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(v1.4.0.9030) as.mo() fix for known lab codes

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  1. 4
      DESCRIPTION
  2. 6
      NEWS.md
  3. 6
      R/aa_helper_functions.R
  4. 2
      R/eucast_rules.R
  5. 2
      R/first_isolate.R
  6. 18
      R/guess_ab_col.R
  7. 58
      R/mo.R
  8. 9
      R/mo_property.R
  9. 4
      R/rsi.R
  10. 2
      docs/404.html
  11. 2
      docs/LICENSE-text.html
  12. 79
      docs/articles/benchmarks.html
  13. BIN
      docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png
  14. 2
      docs/articles/index.html
  15. 2
      docs/authors.html
  16. 2
      docs/index.html
  17. 14
      docs/news/index.html
  18. 2
      docs/pkgdown.yml
  19. 2
      docs/reference/AMR-deprecated.html
  20. 2
      docs/reference/age.html
  21. 2
      docs/reference/age_groups.html
  22. 2
      docs/reference/antibiotic_class_selectors.html
  23. 2
      docs/reference/as.disk.html
  24. 2
      docs/reference/as.mo.html
  25. 2
      docs/reference/as.rsi.html
  26. 2
      docs/reference/bug_drug_combinations.html
  27. 2
      docs/reference/first_isolate.html
  28. 2
      docs/reference/ggplot_pca.html
  29. 2
      docs/reference/ggplot_rsi.html
  30. 4
      docs/reference/guess_ab_col.html
  31. 2
      docs/reference/index.html
  32. 2
      docs/reference/intrinsic_resistant.html
  33. 2
      docs/reference/is_new_episode.html
  34. 2
      docs/reference/key_antibiotics.html
  35. 2
      docs/reference/like.html
  36. 2
      docs/reference/mo_matching_score.html
  37. 2
      docs/reference/mo_property.html
  38. 2
      docs/survey.html
  39. 2
      man/guess_ab_col.Rd
  40. 2
      tests/testthat/test-data.R

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.4.0.9029
Date: 2020-12-01
Version: 1.4.0.9030
Date: 2020-12-03
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

6
NEWS.md

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
# AMR 1.4.0.9029
## <small>Last updated: 1 December 2020</small>
# AMR 1.4.0.9030
## <small>Last updated: 3 December 2020</small>
### New
* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:
@ -30,6 +30,8 @@ @@ -30,6 +30,8 @@
* Fix for using parameter `reference_df` in `as.mo()` and `mo_*()` functions that contain old microbial codes (from previous package versions)
* Fix for using `as.rsi()` on a data.frame in older R versions
* `as.rsi()` on a data.frame will not print a message anymore if the values are already clean R/SI values
* Fixed a bug where `mo_uncertainties()` would not return the results based on the MO matching score
* Fixed a bug where `as.mo()` would not return results for known laboratory codes for microorganisms
### Other
* All messages and warnings thrown by this package now break sentences on whole words

6
R/aa_helper_functions.R

@ -146,7 +146,7 @@ search_type_in_df <- function(x, type, info = TRUE) { @@ -146,7 +146,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
# WHONET support
found <- sort(colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"])[1]
if (!any(class(pm_pull(x, found)) %in% c("Date", "POSIXct"))) {
stop(font_red(paste0("ERROR: Found column `", font_bold(found), "` to be used as input for `col_", type,
stop(font_red(paste0("Found column '", font_bold(found), "' to be used as input for `col_", type,
"`, but this column contains no valid dates. Transform its values to valid dates first.")),
call. = FALSE)
}
@ -178,7 +178,7 @@ search_type_in_df <- function(x, type, info = TRUE) { @@ -178,7 +178,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
if (!is.null(found)) {
# this column should contain logicals
if (!is.logical(x[, found, drop = TRUE])) {
message_("Column `", font_bold(found), "` found as input for `col_", type,
message_("Column '", font_bold(found), "' found as input for `col_", type,
"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.",
add_fn = font_red)
found <- NULL
@ -187,7 +187,7 @@ search_type_in_df <- function(x, type, info = TRUE) { @@ -187,7 +187,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
}
if (!is.null(found) & info == TRUE) {
msg <- paste0("Using column `", font_bold(found), "` as input for `col_", type, "`.")
msg <- paste0("Using column '", found, "' as input for `col_", type, "`.")
if (type %in% c("keyantibiotics", "specimen")) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
}

2
R/eucast_rules.R

@ -454,7 +454,7 @@ eucast_rules <- function(x, @@ -454,7 +454,7 @@ eucast_rules <- function(x,
if (ab_missing(AMP) & !ab_missing(AMX)) {
# ampicillin column is missing, but amoxicillin is available
if (info == TRUE) {
message_("Using column `", font_bold(AMX), "` as input for ampicillin since many EUCAST rules depend on it.")
message_("Using column '", font_bold(AMX), "' as input for ampicillin since many EUCAST rules depend on it.")
}
AMP <- AMX
}

2
R/first_isolate.R

@ -209,7 +209,7 @@ first_isolate <- function(x, @@ -209,7 +209,7 @@ first_isolate <- function(x,
# WHONET support
x$patient_id <- paste(x$`First name`, x$`Last name`, x$Sex)
col_patient_id <- "patient_id"
message_("Using combined columns `", font_bold("First name"), "`, `", font_bold("Last name"), "` and `", font_bold("Sex"), "` as input for `col_patient_id`")
message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
} else {
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
}

18
R/guess_ab_col.R

@ -44,7 +44,7 @@ @@ -44,7 +44,7 @@
#' # [1] "tetr"
#'
#' guess_ab_col(df, "J01AA07", verbose = TRUE)
#' # NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).
#' # NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).
#' # [1] "tetr"
#'
#' # WHONET codes
@ -94,16 +94,16 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) { @@ -94,16 +94,16 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
if (length(ab_result) == 0) {
if (verbose == TRUE) {
message_("No column found as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
message_("No column found as input for ", search_string,
" (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
add_fn = font_black,
as_note = FALSE)
}
return(NULL)
} else {
if (verbose == TRUE) {
message_("Using column `", font_bold(ab_result), "` as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")
message_("Using column '", font_bold(ab_result), "' as input for ", search_string,
" (", ab_name(search_string, language = NULL, tolower = TRUE), ").")
}
return(ab_result)
}
@ -204,12 +204,12 @@ get_column_abx <- function(x, @@ -204,12 +204,12 @@ get_column_abx <- function(x,
for (i in seq_len(length(x))) {
if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message_("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
message_("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
" (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
}
if (info == TRUE & names(x[i]) %in% names(duplicates)) {
warning_(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
warning_(paste0("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
" (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns."),
add_fn = font_red,
call = FALSE,

58
R/mo.R

@ -636,9 +636,7 @@ exec_as.mo <- function(x, @@ -636,9 +636,7 @@ exec_as.mo <- function(x,
}
# WHONET and other common LIS codes ----
found <- lookup(code %in% toupper(c(x_backup_untouched[i], x_backup[i], x_backup_without_spp[i])),
column = "mo",
haystack = microorganisms.codes)
found <- microorganisms.codes[which(microorganisms.codes$code %in% toupper(c(x_backup_untouched[i], x_backup[i], x_backup_without_spp[i]))), "mo", drop = TRUE][1L]
if (!is.na(found)) {
x[i] <- lookup(mo == found)
next
@ -893,10 +891,12 @@ exec_as.mo <- function(x, @@ -893,10 +891,12 @@ exec_as.mo <- function(x,
}
# try any match keeping spaces ----
found <- lookup(fullname_lower %like_case% d.x_withspaces_start_end,
haystack = data_to_check)
if (!is.na(found) & nchar(g.x_backup_without_spp) >= 6) {
return(found[1L])
if (nchar(g.x_backup_without_spp) >= 6) {
found <- lookup(fullname_lower %like_case% d.x_withspaces_start_end,
haystack = data_to_check)
if (!is.na(found)) {
return(found[1L])
}
}
# try any match keeping spaces, not ending with $ ----
@ -905,10 +905,12 @@ exec_as.mo <- function(x, @@ -905,10 +905,12 @@ exec_as.mo <- function(x,
if (!is.na(found)) {
return(found[1L])
}
found <- lookup(fullname_lower %like_case% e.x_withspaces_start_only,
haystack = data_to_check)
if (!is.na(found) & nchar(g.x_backup_without_spp) >= 6) {
return(found[1L])
if (nchar(g.x_backup_without_spp) >= 6) {
found <- lookup(fullname_lower %like_case% e.x_withspaces_start_only,
haystack = data_to_check)
if (!is.na(found)) {
return(found[1L])
}
}
# try any match keeping spaces, not start with ^ ----
@ -919,14 +921,16 @@ exec_as.mo <- function(x, @@ -919,14 +921,16 @@ exec_as.mo <- function(x,
}
# try a trimmed version
found <- lookup(fullname_lower %like_case% b.x_trimmed |
fullname_lower %like_case% c.x_trimmed_without_group,
haystack = data_to_check)
if (!is.na(found) & nchar(g.x_backup_without_spp) >= 6) {
return(found[1L])
if (nchar(g.x_backup_without_spp) >= 6) {
found <- lookup(fullname_lower %like_case% b.x_trimmed |
fullname_lower %like_case% c.x_trimmed_without_group,
haystack = data_to_check)
if (!is.na(found)) {
return(found[1L])
}
}
# try splitting of characters in the middle and then find ID ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
@ -1313,14 +1317,16 @@ exec_as.mo <- function(x, @@ -1313,14 +1317,16 @@ exec_as.mo <- function(x,
if (isTRUE(debug)) {
message("Running '", f.x_withspaces_end_only, "'")
}
found <- lookup(fullname_lower %like_case% f.x_withspaces_end_only, column = "mo")
if (!is.na(found) & nchar(g.x_backup_without_spp) >= 6) {
found_result <- lookup(mo == found)
uncertainties <<- rbind(uncertainties,
attr(found, which = "uncertainties", exact = TRUE),
stringsAsFactors = FALSE)
found <- lookup(mo == found)
return(found)
if (nchar(g.x_backup_without_spp) >= 6) {
found <- lookup(fullname_lower %like_case% f.x_withspaces_end_only, column = "mo")
if (!is.na(found)) {
found_result <- lookup(mo == found)
uncertainties <<- rbind(uncertainties,
attr(found, which = "uncertainties", exact = TRUE),
stringsAsFactors = FALSE)
found <- lookup(mo == found)
return(found)
}
}
}

9
R/mo_property.R

@ -383,9 +383,10 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) { @@ -383,9 +383,10 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
ab <- rep(ab, length(x))
}
if (length(x) != length(ab)) {
stop_("length of 'x' and 'ab' must be equal, or one of them must be of length 1.")
stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
}
# this saves about 50% in calculation time
intrinsic_to_check <- intrinsic_resistant[which(intrinsic_resistant$microorganism %in% x |
intrinsic_resistant$antibiotic %in% ab), , drop = FALSE]
paste(x, ab) %in% paste(intrinsic_to_check$microorganism, intrinsic_to_check$antibiotic)
@ -618,12 +619,12 @@ find_mo_col <- function(fn) { @@ -618,12 +619,12 @@ find_mo_col <- function(fn) {
mo <- suppressMessages(search_type_in_df(df, "mo"))
}, silent = TRUE)
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
message_("Using column `", font_bold(mo), "` as input for ", fn, "()")
message_("Using column '", font_bold(mo), "' as input for ", fn, "()")
return(df[, mo, drop = TRUE])
} else {
stop_("Argument 'x' is missing and no column with info about microorganisms could be found.", call = -2)
stop_("Argument `x` is missing and no column with info about microorganisms could be found.", call = -2)
}
} else {
stop_("Argument 'x' is missing.", call = -2)
stop_("Argument `x` is missing.", call = -2)
}
}

4
R/rsi.R

@ -1087,11 +1087,11 @@ check_reference_data <- function(reference_data) { @@ -1087,11 +1087,11 @@ check_reference_data <- function(reference_data) {
class_rsi <- sapply(rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))
class_ref <- sapply(reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
if (!all(names(class_rsi) == names(class_ref))) {
stop_("'reference_data' must have the same column names as the 'rsi_translation' data set.", call = -2)
stop_("`reference_data` must have the same column names as the 'rsi_translation' data set.", call = -2)
}
if (!all(class_rsi == class_ref)) {
class_rsi[class_rsi != class_ref][1]
stop_("'reference_data' must be the same structure as the 'rsi_translation' data set. Column '", names(class_ref[class_rsi != class_ref][1]), "' is of class ", class_ref[class_rsi != class_ref][1], ", but should be of class ", class_rsi[class_rsi != class_ref][1], ".", call = -2)
stop_("`reference_data` must be the same structure as the 'rsi_translation' data set. Column '", names(class_ref[class_rsi != class_ref][1]), "' is of class ", class_ref[class_rsi != class_ref][1], ", but should be of class ", class_rsi[class_rsi != class_ref][1], ".", call = -2)
}
}
}

2
docs/404.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/LICENSE-text.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

79
docs/articles/benchmarks.html

@ -39,7 +39,7 @@ @@ -39,7 +39,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>
@ -187,8 +187,7 @@ @@ -187,8 +187,7 @@
</header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><link href="benchmarks_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
<script src="benchmarks_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
</header><script src="benchmarks_files/header-attrs-2.4/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Benchmarks</h1>
@ -228,20 +227,20 @@ @@ -228,20 +227,20 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 26.0 26.0 50.0 26.0 26.0 180</span>
<span class="co"># as.mo("stau") 430.0 430.0 470.0 440.0 490.0 630</span>
<span class="co"># as.mo("STAU") 430.0 440.0 470.0 500.0 500.0 500</span>
<span class="co"># as.mo("staaur") 26.0 26.0 32.0 26.0 26.0 76</span>
<span class="co"># as.mo("STAAUR") 26.0 26.0 44.0 26.0 81.0 83</span>
<span class="co"># as.mo("S. aureus") 60.0 60.0 77.0 61.0 110.0 120</span>
<span class="co"># as.mo("S aureus") 60.0 61.0 94.0 110.0 120.0 120</span>
<span class="co"># as.mo("Staphylococcus aureus") 4.1 4.1 9.6 4.1 4.2 59</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 2200.0 2200.0 2200.0 2200.0 2300.0 2300</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 760.0 800.0 810.0 800.0 810.0 840</span>
<span class="co"># as.mo("MRSA") 26.0 26.0 37.0 26.0 26.0 83</span>
<span class="co"># as.mo("VISA") 42.0 42.0 59.0 42.0 92.0 97</span>
<span class="co"># as.mo("VRSA") 42.0 42.0 68.0 67.0 92.0 97</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 11.0 12 16.0 14.0 15.0 40.0</span>
<span class="co"># as.mo("stau") 110.0 120 140.0 140.0 150.0 160.0</span>
<span class="co"># as.mo("STAU") 110.0 120 140.0 140.0 140.0 150.0</span>
<span class="co"># as.mo("staaur") 12.0 13 20.0 15.0 16.0 45.0</span>
<span class="co"># as.mo("STAAUR") 15.0 15 26.0 16.0 41.0 58.0</span>
<span class="co"># as.mo("S. aureus") 31.0 35 50.0 59.0 62.0 65.0</span>
<span class="co"># as.mo("S aureus") 27.0 33 59.0 59.0 62.0 160.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.9 2 2.4 2.4 2.7 2.9</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 910.0 960 980.0 970.0 1000.0 1100.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 400.0 410 430.0 420.0 440.0 560.0</span>
<span class="co"># as.mo("MRSA") 12.0 13 19.0 15.0 15.0 42.0</span>
<span class="co"># as.mo("VISA") 20.0 22 31.0 24.0 47.0 54.0</span>
<span class="co"># as.mo("VRSA") 22.0 23 35.0 24.0 52.0 56.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@ -285,8 +284,8 @@ @@ -285,8 +284,8 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 308 326 399 331 370 676 10</span></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.331 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 165 176 223 202 274 318 10</span></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.202 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -299,11 +298,11 @@ @@ -299,11 +298,11 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 16.20 16.20 18.60 17.90 18.90 28.00 10</span>
<span class="co"># B 50.90 51.10 57.70 51.20 53.10 108.00 10</span>
<span class="co"># C 3.58 3.72 4.03 4.06 4.14 4.91 10</span></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0041 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.83 8.05 9.56 9.43 10.90 12.90 10</span>
<span class="co"># B 23.50 24.40 30.20 25.50 26.80 74.50 10</span>
<span class="co"># C 2.00 2.19 2.42 2.41 2.56 3.06 10</span></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0024 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@ -317,14 +316,14 @@ @@ -317,14 +316,14 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 3.62 3.62 3.66 3.64 3.67 3.80 10</span>
<span class="co"># B 3.57 3.59 3.68 3.64 3.72 4.01 10</span>
<span class="co"># C 3.63 3.64 3.65 3.64 3.67 3.71 10</span>
<span class="co"># D 3.57 3.58 3.62 3.61 3.67 3.69 10</span>
<span class="co"># E 3.56 3.57 3.60 3.59 3.60 3.68 10</span>
<span class="co"># F 3.55 3.58 3.73 3.65 3.85 4.01 10</span>
<span class="co"># G 3.54 3.56 3.62 3.58 3.61 3.93 10</span>
<span class="co"># H 3.53 3.57 3.59 3.58 3.63 3.66 10</span></pre></div>
<span class="co"># A 1.69 1.75 1.90 1.86 2.00 2.25 10</span>
<span class="co"># B 1.69 1.72 1.86 1.79 1.87 2.43 10</span>
<span class="co"># C 1.67 1.75 1.89 1.81 1.93 2.67 10</span>
<span class="co"># D 1.64 1.73 1.87 1.87 1.94 2.23 10</span>
<span class="co"># E 1.65 1.75 1.90 1.83 1.92 2.35 10</span>
<span class="co"># F 1.70 1.75 1.87 1.85 1.93 2.20 10</span>
<span class="co"># G 1.73 1.83 1.93 1.93 2.01 2.25 10</span>
<span class="co"># H 1.65 1.73 1.85 1.77 2.06 2.11 10</span></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -351,14 +350,14 @@ @@ -351,14 +350,14 @@
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 35.85 36.13 41.92 36.29 36.84 318.20 100</span>
<span class="co"># de 42.37 42.67 45.11 42.91 43.19 95.04 100</span>
<span class="co"># nl 70.13 70.65 75.92 70.95 71.50 140.20 100</span>
<span class="co"># es 42.16 42.46 46.88 42.64 43.20 95.37 100</span>
<span class="co"># it 41.85 42.24 46.84 42.40 42.84 95.92 100</span>
<span class="co"># fr 42.13 42.53 48.41 42.71 43.27 95.21 100</span>
<span class="co"># pt 42.25 42.47 48.56 42.71 43.12 96.60 100</span></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 16.23 16.62 21.00 17.00 18.51 59.06 100</span>
<span class="co"># de 19.27 19.96 22.73 20.36 21.08 69.70 100</span>
<span class="co"># nl 31.40 32.54 38.76 33.16 35.34 82.43 100</span>
<span class="co"># es 19.36 19.75 23.61 20.26 20.88 67.39 100</span>
<span class="co"># it 19.24 19.64 21.23 20.00 20.72 62.92 100</span>
<span class="co"># fr 19.19 19.82 25.12 20.16 21.49 70.00 100</span>
<span class="co"># pt 19.18 19.64 22.44 20.23 21.47 60.56 100</span></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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2
docs/articles/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/authors.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/index.html

@ -43,7 +43,7 @@ @@ -43,7 +43,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

14
docs/news/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>
@ -236,13 +236,13 @@ @@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409029" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9029">
<a href="#amr-1409029" class="anchor"></a>AMR 1.4.0.9029<small> Unreleased </small>
<div id="amr-1409030" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9030">
<a href="#amr-1409030" class="anchor"></a>AMR 1.4.0.9030<small> Unreleased </small>
</h1>
<div id="last-updated-1-december-2020" class="section level2">
<div id="last-updated-3-december-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-1-december-2020" class="anchor"></a><small>Last updated: 1 December 2020</small>
<a href="#last-updated-3-december-2020" class="anchor"></a><small>Last updated: 3 December 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -284,6 +284,8 @@ @@ -284,6 +284,8 @@
<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame in older R versions</li>
<li>
<code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame will not print a message anymore if the values are already clean R/SI values</li>
<li>Fixed a bug where <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> would not return the results based on the MO matching score</li>
<li>Fixed a bug where <code><a href="../reference/as.mo.html">as.mo()</a></code> would not return results for known laboratory codes for microorganisms</li>
</ul>
</div>
<div id="other" class="section level3">

2
docs/pkgdown.yml

@ -12,7 +12,7 @@ articles: @@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-12-01T15:59Z
last_built: 2020-12-03T15:56Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/AMR-deprecated.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/age.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/age_groups.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/antibiotic_class_selectors.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/as.disk.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/as.mo.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/as.rsi.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/first_isolate.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/ggplot_pca.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

4
docs/reference/guess_ab_col.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>
@ -290,7 +290,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s @@ -290,7 +290,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># [1] "tetr"</span>
<span class='fu'>guess_ab_col</span><span class='op'>(</span><span class='va'>df</span>, <span class='st'>"J01AA07"</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='co'># NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).</span>
<span class='co'># NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).</span>
<span class='co'># [1] "tetr"</span>
<span class='co'># WHONET codes</span>

2
docs/reference/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/intrinsic_resistant.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/is_new_episode.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/key_antibiotics.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/like.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/mo_matching_score.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/reference/mo_property.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
docs/survey.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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">1.4.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
</span>
</div>

2
man/guess_ab_col.Rd

@ -45,7 +45,7 @@ guess_ab_col(df, "J01AA07") # ATC code of tetracycline @@ -45,7 +45,7 @@ guess_ab_col(df, "J01AA07") # ATC code of tetracycline
# [1] "tetr"
guess_ab_col(df, "J01AA07", verbose = TRUE)
# NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).
# NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).
# [1] "tetr"
# WHONET codes

2
tests/testthat/test-data.R

@ -40,6 +40,8 @@ test_that("data sets are valid", { @@ -40,6 +40,8 @@ test_that("data sets are valid", {
expect_true(all(example_isolates$mo %in% microorganisms$mo))
expect_true(all(microorganisms.translation$mo_new %in% microorganisms$mo))
expect_true(all(rsi_translation$mo %in% microorganisms$mo))
expect_true(all(intrinsic_resistant$microorganism %in% microorganisms$fullname)) # also important for mo_is_intrinsic_resistant()
expect_true(all(intrinsic_resistant$antibiotic %in% antibiotics$name))
expect_false(any(is.na(microorganisms.codes$code)))
expect_false(any(is.na(microorganisms.codes$mo)))
expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))

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