(v0.7.1.9076) mo codes

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dr. M.S. (Matthijs) Berends
2019-09-20 12:33:05 +02:00
parent e2aa4f996b
commit 3596adb295
41 changed files with 465 additions and 520 deletions
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53
R/mo.R
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@ -1065,30 +1065,33 @@ exec_as.mo <- function(x,
}
# MISCELLANEOUS ----
# look for old taxonomic names ----
found <- microorganisms.oldDT[fullname_lower == tolower(a.x_backup)
| fullname_lower %like_case% d.x_withspaces_start_end,]
if (NROW(found) > 0) {
col_id_new <- found[1, col_id_new]
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
# mo_ref("Chlamydia psittaci") = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci") = "Everett et al., 1999"
if (property == "ref") {
x[i] <- found[1, ref]
} else {
x[i] <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
# wait until prevalence == 2 to run the old taxonomic results on both prevalence == 1 and prevalence == 2
if (nrow(data_to_check) == nrow(microorganismsDT[prevalence == 2])) {
found <- microorganisms.oldDT[fullname_lower == tolower(a.x_backup)
| fullname_lower %like_case% d.x_withspaces_start_end,]
if (NROW(found) > 0) {
col_id_new <- found[1, col_id_new]
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
# mo_ref("Chlamydia psittaci") = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci") = "Everett et al., 1999"
if (property == "ref") {
x[i] <- found[1, ref]
} else {
x[i] <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
}
options(mo_renamed_last_run = found[1, fullname])
was_renamed(name_old = found[1, fullname],
name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
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)
}
return(x[i])
}
options(mo_renamed_last_run = found[1, fullname])
was_renamed(name_old = found[1, fullname],
name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
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)
}
return(x[i])
}
# check for uncertain results ----
@ -1851,7 +1854,7 @@ as.data.frame.mo <- function(x, ...) {
"[<-.mo" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
class_integrity_check(y, "microbial code", c(as.character(AMR::microorganisms$mo), as.character(microorganisms.translation$mo_old)))
class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo), as.character(microorganisms.translation$mo_old)))
}
#' @exportMethod [[<-.mo
#' @export
@ -1859,7 +1862,7 @@ as.data.frame.mo <- function(x, ...) {
"[[<-.mo" <- function(i, j, ..., value) {
y <- NextMethod()
attributes(y) <- attributes(i)
class_integrity_check(y, "microbial code", c(as.character(AMR::microorganisms$mo), as.character(microorganisms.translation$mo_old)))
class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo), as.character(microorganisms.translation$mo_old)))
}
#' @exportMethod c.mo
#' @export
@ -1867,7 +1870,7 @@ as.data.frame.mo <- function(x, ...) {
c.mo <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
class_integrity_check(y, "microbial code", c(as.character(AMR::microorganisms$mo), as.character(microorganisms.translation$mo_old)))
class_integrity_check(y, "microorganism code", c(as.character(AMR::microorganisms$mo), as.character(microorganisms.translation$mo_old)))
}
#' @rdname as.mo