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(v0.7.1.9083) LIS code improvement
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Package: AMR
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Version: 0.7.1.9082
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Version: 0.7.1.9083
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Date: 2019-09-23
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.1.9082
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# AMR 0.7.1.9083
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<small>Last updated: 23-Sep-2019</small>
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### Breaking
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64
R/mo.R
64
R/mo.R
@ -490,8 +490,8 @@ exec_as.mo <- function(x,
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x_backup[grepl("^(fungus|fungi)$", x)] <- "F_FUNGUS" # will otherwise become the kingdom
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# remove spp and species
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x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x, ignore.case = TRUE)
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x <- gsub("(spp.?|ssp.?|subsp.?|subspecies|biovar|serovar|species)", "", x, ignore.case = TRUE)
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x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x)
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x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x)
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x <- strip_whitespace(x, dyslexia_mode)
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x_backup_without_spp <- x
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@ -582,7 +582,7 @@ exec_as.mo <- function(x,
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progress$tick()$print()
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mo_hist <- get_mo_history(x, uncertainty_level, force = force_mo_history, disable = disable_mo_history)
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mo_hist <- get_mo_history(x_backup[i], uncertainty_level, force = force_mo_history, disable = disable_mo_history)
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if (initial_search == TRUE & !any(is.na(mo_hist))) {
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# previously found code
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found <- data.frame(mo = mo_hist,
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@ -638,6 +638,29 @@ exec_as.mo <- function(x,
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next
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}
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# WHONET and other common LIS codes
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if (any(toupper(c(x_backup[i], x_backup_without_spp[i])) %in% AMR::microorganisms.codes$code)) {
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mo_found <- AMR::microorganisms.codes[which(AMR::microorganisms.codes$code %in% toupper(c(x_backup[i], x_backup_without_spp[i]))), "mo"][1L]
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if (length(mo_found) > 0) {
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x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
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if (initial_search == TRUE) {
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
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}
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next
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}
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}
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if (!is.null(reference_df)) {
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# self-defined reference
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if (x_backup[i] %in% reference_df[, 1]) {
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ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"]
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if (ref_mo %in% data_to_check[, mo]) {
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x[i] <- data_to_check[mo == ref_mo, ..property][[1]][1L]
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next
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} else {
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warning("Value '", x_backup[i], "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE)
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}
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}
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}
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# WHONET: xxx = no growth
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if (tolower(as.character(paste0(x_backup_without_spp[i], ""))) %in% c("", "xxx", "na", "nan")) {
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@ -688,13 +711,6 @@ exec_as.mo <- function(x,
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x[i] <- NA_character_
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next
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}
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# x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
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# if (initial_search == TRUE) {
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# failures <- c(failures, x_backup[i])
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# set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
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# }
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# next
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# }
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# translate known trivial abbreviations to genus + species ----
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if (!is.na(x_trimmed[i])) {
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@ -961,32 +977,7 @@ exec_as.mo <- function(x,
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# rest of genus only is in allow_uncertain part.
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}
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# TRY OTHER SOURCES ----
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# WHONET and other common LIS codes
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if (toupper(a.x_backup) %in% AMR::microorganisms.codes[, 1]) {
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mo_found <- AMR::microorganisms.codes[toupper(a.x_backup) == AMR::microorganisms.codes[, 1], "mo"][1L]
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if (length(mo_found) > 0) {
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x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
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if (initial_search == TRUE) {
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set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
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}
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return(x[i])
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}
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}
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if (!is.null(reference_df)) {
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# self-defined reference
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if (a.x_backup %in% reference_df[, 1]) {
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ref_mo <- reference_df[reference_df[, 1] == a.x_backup, "mo"]
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if (ref_mo %in% data_to_check[, mo]) {
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x[i] <- data_to_check[mo == ref_mo, ..property][[1]][1L]
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return(x[i])
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} else {
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warning("Value '", a.x_backup, "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE)
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}
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}
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}
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# allow no codes less than 4 characters long, was already checked for WHONET above
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# allow no codes less than 4 characters long, was already checked for WHONET earlier
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if (nchar(g.x_backup_without_spp) < 4) {
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x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
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if (initial_search == TRUE) {
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@ -1565,7 +1556,6 @@ exec_as.mo <- function(x,
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next
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}
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# no results found: make them UNKNOWN ----
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x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
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if (initial_search == TRUE) {
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@ -27,6 +27,10 @@ set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FA
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return(base::invisible())
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}
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# don't save codes that are in a code data set already
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mo <- mo[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
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x <- x[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
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if (base::interactive() | force == TRUE) {
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mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
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warning_new_write <- FALSE
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Binary file not shown.
@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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@ -225,9 +225,9 @@
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</div>
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<div id="amr-0-7-1-9082" class="section level1">
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<div id="amr-0-7-1-9083" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9082" class="anchor"></a>AMR 0.7.1.9082<small> Unreleased </small>
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<a href="#amr-0-7-1-9083" class="anchor"></a>AMR 0.7.1.9083<small> Unreleased </small>
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</h1>
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<p><small>Last updated: 23-Sep-2019</small></p>
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<div id="breaking" class="section level3">
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@ -1280,7 +1280,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-7-1-9082">0.7.1.9082</a></li>
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<li><a href="#amr-0-7-1-9083">0.7.1.9083</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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<li><a href="#amr-0-6-1">0.6.1</a></li>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9081</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9082</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9083</span>
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</span>
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</div>
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