Browse Source

as.mo improvement

new-mo-algorithm
parent
commit
e18a1f1f17
  1. 5
      .gitlab-ci.yml
  2. 111
      R/mo.R
  3. 28
      R/mo_history.R
  4. 3
      man/as.mo.Rd
  5. 2
      tests/testthat/test-mo_history.R

5
.gitlab-ci.yml

@ -86,7 +86,10 @@ coverage: @@ -86,7 +86,10 @@ coverage:
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
- Rscript -e 'print("${codecov_token}")'
- Rscript -e 'print("$codecov_token")'
- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "$codecov_token"); cat("Code coverage:", covr::percent_coverage(cc))'
- Rscript -e 'print("$${codecov_token}")'
- Rscript -e 'print("$$codecov_token")'
- echo $codecov_token
- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "$$codecov_token"); cat("Code coverage:", covr::percent_coverage(cc))'
coverage: '/Code coverage: \d+\.\d+/'
pages:

111
R/mo.R

@ -57,7 +57,8 @@ @@ -57,7 +57,8 @@
#'
#' Use the \code{\link{mo_property}_*} functions to get properties based on the returned code, see Examples.
#'
#' All IDs that are found with zero uncertainty are saved to a local file (\code{"~/.Rhistory_mo"}) to improve speed for every next time. Use \code{clean_mo_history()} to delete this file, which resets the algorithms. Only previous results will be used from this version of the \code{AMR} package, since the taxonomic tree may change in the future for any organism.
#' \strong{Self-learning algoritm} \cr
#' The \code{as.mo()} function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use \code{clean_mo_history()} to reset the algorithms. Only experience from your current \code{AMR} package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge. Usually, any guess after the first try runs 90-95\% faster than the first try. The algorithm saves its previous findings to \code{~/.Rhistory_mo}.
#'
#' \strong{Intelligent rules} \cr
#' This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:
@ -218,7 +219,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, @@ -218,7 +219,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
y <- x
} else if (sum(is.na(mo_hist)) == 0
} else if (!any(is.na(mo_hist))
& isFALSE(Becker)
& isFALSE(Lancefield)) {
# check previously found results
@ -242,13 +243,8 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, @@ -242,13 +243,8 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
on = "fullname_lower",
"mo"][[1]]
}
# save them too
mo_hist <- read_mo_history(force = isTRUE(list(...)$force_mo_history))
if (any(!x %in% mo_hist$x)) {
for (i in 1:length(y)) {
set_mo_history(x[i], y[i], force = isTRUE(list(...)$force_mo_history))
}
}
# save them to history
set_mo_history(x, y, force = isTRUE(list(...)$force_mo_history))
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
@ -271,13 +267,16 @@ is.mo <- function(x) { @@ -271,13 +267,16 @@ is.mo <- function(x) {
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
#' @importFrom data.table data.table as.data.table setkey
#' @importFrom crayon magenta red blue silver italic has_color
# param property a column name of AMR::microorganisms
# param initial_search logical - is FALSE when coming from uncertain tries, which uses exec_as.mo internally too
# param force_mo_history logical - whether found result must be saved with set_mo_history (default FALSE on non-interactive sessions)
exec_as.mo <- function(x,
Becker = FALSE,
Lancefield = FALSE,
allow_uncertain = TRUE,
reference_df = get_mo_source(),
property = "mo",
clear_options = TRUE,
initial_search = TRUE,
force_mo_history = FALSE) {
if (!"AMR" %in% base::.packages()) {
@ -285,7 +284,7 @@ exec_as.mo <- function(x, @@ -285,7 +284,7 @@ exec_as.mo <- function(x,
# check onLoad() in R/zzz.R: data tables are created there.
}
if (clear_options == TRUE) {
if (initial_search == TRUE) {
options(mo_failures = NULL)
options(mo_uncertainties = NULL)
options(mo_renamed = NULL)
@ -401,6 +400,10 @@ exec_as.mo <- function(x, @@ -401,6 +400,10 @@ exec_as.mo <- function(x,
}
x <- y
} else if (all(x %in% read_mo_history(force = force_mo_history)$x)) {
# previously found code
x <- microorganismsDT[data.table(mo = get_mo_history(x, force = force_mo_history)), on = "mo", ..property][[1]]
} else if (all(tolower(x) %in% microorganismsDT$fullname_lower)) {
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
@ -420,6 +423,9 @@ exec_as.mo <- function(x, @@ -420,6 +423,9 @@ exec_as.mo <- function(x,
} else if (all(toupper(x) %in% AMR::microorganisms.codes$code)) {
# commonly used MO codes
y <- as.data.table(AMR::microorganisms.codes)[data.table(code = toupper(x)), on = "code", ]
# save them to history
set_mo_history(x, y$mo, force = force_mo_history)
x <- microorganismsDT[data.table(mo = y[["mo"]]), on = "mo", ..property][[1]]
} else if (!all(x %in% AMR::microorganisms[, property])) {
@ -503,7 +509,7 @@ exec_as.mo <- function(x, @@ -503,7 +509,7 @@ exec_as.mo <- function(x,
# most probable: is exact match in fullname
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -517,6 +523,9 @@ exec_as.mo <- function(x, @@ -517,6 +523,9 @@ exec_as.mo <- function(x,
if (tolower(x_backup_without_spp[i]) %in% c("other", "none", "unknown")) {
# empty and nonsense values, ignore without warning
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
@ -531,7 +540,7 @@ exec_as.mo <- function(x, @@ -531,7 +540,7 @@ exec_as.mo <- function(x,
# return first genus that begins with x_trimmed, e.g. when "E. spp."
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -541,6 +550,9 @@ exec_as.mo <- function(x, @@ -541,6 +550,9 @@ exec_as.mo <- function(x,
# fewer than 3 chars and not looked for species, add as failure
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
failures <- c(failures, x_backup[i])
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
@ -548,6 +560,9 @@ exec_as.mo <- function(x, @@ -548,6 +560,9 @@ exec_as.mo <- function(x,
# there is no fullname like virus, so don't try to coerce it
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
failures <- c(failures, x_backup[i])
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
@ -555,14 +570,14 @@ exec_as.mo <- function(x, @@ -555,14 +570,14 @@ exec_as.mo <- function(x,
if (!is.na(x_trimmed[i])) {
if (toupper(x_backup_without_spp[i]) %in% c('MRSA', 'MSSA', 'VISA', 'VRSA')) {
x[i] <- microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c('MRSE', 'MSSE')) {
x[i] <- microorganismsDT[mo == 'B_STPHY_EPI', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -570,14 +585,14 @@ exec_as.mo <- function(x, @@ -570,14 +585,14 @@ exec_as.mo <- function(x,
if (toupper(x_backup_without_spp[i]) == "VRE"
| x_backup_without_spp[i] %like% '(enterococci|enterokok|enterococo)[a-z]*?$') {
x[i] <- microorganismsDT[mo == 'B_ENTRC', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c("EHEC", "EPEC", "EIEC", "STEC", "ATEC")) {
x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -585,7 +600,7 @@ exec_as.mo <- function(x, @@ -585,7 +600,7 @@ exec_as.mo <- function(x,
if (toupper(x_backup_without_spp[i]) == 'MRPA') {
# multi resistant P. aeruginosa
x[i] <- microorganismsDT[mo == 'B_PSDMN_AER', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -594,7 +609,7 @@ exec_as.mo <- function(x, @@ -594,7 +609,7 @@ exec_as.mo <- function(x,
| toupper(x_backup_without_spp[i]) == 'CRSM') {
# co-trim resistant S. maltophilia
x[i] <- microorganismsDT[mo == 'B_STNTR_MAL', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -602,7 +617,7 @@ exec_as.mo <- function(x, @@ -602,7 +617,7 @@ exec_as.mo <- function(x,
if (toupper(x_backup_without_spp[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x[i] <- microorganismsDT[mo == 'B_STRPT_PNE', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -610,7 +625,7 @@ exec_as.mo <- function(x, @@ -610,7 +625,7 @@ exec_as.mo <- function(x,
if (x_backup_without_spp[i] %like% '^G[ABCDFGHK]S$') {
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRB)
x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPT_GR\\1", x_backup_without_spp[i], ignore.case = TRUE), ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -618,7 +633,7 @@ exec_as.mo <- function(x, @@ -618,7 +633,7 @@ exec_as.mo <- function(x,
if (x_backup_without_spp[i] %like% '(streptococ|streptokok).* [ABCDFGHK]$') {
# Streptococci in different languages, like "estreptococos grupo B"
x[i] <- microorganismsDT[mo == gsub(".*(streptococ|streptokok|estreptococ).* ([ABCDFGHK])$", "B_STRPT_GR\\2", x_backup_without_spp[i], ignore.case = TRUE), ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -626,7 +641,7 @@ exec_as.mo <- function(x, @@ -626,7 +641,7 @@ exec_as.mo <- function(x,
if (x_backup_without_spp[i] %like% 'group [ABCDFGHK] (streptococ|streptokok|estreptococ)') {
# Streptococci in different languages, like "Group A Streptococci"
x[i] <- microorganismsDT[mo == gsub(".*group ([ABCDFGHK]) (streptococ|streptokok|estreptococ).*", "B_STRPT_GR\\1", x_backup_without_spp[i], ignore.case = TRUE), ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -637,7 +652,7 @@ exec_as.mo <- function(x, @@ -637,7 +652,7 @@ exec_as.mo <- function(x,
| x_backup_without_spp[i] %like% '[ck]o?ns[^a-z]?$') {
# coerce S. coagulase negative
x[i] <- microorganismsDT[mo == 'B_STPHY_CNS', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -647,7 +662,7 @@ exec_as.mo <- function(x, @@ -647,7 +662,7 @@ exec_as.mo <- function(x,
| x_backup_without_spp[i] %like% '[ck]o?ps[^a-z]?$') {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -657,7 +672,7 @@ exec_as.mo <- function(x, @@ -657,7 +672,7 @@ exec_as.mo <- function(x,
| x_trimmed[i] %like% 'gram[ -]?neg.*') {
# coerce Gram negatives
x[i] <- microorganismsDT[mo == 'B_GRAMN', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -667,7 +682,7 @@ exec_as.mo <- function(x, @@ -667,7 +682,7 @@ exec_as.mo <- function(x,
| x_trimmed[i] %like% 'gram[ -]?pos.*') {
# coerce Gram positives
x[i] <- microorganismsDT[mo == 'B_GRAMP', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -676,7 +691,7 @@ exec_as.mo <- function(x, @@ -676,7 +691,7 @@ exec_as.mo <- function(x,
if (x_backup_without_spp[i] %like% "Salmonella group") {
# Salmonella Group A to Z, just return S. species for now
x[i] <- microorganismsDT[mo == 'B_SLMNL', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
options(mo_renamed = c(getOption("mo_renamed"),
@ -688,7 +703,7 @@ exec_as.mo <- function(x, @@ -688,7 +703,7 @@ exec_as.mo <- function(x,
} else {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
options(mo_renamed = c(getOption("mo_renamed"),
@ -708,7 +723,7 @@ exec_as.mo <- function(x, @@ -708,7 +723,7 @@ exec_as.mo <- function(x,
found <- microorganismsDT[fullname_lower %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -717,7 +732,7 @@ exec_as.mo <- function(x, @@ -717,7 +732,7 @@ exec_as.mo <- function(x,
found <- microorganismsDT[fullname_lower %like% paste0("^", unregex(x_backup_without_spp[i]), "[a-z]+"), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -732,7 +747,7 @@ exec_as.mo <- function(x, @@ -732,7 +747,7 @@ exec_as.mo <- function(x,
mo_found <- AMR::microorganisms.codes[toupper(x_backup[i]) == AMR::microorganisms.codes[, 1], "mo"][1L]
if (length(mo_found) > 0) {
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -755,6 +770,9 @@ exec_as.mo <- function(x, @@ -755,6 +770,9 @@ exec_as.mo <- function(x,
if (nchar(x_backup_without_spp[i]) < 4) {
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
failures <- c(failures, x_backup[i])
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
@ -836,7 +854,7 @@ exec_as.mo <- function(x, @@ -836,7 +854,7 @@ exec_as.mo <- function(x,
f.x_withspaces_end_only = x_withspaces_end_only[i],
g.x_backup_without_spp = x_backup_without_spp[i])
if (!empty_result(x[i])) {
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -851,7 +869,7 @@ exec_as.mo <- function(x, @@ -851,7 +869,7 @@ exec_as.mo <- function(x,
f.x_withspaces_end_only = x_withspaces_end_only[i],
g.x_backup_without_spp = x_backup_without_spp[i])
if (!empty_result(x[i])) {
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -866,7 +884,7 @@ exec_as.mo <- function(x, @@ -866,7 +884,7 @@ exec_as.mo <- function(x,
f.x_withspaces_end_only = x_withspaces_end_only[i],
g.x_backup_without_spp = x_backup_without_spp[i])
if (!empty_result(x[i])) {
if (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -892,7 +910,7 @@ exec_as.mo <- function(x, @@ -892,7 +910,7 @@ 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 (property == "mo") {
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
@ -938,7 +956,7 @@ exec_as.mo <- function(x, @@ -938,7 +956,7 @@ exec_as.mo <- function(x,
}
# (2) not yet implemented taxonomic changes in Catalogue of Life ----
found <- suppressMessages(suppressWarnings(exec_as.mo(TEMPORARY_TAXONOMY(b.x_trimmed), clear_options = FALSE, allow_uncertain = FALSE)))
found <- suppressMessages(suppressWarnings(exec_as.mo(TEMPORARY_TAXONOMY(b.x_trimmed), initial_search = FALSE, allow_uncertain = FALSE)))
if (!empty_result(found)) {
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
@ -972,7 +990,7 @@ exec_as.mo <- function(x, @@ -972,7 +990,7 @@ exec_as.mo <- function(x,
# (4) strip values between brackets ----
a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup)
a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped))
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_stripped, clear_options = FALSE, allow_uncertain = FALSE)))
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_stripped, initial_search = FALSE, allow_uncertain = FALSE)))
if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) {
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
@ -990,7 +1008,7 @@ exec_as.mo <- function(x, @@ -990,7 +1008,7 @@ exec_as.mo <- function(x,
for (i in 1:(length(x_strip) - 1)) {
x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ")
if (nchar(x_strip_collapsed) >= 4) {
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE, allow_uncertain = FALSE)))
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE)))
if (!empty_result(found)) {
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
@ -1012,7 +1030,7 @@ exec_as.mo <- function(x, @@ -1012,7 +1030,7 @@ exec_as.mo <- function(x,
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
for (i in 2:(length(x_strip))) {
x_strip_collapsed <- paste(x_strip[i:length(x_strip)], collapse = " ")
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE, allow_uncertain = FALSE)))
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE)))
if (!empty_result(found)) {
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
@ -1059,12 +1077,15 @@ exec_as.mo <- function(x, @@ -1059,12 +1077,15 @@ exec_as.mo <- function(x,
# not found ----
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
failures <- c(failures, x_backup[i])
if (property == "mo" & initial_search == TRUE) {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
}
}
# failures
failures <- failures[!failures %in% c(NA, NULL, NaN)]
if (length(failures) > 0 & clear_options == TRUE) {
# handling failures ----
failures <- x_input[x == "UNKNOWN"] # failures[!failures %in% c(NA, NULL, NaN)]
if (length(failures) > 0 & initial_search == TRUE) {
options(mo_failures = sort(unique(failures)))
plural <- c("value", "it", "was")
if (n_distinct(failures) > 1) {
@ -1083,8 +1104,8 @@ exec_as.mo <- function(x, @@ -1083,8 +1104,8 @@ exec_as.mo <- function(x,
call. = FALSE,
immediate. = TRUE) # thus will always be shown, even if >= warnings
}
# uncertainties
if (NROW(uncertainties) > 0 & clear_options == TRUE) {
# handling uncertainties ----
if (NROW(uncertainties) > 0 & initial_search == TRUE) {
options(mo_uncertainties = as.list(distinct(uncertainties, input, .keep_all = TRUE)))
plural <- c("value", "it")

28
R/mo_history.R

@ -20,17 +20,22 @@ @@ -20,17 +20,22 @@
# ==================================================================== #
# print successful as.mo coercions to file, not uncertain ones
#' @importFrom dplyr %>% filter
#' @importFrom dplyr distinct
set_mo_history <- function(x, mo, force = FALSE) {
file_location <- base::path.expand('~/.Rhistory_mo')
if ((base::interactive() & mo != "UNKNOWN") | force == TRUE) {
if (base::interactive() | force == TRUE) {
mo_hist <- read_mo_history(force = force)
if (NROW(mo_hist[base::which(mo_hist$x == x & mo_hist$package_version == utils::packageVersion("AMR")),]) == 0) {
base::write(x = c(x, mo, base::as.character(utils::packageVersion("AMR"))),
file = file_location,
ncolumns = 3,
append = TRUE,
sep = "\t")
df <- distinct(data.frame(x, mo, stringsAsFactors = FALSE), x, .keep_all = TRUE)
x <- df$x
mo <- df$mo
for (i in 1:length(x)) {
if (NROW(mo_hist[base::which(mo_hist$x == x[i] & mo_hist$package_version == utils::packageVersion("AMR")),]) == 0) {
base::write(x = c(x[i], mo[i], base::as.character(utils::packageVersion("AMR"))),
file = file_location,
ncolumns = 3,
append = TRUE,
sep = "\t")
}
}
}
return(base::invisible())
@ -47,6 +52,7 @@ get_mo_history <- function(x, force = FALSE) { @@ -47,6 +52,7 @@ get_mo_history <- function(x, force = FALSE) {
}
}
#' @importFrom dplyr %>% filter distinct
read_mo_history <- function(force = FALSE) {
file_location <- base::path.expand('~/.Rhistory_mo')
if (!base::file.exists(file_location) | (!base::interactive() & force == FALSE)) {
@ -58,9 +64,11 @@ read_mo_history <- function(force = FALSE) { @@ -58,9 +64,11 @@ read_mo_history <- function(force = FALSE) {
col.names = c("x", "mo", "package_version"),
stringsAsFactors = FALSE)
# Below: filter on current package version.
# Future fullnames may even be replaced by new taxonomic names, so new versions of
# Even current fullnames may be replaced by new taxonomic names, so new versions of
# the Catalogue of Life must not lead to data corruption.
file_read[base::which(file_read$package_version == utils::packageVersion("AMR")), c("x", "mo")]
file_read %>%
filter(package_version == utils::packageVersion("AMR")) %>%
distinct(x, mo, .keep_all = TRUE)
}
#' @rdname as.mo

3
man/as.mo.Rd

@ -68,7 +68,8 @@ Values that cannot be coered will be considered 'unknown' and have an MO code \c @@ -68,7 +68,8 @@ Values that cannot be coered will be considered 'unknown' and have an MO code \c
Use the \code{\link{mo_property}_*} functions to get properties based on the returned code, see Examples.
All IDs that are found with zero uncertainty are saved to a local file (\code{"~/.Rhistory_mo"}) to improve speed for every next time. Use \code{clean_mo_history()} to delete this file, which resets the algorithms. Only previous results will be used from this version of the \code{AMR} package, since the taxonomic tree may change in the future for any organism.
\strong{Self-learning algoritm} \cr
The \code{as.mo()} function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use \code{clean_mo_history()} to reset the algorithms. Only experience from your current \code{AMR} package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge. Usually, any guess after the first try runs 90-95\% faster than the first try. The algorithm saves its previous findings to \code{~/.Rhistory_mo}.
\strong{Intelligent rules} \cr
This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:

2
tests/testthat/test-mo_history.R

@ -30,5 +30,5 @@ test_that("mo_history works", { @@ -30,5 +30,5 @@ test_that("mo_history works", {
expect_equal(get_mo_history("testsubject", force = TRUE),
"B_ESCHR_COL")
expect_equal(colnames(read_mo_history(force = TRUE)),
c("x", "mo"))
c("x", "mo", "package_version"))
})

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