(v0.9.0.9018) Remove mo_history

v1.8.2
parent 1b80773c22
commit f152ab9a48
  1. 4
      DESCRIPTION
  2. 3
      NAMESPACE
  3. 5
      NEWS.md
  4. 2
      R/ab.R
  5. 5
      R/ab_property.R
  6. 216
      R/mo.R
  7. 200
      R/mo_history.R
  8. 4
      cran-comments.md
  9. 2
      docs/404.html
  10. 2
      docs/LICENSE-text.html
  11. BIN
      docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
  12. BIN
      docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png
  13. 2
      docs/articles/index.html
  14. 2
      docs/authors.html
  15. 2
      docs/index.html
  16. 13
      docs/reference/as.mo.html
  17. 2
      docs/reference/example_isolates.html
  18. 4
      docs/reference/index.html
  19. 2
      docs/reference/microorganisms.html
  20. 2
      docs/reference/mo_property.html
  21. 2
      docs/reference/rsi_translation.html
  22. 1
      inst/mo_history/mo_history.csv
  23. 14
      man/as.mo.Rd
  24. 4
      tests/testthat/test-mo.R
  25. 38
      vignettes/benchmarks.Rmd

@ -1,6 +1,6 @@
Package: AMR
Version: 0.9.0.9017
Date: 2020-01-27
Version: 0.9.0.9018
Date: 2020-01-31
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

@ -86,7 +86,6 @@ export(availability)
export(brmo)
export(bug_drug_combinations)
export(catalogue_of_life_version)
export(clear_mo_history)
export(count_I)
export(count_IR)
export(count_R)
@ -329,5 +328,3 @@ importFrom(tidyr,pivot_wider)
importFrom(utils,adist)
importFrom(utils,browseURL)
importFrom(utils,menu)
importFrom(utils,read.csv)
importFrom(utils,write.csv)

@ -1,5 +1,5 @@
# AMR 0.9.0.9017
## <small>Last updated: 27-Jan-2020</small>
# AMR 0.9.0.9018
## <small>Last updated: 31-Jan-2020</small>
### New
* Support for LOINC and SNOMED codes
@ -24,6 +24,7 @@
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2019 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
### Changes
* The `as.mo()` function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the function `clear_mo_history()` was removed.
* Bugfix for some WHONET microorganism codes that were not interpreted correctly when using `as.rsi()`
* Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae*
* Better support for determination of *Salmonella* biovars

@ -327,7 +327,7 @@ as.ab <- function(x, ...) {
#' @rdname as.ab
#' @export
is.ab <- function(x) {
identical(class(x), "ab")
inherits(x, "ab")
}
#' @exportMethod print.ab

@ -197,11 +197,6 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
}
ab_validate <- function(x, property, ...) {
if (!"AMR" %in% base::.packages()) {
library("AMR")
# check onLoad() in R/zzz.R: data tables are created there.
}
# try to catch an error when inputting an invalid parameter
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% AMR::antibiotics[1, property],

216
R/mo.R

@ -98,14 +98,6 @@
#' Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is *Aspergillus*, *Bacteroides*, *Candida*, *Capnocytophaga*, *Chryseobacterium*, *Cryptococcus*, *Elisabethkingia*, *Flavobacterium*, *Fusobacterium*, *Giardia*, *Leptotrichia*, *Mycoplasma*, *Prevotella*, *Rhodotorula*, *Treponema*, *Trichophyton* or *Ureaplasma*.
#'
#' Group 3 (least prevalent microorganisms) consists of all other microorganisms.
#'
#' ## Self-learning algorithm
#'
#' The [as.mo()] function gains experience from previously determined microorganism IDs and learns from it. This drastically improves both speed and reliability. Use [clear_mo_history()] to reset the algorithms. Only experience from your current `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 80-95% faster than the first try.
#'
#' This resets with every update of this `AMR` package since results are saved to your local package library folder.
#' @inheritSection catalogue_of_life Catalogue of Life
# (source as a section here, so it can be inherited by other man pages:)
#' @section Source:
@ -189,11 +181,7 @@ as.mo <- function(x,
x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
mo_hist <- get_mo_history(x,
uncertainty_level,
force = isTRUE(list(...)$force_mo_history),
disable = isTRUE(list(...)$disable_mo_history))
if (mo_source_isvalid(reference_df)
& isFALSE(Becker)
& isFALSE(Lancefield)
@ -225,12 +213,6 @@ as.mo <- function(x,
& isFALSE(Lancefield)) {
y <- x
} else if (!any(is.na(mo_hist))
& isFALSE(Becker)
& isFALSE(Lancefield)) {
# check previously found results
y <- mo_hist
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
y <- mo_validate(x = x, property = "mo",
@ -249,7 +231,7 @@ to_class_mo <- function(x) {
#' @rdname as.mo
#' @export
is.mo <- function(x) {
identical(class(x), class(to_class_mo(x)))
inherits(x, "mo")
}
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
@ -259,8 +241,6 @@ is.mo <- function(x) {
# 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 dyslexia_mode logical - also check for characters that resemble others
# param force_mo_history logical - whether found result must be saved with set_mo_history (default FALSE on non-interactive sessions)
# param disable_mo_history logical - whether set_mo_history and get_mo_history should be ignored
# param debug logical - show different lookup texts while searching
# param reference_data_to_use data.frame - the data set to check for
exec_as.mo <- function(x,
@ -271,8 +251,6 @@ exec_as.mo <- function(x,
property = "mo",
initial_search = TRUE,
dyslexia_mode = FALSE,
force_mo_history = FALSE,
disable_mo_history = getOption("AMR_disable_mo_history", FALSE),
debug = FALSE,
reference_data_to_use = microorganismsDT) {
@ -408,19 +386,6 @@ exec_as.mo <- function(x,
}
x <- y
} else if (all(toupper(x) %in% read_mo_history(uncertainty_level,
force = force_mo_history,
disable = disable_mo_history)$x)) {
# previously found code
x <- data.frame(mo = get_mo_history(x,
uncertainty_level,
force = force_mo_history,
disable = disable_mo_history),
stringsAsFactors = FALSE) %>%
left_join(AMR::microorganisms, by = "mo") %>%
pull(property)
} else if (all(tolower(x) %in% reference_data_to_use$fullname_lower)) {
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
@ -432,8 +397,6 @@ exec_as.mo <- function(x,
# 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$mo, 0, force = force_mo_history, disable = disable_mo_history)
x <- reference_data_to_use[data.table(mo = y[["mo"]]),
on = "mo",
@ -447,7 +410,6 @@ exec_as.mo <- function(x,
y <- reference_data_to_use[data.table(mo = y),
on = "mo",
..property][[1]]
# don't save to history, as all items are already in microorganisms.translation
x <- y
} else if (!all(x %in% AMR::microorganisms[, property])) {
@ -592,19 +554,6 @@ exec_as.mo <- function(x,
}
}
mo_hist <- get_mo_history(x_backup[i], uncertainty_level, force = force_mo_history, disable = disable_mo_history)
if (initial_search == TRUE & !any(is.na(mo_hist))) {
# previously found code
found <- data.frame(mo = mo_hist,
stringsAsFactors = FALSE) %>%
left_join(reference_data_to_use, by = "mo") %>%
pull(property)
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
if (x_backup[i] %like_case% "\\(unknown [a-z]+\\)") {
x[i] <- "UNKNOWN"
next
@ -625,7 +574,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
# don't save to history, as all items are already in microorganisms.translation
next
}
}
@ -636,7 +584,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
# don't save to history, as all items are already in microorganisms.codes
next
}
}
@ -646,9 +593,6 @@ exec_as.mo <- function(x,
# most probable: is exact match in fullname
if (length(found) > 0) {
x[i] <- found[1L]
if (initial_search == TRUE) {
# don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
}
next
}
@ -664,7 +608,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
# don't save to history, as all items are already in microorganisms
next
}
}
@ -675,9 +618,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -686,9 +626,6 @@ exec_as.mo <- function(x,
# is a valid Catalogue of Life ID
if (NROW(found) > 0) {
x[i] <- found[1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -698,9 +635,6 @@ exec_as.mo <- function(x,
if (length(mo_found) > 0) {
x[i] <- microorganismsDT[mo == mo_found,
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
}
@ -729,9 +663,6 @@ exec_as.mo <- function(x,
# empty and nonsense values, ignore without warning
x[i] <- microorganismsDT[mo == "UNKNOWN",
..property][[1]]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -743,7 +674,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (initial_search == TRUE) {
failures <- c(failures, x_backup[i])
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -760,18 +690,12 @@ exec_as.mo <- function(x,
| x_backup_without_spp[i] %like_case% " (mrsa|mssa|visa|vrsa) ") {
x[i] <- microorganismsDT[mo == "B_STPHY_AURS",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c("MRSE", "MSSE")
| x_backup_without_spp[i] %like_case% " (mrse|msse) ") {
x[i] <- microorganismsDT[mo == "B_STPHY_EPDR",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) == "VRE"
@ -779,9 +703,6 @@ exec_as.mo <- function(x,
| x_backup_without_spp[i] %like_case% "(enterococci|enterokok|enterococo)[a-z]*?$") {
x[i] <- microorganismsDT[mo == "B_ENTRC",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
# support for:
@ -801,9 +722,6 @@ exec_as.mo <- function(x,
| x_backup_without_spp[i] %like_case% "o?(26|103|104|111|121|145|157)") {
x[i] <- microorganismsDT[mo == "B_ESCHR_COLI",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) == "MRPA"
@ -811,18 +729,12 @@ exec_as.mo <- function(x,
# multi resistant P. aeruginosa
x[i] <- microorganismsDT[mo == "B_PSDMN_ARGN",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) == "CRSM") {
# co-trim resistant S. maltophilia
x[i] <- microorganismsDT[mo == "B_STNTR_MLTP",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c("PISP", "PRSP", "VISP", "VRSP")
@ -830,45 +742,30 @@ exec_as.mo <- function(x,
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x[i] <- microorganismsDT[mo == "B_STRPT_PNMN",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "^g[abcdfghk]s$") {
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
x[i] <- microorganismsDT[mo == toupper(gsub("g([abcdfghk])s", "B_STRPT_GRP\\1", x_backup_without_spp[i])),
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "(streptococ|streptokok).* [abcdfghk]$") {
# Streptococci in different languages, like "estreptococos grupo B"
x[i] <- microorganismsDT[mo == toupper(gsub(".*(streptococ|streptokok|estreptococ).* ([abcdfghk])$", "B_STRPT_GRP\\2", x_backup_without_spp[i])),
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "group [abcdfghk] (streptococ|streptokok|estreptococ)") {
# Streptococci in different languages, like "Group A Streptococci"
x[i] <- microorganismsDT[mo == toupper(gsub(".*group ([abcdfghk]) (streptococ|streptokok|estreptococ).*", "B_STRPT_GRP\\1", x_backup_without_spp[i])),
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "haemoly.*strept") {
# Haemolytic streptococci in different languages
x[i] <- microorganismsDT[mo == "B_STRPT_HAEM",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
@ -878,9 +775,6 @@ exec_as.mo <- function(x,
# coerce S. coagulase negative
x[i] <- microorganismsDT[mo == "B_STPHY_CONS",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "[ck]oagulas[ea] positie?[vf]"
@ -889,9 +783,6 @@ exec_as.mo <- function(x,
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == "B_STPHY_COPS",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
# streptococcal groups: milleri and viridans
@ -901,9 +792,6 @@ exec_as.mo <- function(x,
# Milleri Group Streptococcus (MGS)
x[i] <- microorganismsDT[mo == "B_STRPT_MILL",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_trimmed[i] %like_case% "strepto.* viridans"
@ -912,9 +800,6 @@ exec_as.mo <- function(x,
# Viridans Group Streptococcus (VGS)
x[i] <- microorganismsDT[mo == "B_STRPT_VIRI",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "gram[ -]?neg.*"
@ -923,9 +808,6 @@ exec_as.mo <- function(x,
# coerce Gram negatives
x[i] <- microorganismsDT[mo == "B_GRAMN",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "gram[ -]?pos.*"
@ -934,18 +816,12 @@ exec_as.mo <- function(x,
# coerce Gram positives
x[i] <- microorganismsDT[mo == "B_GRAMP",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (x_backup_without_spp[i] %like_case% "mycoba[ck]teri.[nm]?$") {
# coerce Gram positives
x[i] <- microorganismsDT[mo == "B_MYCBC",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -954,9 +830,6 @@ exec_as.mo <- function(x,
# Salmonella Group A to Z, just return S. species for now
x[i] <- microorganismsDT[mo == "B_SLMNL",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE) &
!x_backup[i] %like% "t[iy](ph|f)[iy]") {
@ -964,9 +837,6 @@ exec_as.mo <- function(x,
# except for S. typhi, S. paratyphi, S. typhimurium
x[i] <- microorganismsDT[mo == "B_SLMNL_ENTR",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
uncertainties <- rbind(uncertainties,
format_uncertainty_as_df(uncertainty_level = 1,
input = x_backup[i],
@ -980,27 +850,18 @@ exec_as.mo <- function(x,
# coerce Neisseria meningitidis
x[i] <- microorganismsDT[mo == "B_NESSR_MNNG",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if ("gonococcus" %like_case% x_trimmed[i]) {
# coerce Neisseria gonorrhoeae
x[i] <- microorganismsDT[mo == "B_NESSR_GNRR",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if ("pneumococcus" %like_case% x_trimmed[i]) {
# coerce Streptococcus penumoniae
x[i] <- microorganismsDT[mo == "B_STRPT_PNMN",
..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
}
@ -1026,9 +887,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
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])
}
if (nchar(g.x_backup_without_spp) >= 6) {
@ -1036,9 +894,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
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])
}
}
@ -1051,7 +906,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (initial_search == TRUE) {
failures <- c(failures, a.x_backup)
set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
return(x[i])
}
@ -1145,7 +999,6 @@ 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])
# no set history on renames
return(x[i])
}
@ -1196,7 +1049,6 @@ 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]))
# no set history on renames
return(x)
}
@ -1222,9 +1074,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 1, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
}
@ -1251,9 +1100,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(x, property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(x)
}
}
@ -1282,9 +1128,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
@ -1310,9 +1153,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
@ -1345,9 +1185,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
}
@ -1378,9 +1215,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
}
@ -1399,9 +1233,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
if (b.x_trimmed %like_case% "(fungus|fungi)" & !b.x_trimmed %like_case% "fungiphrya") {
@ -1413,9 +1244,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
# (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
@ -1445,9 +1273,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
}
@ -1484,9 +1309,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 3, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
}
@ -1516,9 +1338,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
}
@ -1541,9 +1360,6 @@ exec_as.mo <- function(x,
format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
input = a.x_backup,
result_mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 3, force = force_mo_history, disable = disable_mo_history)
}
return(found[1L])
}
}
@ -1564,7 +1380,6 @@ exec_as.mo <- function(x,
g.x_backup_without_spp = g.x_backup_without_spp,
uncertain.reference_data_to_use = microorganismsDT[prevalence %in% c(1, 2)])
if (!empty_result(x[i])) {
# no set_mo_history here - it is already set in uncertain_fn()
return(x[i])
}
} else if (nrow(data_to_check) == nrow(microorganismsDT[prevalence == 3])) {
@ -1576,7 +1391,6 @@ exec_as.mo <- function(x,
g.x_backup_without_spp = g.x_backup_without_spp,
uncertain.reference_data_to_use = microorganismsDT[prevalence == 3])
if (!empty_result(x[i])) {
# no set_mo_history here - it is already set in uncertain_fn()
return(x[i])
}
}
@ -1598,9 +1412,6 @@ exec_as.mo <- function(x,
h.x_species = x_species[i],
i.x_trimmed_species = x_trimmed_species[i])
if (!empty_result(x[i])) {
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -1618,9 +1429,6 @@ exec_as.mo <- function(x,
h.x_species = x_species[i],
i.x_trimmed_species = x_trimmed_species[i])
if (!empty_result(x[i])) {
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -1637,9 +1445,6 @@ exec_as.mo <- function(x,
h.x_species = x_species[i],
i.x_trimmed_species = x_trimmed_species[i])
if (!empty_result(x[i])) {
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
@ -1648,7 +1453,6 @@ exec_as.mo <- function(x,
..property][[1]]
if (initial_search == TRUE) {
failures <- c(failures, x_backup[i])
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
}
}
@ -2071,22 +1875,6 @@ unregex <- function(x) {
gsub("[^a-zA-Z0-9 -]", "", x)
}
get_mo_code <- function(x, property) {
if (property == "mo") {
unique(x)
} else if (property == "snomed") {
found <- unlist(lapply(microorganismsDT$snomed,
function(s) if (any(x %in% s, na.rm = TRUE)) {
TRUE
} else {
FALSE
}))
microorganismsDT$mo[found == TRUE]
} else {
microorganismsDT[get(property) == x, "mo"][[1]]
}
}
translate_allow_uncertain <- function(allow_uncertain) {
if (isTRUE(allow_uncertain)) {
# default to uncertainty level 2

@ -1,200 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
# print successful as.mo coercions to a options entry
#' @inheritSection lifecycle Stable lifecycle
#' @importFrom dplyr %>% distinct filter
#' @importFrom utils write.csv
set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FALSE) {
if (isTRUE(disable)) {
return(base::invisible())
}
# don't save codes that are in a code data set already
mo <- mo[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
x <- x[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
warning_new_write <- FALSE
if (base::interactive() | force == TRUE) {
mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
distinct(x, .keep_all = TRUE) %>%
filter(!is.na(x) & !is.na(mo))
if (nrow(df) == 0) {
return(base::invisible())
}
x <- toupper(df$x)
mo <- df$mo
for (i in seq_len(length(x))) {
# save package version too, as both the as.mo() algorithm and the reference data set may change
if (NROW(mo_hist[base::which(mo_hist$x == x[i] &
mo_hist$uncertainty_level >= uncertainty_level &
mo_hist$package_version == utils::packageVersion("AMR")), ]) == 0) {
if (is.null(mo_hist) & interactive()) {
warning_new_write <- TRUE
}
tryCatch(write.csv(rbind(mo_hist,
data.frame(
x = x[i],
mo = mo[i],
uncertainty_level = uncertainty_level,
package_version = base::as.character(utils::packageVersion("AMR")),
stringsAsFactors = FALSE)),
row.names = FALSE,
file = mo_history_file()),
error = function(e) {
warning_new_write <- FALSE; base::invisible()
})
}
}
}
if (warning_new_write == TRUE) {
message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
}
return(base::invisible())
}
get_mo_history <- function(x, uncertainty_level, force = FALSE, disable = FALSE) {
if (isTRUE(disable)) {
return(to_class_mo(NA))
}
history <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
if (base::is.null(history)) {
result <- NA
} else {
result <- data.frame(x = as.character(toupper(x)), stringsAsFactors = FALSE) %>%
left_join(history, by = "x") %>%
pull(mo)
}
to_class_mo(result)
}
#' @importFrom dplyr %>% filter distinct
#' @importFrom utils read.csv
read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE, disable = FALSE) {
if (isTRUE(disable)) {
return(NULL)
}
if ((!base::interactive() & force == FALSE)) {
return(NULL)
}
uncertainty_level_param <- uncertainty_level
history <- tryCatch(read.csv(mo_history_file(), stringsAsFactors = FALSE),
warning = function(w) invisible(),
error = function(e) NULL)
if (is.null(history)) {
return(NULL)
}
# Below: filter on current package version.
# Even current fullnames may be replaced by new taxonomic names, so new versions of
# the Catalogue of Life must not lead to data corruption.
if (unfiltered == FALSE) {
history <- history %>%
filter(package_version == as.character(utils::packageVersion("AMR")),
# only take unknowns if uncertainty_level_param is higher
((mo == "UNKNOWN" & uncertainty_level_param == uncertainty_level) |
(mo != "UNKNOWN" & uncertainty_level_param >= uncertainty_level))) %>%
arrange(desc(uncertainty_level)) %>%
distinct(x, mo, .keep_all = TRUE)
}
if (nrow(history) == 0) {
NULL
} else {
history
}
}
#' @rdname as.mo
#' @importFrom crayon red
#' @importFrom utils menu
#' @export
clear_mo_history <- function(...) {
if (!is.null(read_mo_history())) {
if (interactive() & !isTRUE(list(...)$force)) {
q <- menu(title = paste("This will clear all",
format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
"previously determined microbial IDs. Are you sure?"),
choices = c("Yes", "No"),
graphics = FALSE)
if (q != 1) {
return(invisible())
}
}
success <- create_blank_mo_history()
if (!isFALSE(success)) {
cat(red(paste("File", mo_history_file(), "cleared.")))
}
}
}
#' @importFrom utils write.csv
create_blank_mo_history <- function() {
tryCatch(
write.csv(x = data.frame(x = character(0),
mo = character(0),
uncertainty_level = integer(0),
package_version = character(0),
stringsAsFactors = FALSE),
row.names = FALSE,
file = mo_history_file()),
warning = function(w) invisible(),
error = function(e) TRUE)
}
# Borrowed all below code from the extrafont package,
# https://github.com/wch/extrafont/blob/254c3f99b02f11adb59affbda699a92aec8624f5/R/utils.r
inst_path <- function() {
envname <- environmentName(parent.env(environment()))
# If installed in package, envname == "AMR"
# If loaded with load_all, envname == "package:AMR"
# (This is kind of strange)
if (envname == "AMR") {
system.file(package = "AMR")
} else {
srcfile <- attr(attr(inst_path, "srcref"), "srcfile")
file.path(dirname(dirname(srcfile$filename)), "inst")
}
}
# Get the path where extrafontdb is installed
db_path <- function() {
system.file(package = "AMR")
}
# fonttable file
mo_history_file <- function() {
file.path(mo_history_path(), "mo_history.csv")
}
# Path of fontmap directory
mo_history_path <- function() {
file.path(db_path(), "mo_history")
}

@ -1,7 +1,5 @@
# Version 0.9.0
# Version 0.10.0
* For this specific version, nothing to mention.
* Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.
* Since version 0.8.0, this package writes lines to `[library path]/AMR/mo_history/mo_history.csv` when using the `as.mo()` function, in the exact same way (and borrowed from) the `extrafont` package on CRAN (version 0.17) writes to the user library path. Users are notified about this with a `message()`, and staged install on R >= 3.6.0 still works. The CSV file is never newly created or deleted by this package, it only changes this file to improve speed and reliability of the `as.mo()` function. See the source code of functions `set_mo_history()` and `clear_mo_history()` in file `R/mo_history.R`.

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -45,7 +45,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>
@ -252,9 +252,7 @@
<span class='fu'>mo_uncertainties</span>()
<span class='fu'>mo_renamed</span>()
<span class='fu'>clear_mo_history</span>(<span class='no'>...</span>)</pre>
<span class='fu'>mo_renamed</span>()</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -353,13 +351,6 @@
<p>Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is <em>Aspergillus</em>, <em>Bacteroides</em>, <em>Candida</em>, <em>Capnocytophaga</em>, <em>Chryseobacterium</em>, <em>Cryptococcus</em>, <em>Elisabethkingia</em>, <em>Flavobacterium</em>, <em>Fusobacterium</em>, <em>Giardia</em>, <em>Leptotrichia</em>, <em>Mycoplasma</em>, <em>Prevotella</em>, <em>Rhodotorula</em>, <em>Treponema</em>, <em>Trichophyton</em> or <em>Ureaplasma</em>.</p>
<p>Group 3 (least prevalent microorganisms) consists of all other microorganisms.</p>
<h3>Self-learning algorithm</h3>
<p>The <code>as.mo()</code> function gains experience from previously determined microorganism IDs and learns from it. This drastically improves both speed and reliability. Use <code>clear_mo_history()</code> to reset the algorithms. Only experience from your current <code>AMR</code> 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.</p>
<p>Usually, any guess after the first try runs 80-95% faster than the first try.</p>
<p>This resets with every update of this <code>AMR</code> package since results are saved to your local package library folder.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>
@ -266,7 +266,7 @@
</tr><tr>
<td>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">clear_mo_history()</a></code> </p>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
</td>
<td><p>Transform to microorganism ID</p></td>
</tr><tr>

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -85,7 +85,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9018</span>
</span>
</div>

@ -1 +0,0 @@
"x","mo","uncertainty_level","package_version"
unable to load file from head commit

@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo.R, R/mo_history.R
% Please edit documentation in R/mo.R
\name{as.mo}
\alias{as.mo}
\alias{mo}
@ -7,7 +7,6 @@
\alias{mo_failures}
\alias{mo_uncertainties}
\alias{mo_renamed}
\alias{clear_mo_history}
\title{Transform to microorganism ID}
\usage{
as.mo(
@ -26,8 +25,6 @@ mo_failures()
mo_uncertainties()
mo_renamed()
clear_mo_history(...)
}
\arguments{
\item{x}{a character vector or a \code{\link{data.frame}} with one or two columns}
@ -122,15 +119,6 @@ Group 2 consists of all microorganisms where the taxonomic phylum is Proteobacte