(v1.2.0.9023) ab_from_text() improvement

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.2.0.9022
+Version: 1.2.0.9023
-Date: 2020-07-01
+Date: 2020-07-02
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.2.0.9022
+# AMR 1.2.0.9023
-## <small>Last updated: 01-Jul-2020</small>
+## <small>Last updated: 02-Jul-2020</small>
 
 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@@ -19,9 +19,9 @@
 * Added Monuril as trade name for fosfomycin
 
 ### Changed
-* Using unexisting columns in all `count_*()`, `proportion_*()`, `susceptibility()` and `resistance()` functions wil now return an error instead of dropping them silently
+* Using unexisting columns in all `count_*()`, `proportion_*()`, `susceptibility()` and `resistance()` functions wil now return an error instead of dropping them silently. Using variables for column names (as well as `dplyr::all_of()`) now works again.
 * Improvements for `as.ab()`:
-  * Dramatic improvement of the algorithm behind `as.ab()`, making many more input errors translatable like from digitalised health care records, using too few or too many vowels or consonants and many more
+  * Dramatic improvement of the algorithm behind `as.ab()`, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more
   * Added progress bar
   * Fixed a bug where `as.ab()` would return an error on invalid input values
   * The `as.ab()` function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.
@@ -32,7 +32,7 @@
 * Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
 * Changed the summary for class `<mo>`, to highlight the %SI vs. %R
 * Improved error handling, giving more useful info when functions return an error
-
+* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
 
 # AMR 1.2.0
 

R/aa_helper_functions.R

@@ -184,7 +184,7 @@ stop_ifnot_installed <- function(package) {
   # https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
   sapply(package, function(pkg)
     tryCatch(get(".packageName", envir = asNamespace(pkg)),
-             error = function(e) { 
+             error = function(e) {
                if (package == "rstudioapi") {
                  stop("This function only works in RStudio.", call. = FALSE)
                } else if (pkg != "base") {

R/ab_from_text.R

@@ -27,6 +27,7 @@
 #' @param type type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
 #' @param collapse character to pass on to `paste(..., collapse = ...)` to only return one character per element of `text`, see *Examples*
 #' @param translate_ab if `type = "drug"`: a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
+#' @param thorough_search logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
 #' @param ... parameters passed on to [as.ab()]
 #' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned.
 #' 
@@ -85,6 +86,7 @@ ab_from_text <- function(text,
                          type = c("drug", "dose", "administration"),
                          collapse = NULL,
                          translate_ab = FALSE,
+                         thorough_search = NULL,
                          ...) {
   
   if (missing(type)) {
@@ -95,30 +97,54 @@ ab_from_text <- function(text,
   
   text <- tolower(as.character(text))
   text_split_all <- strsplit(text, "[ ;.,:\\|]")
+  progress <- progress_estimated(n = length(text_split_all), n_min = 5)
+  on.exit(close(progress))
   
   if (type %like% "(drug|ab|anti)") {
     
     translate_ab <- get_translate_ab(translate_ab)
     
-    abbr <- unlist(antibiotics$abbreviations)
+    if (isTRUE(thorough_search) | 
-    abbr <- abbr[nchar(abbr) >= 4]
+        (isTRUE(is.null(thorough_search)) & max(sapply(text_split_all, length), na.rm = TRUE) <= 3)) {
-    names_atc <- substr(c(antibiotics$name, antibiotics$atc), 1, 5)
+      text_split_all <- text_split_all[nchar(text_split_all) >= 4 & grepl("[a-z]+", text_split_all)]
-    synonyms <- unlist(antibiotics$synonyms)
+      result <- lapply(text_split_all, function(text_split) {
-    synonyms <- synonyms[nchar(synonyms) >= 4]
+        progress$tick()
-    to_regex <- function(x) {
+        suppressWarnings(
-      paste0("^(",
+          out <- as.ab(text_split, ...)
-             paste0(unique(gsub("[^a-z0-9]", ".*", sort(tolower(x)))), collapse = "|"),
+        )
-             ").*")
+      })
+      
+    } else {
+      # no thorough search
+      abbr <- unlist(antibiotics$abbreviations)
+      abbr <- abbr[nchar(abbr) >= 4]
+      names_atc <- substr(c(antibiotics$name, antibiotics$atc), 1, 5)
+      synonyms <- unlist(antibiotics$synonyms)
+      synonyms <- synonyms[nchar(synonyms) >= 4]
+      # regular expression must not be too long, so split synonyms in two:
+      synonyms_part1 <- synonyms[seq_len(0.5 * length(synonyms))]
+      synonyms_part2 <- synonyms[!synonyms %in% synonyms_part1]
+      to_regex <- function(x) {
+        paste0("^(",
+               paste0(unique(gsub("[^a-z0-9]+", "", sort(tolower(x)))), collapse = "|"),
+               ").*")
+      }
+      result <- lapply(text_split_all, function(text_split) {
+        progress$tick()
+        suppressWarnings(
+          out <- as.ab(unique(c(text_split[text_split %like_case% to_regex(abbr)],
+                                text_split[text_split %like_case% to_regex(names_atc)],
+                                text_split[text_split %like_case% to_regex(synonyms_part1)],
+                                text_split[text_split %like_case% to_regex(synonyms_part2)])
+                              ),
+                       ...)
+        )
+      })
     }
     
-    result <- lapply(text_split_all, function(text_split) {
+    close(progress)
-      suppressWarnings(
+    
-        out <- as.ab(unique(c(text_split[grep(to_regex(abbr), text_split)],
+    result <- lapply(result, function(out) {
-                              text_split[grep(to_regex(names_atc), text_split)],
-                              # regular expression must not be too long, so split synonyms in two:
-                              text_split[grep(to_regex(synonyms[c(1:0.5 * length(synonyms))]), text_split)],
-                              text_split[grep(to_regex(synonyms[c(0.5 * length(synonyms):length(synonyms))]), text_split)])),
-                     ...))
       out <- out[!is.na(out)]
       if (length(out) == 0) {
         as.ab(NA)
@@ -128,6 +154,7 @@ ab_from_text <- function(text,
         }
         out
       }
+      
     })
     
   } else if (type %like% "dos") {
@@ -167,7 +194,7 @@ ab_from_text <- function(text,
   # collapse text if needed
   if (!is.null(collapse)) {
     result <- sapply(result, function(x) {
-      if(length(x) == 1 & all(is.na(x))) {
+      if (length(x) == 1 & all(is.na(x))) {
         NA_character_
       } else {
         paste0(x, collapse = collapse)

R/bug_drug_combinations.R

@@ -135,7 +135,7 @@ format.bug_drug_combinations <- function(x,
     format <- tolower(format)
     ab_txt <- rep(format, length(ab))
     for (i in seq_len(length(ab_txt))) {
-      ab_txt[i] <- gsub("ab", ab[i], ab_txt[i])
+      ab_txt[i] <- gsub("ab", as.character(as.ab(ab[i])), ab_txt[i])
       ab_txt[i] <- gsub("cid", ab_cid(ab[i]), ab_txt[i])
       ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i])
       ab_txt[i] <- gsub("atc_group1", ab_atc_group1(ab[i], language = language), ab_txt[i])

R/first_isolate.R

@@ -259,25 +259,25 @@ first_isolate <- function(x,
   
   # arrange data to the right sorting
   if (is.null(specimen_group)) {
-      x <- x[order(x$newvar_patient_id, 
+    x <- x[order(x$newvar_patient_id, 
-                   x$newvar_genus_species,
+                 x$newvar_genus_species,
-                   x$newvar_date), ]
+                 x$newvar_date), ]
-      rownames(x) <- NULL
+    rownames(x) <- NULL
-      row.start <- 1
+    row.start <- 1
-      row.end <- nrow(x)
+    row.end <- nrow(x)
   } else {
     # filtering on specimen and only analyse these rows to save time
-      x <- x[order(pull(x, col_specimen),
+    x <- x[order(pull(x, col_specimen),
-                   x$newvar_patient_id, 
+                 x$newvar_patient_id, 
-                   x$newvar_genus_species,
+                 x$newvar_genus_species,
-                   x$newvar_date), ]
+                 x$newvar_date), ]
-      rownames(x) <- NULL
+    rownames(x) <- NULL
-      suppressWarnings(
+    suppressWarnings(
-        row.start <- which(x %>% pull(col_specimen) == specimen_group) %>% min(na.rm = TRUE)
+      row.start <- which(x %>% pull(col_specimen) == specimen_group) %>% min(na.rm = TRUE)
-      )
+    )
-      suppressWarnings(
+    suppressWarnings(
-        row.end <- which(x %>% pull(col_specimen) == specimen_group) %>% max(na.rm = TRUE)
+      row.end <- which(x %>% pull(col_specimen) == specimen_group) %>% max(na.rm = TRUE)
-      )
+    )
   }
   
   # no isolates found
@@ -290,7 +290,7 @@ first_isolate <- function(x,
   
   # did find some isolates - add new index numbers of rows
   x$newvar_row_index_sorted <- seq_len(nrow(x))
-
+  
   scope.size <- nrow(x[which(x$newvar_row_index_sorted %in% c(row.start + 1:row.end) &
                                !is.na(x$newvar_mo)), , drop = FALSE])
   
@@ -318,17 +318,17 @@ first_isolate <- function(x,
   
   # Analysis of first isolate ----
   x$other_pat_or_mo <- if_else(x$newvar_patient_id == lag(x$newvar_patient_id) &
-                                         x$newvar_genus_species == lag(x$newvar_genus_species),
+                                 x$newvar_genus_species == lag(x$newvar_genus_species),
-                                       FALSE,
+                               FALSE,
-                                       TRUE)
+                               TRUE)
   x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
-  x$more_than_episode_ago <- unname(unlist(lapply(unique(x$episode_group), 
+  x$more_than_episode_ago <- unlist(lapply(unique(x$episode_group),
-                                                          function(g, 
+                                           function(g,
-                                                                   df = x,
+                                                    df = x,
-                                                                   days = episode_days) {
+                                                    days = episode_days) {
-                                                            identify_new_year(x = df[which(df$episode_group == g), "newvar_date"],
+                                             identify_new_year(x = df[which(df$episode_group == g), "newvar_date", drop = TRUE],
-                                                                              episode_days = days)
+                                                               episode_days = days)
-                                                          })))
+                                           }))
   
   weighted.notice <- ""
   if (!is.null(col_keyantibiotics)) {
@@ -336,38 +336,38 @@ first_isolate <- function(x,
     if (info == TRUE) {
       if (type == "keyantibiotics") {
         message(font_black(paste0("[Criterion] Base inclusion on key antibiotics, ",
-                            ifelse(ignore_I == FALSE, "not ", ""),
+                                  ifelse(ignore_I == FALSE, "not ", ""),
-                            "ignoring I")))
+                                  "ignoring I")))
       }
       if (type == "points") {
         message(font_black(paste0("[Criterion] Base inclusion on key antibiotics, using points threshold of "
-                            , points_threshold)))
+                                  , points_threshold)))
       }
     }
     type_param <- type
     
     x$other_key_ab <- !key_antibiotics_equal(y = x$newvar_key_ab,
-                                                     z = lag(x$newvar_key_ab),
+                                             z = lag(x$newvar_key_ab),
-                                                     type = type_param,
+                                             type = type_param,
-                                                     ignore_I = ignore_I,
+                                             ignore_I = ignore_I,
-                                                     points_threshold = points_threshold,
+                                             points_threshold = points_threshold,
-                                                     info = info)
+                                             info = info)
     # with key antibiotics
     x$newvar_first_isolate <- if_else(x$newvar_row_index_sorted >= row.start &
-                                              x$newvar_row_index_sorted <= row.end &
+                                        x$newvar_row_index_sorted <= row.end &
-                                              x$newvar_genus_species != "" & 
+                                        x$newvar_genus_species != "" & 
-                                              (x$other_pat_or_mo | x$more_than_episode_ago | x$other_key_ab),
+                                        (x$other_pat_or_mo | x$more_than_episode_ago | x$other_key_ab),
-                                            TRUE,
+                                      TRUE,
-                                            FALSE)
+                                      FALSE)
     
   } else {
     # no key antibiotics
     x$newvar_first_isolate <- if_else(x$newvar_row_index_sorted >= row.start &
-                                              x$newvar_row_index_sorted <= row.end &
+                                        x$newvar_row_index_sorted <= row.end &
-                                              x$newvar_genus_species != "" & 
+                                        x$newvar_genus_species != "" & 
-                                              (x$other_pat_or_mo | x$more_than_episode_ago),
+                                        (x$other_pat_or_mo | x$more_than_episode_ago),
-                                            TRUE,
+                                      TRUE,
-                                            FALSE)
+                                      FALSE)
   }
   
   # first one as TRUE
@@ -391,17 +391,17 @@ first_isolate <- function(x,
   # handle empty microorganisms
   if (any(x$newvar_mo == "UNKNOWN", na.rm = TRUE) & info == TRUE) {
     message(font_blue(paste0("NOTE: ", ifelse(include_unknown == TRUE, "Included ", "Excluded "), 
-                        format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
+                             format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
-                               decimal.mark = decimal.mark, big.mark = big.mark), 
+                                    decimal.mark = decimal.mark, big.mark = big.mark), 
-                        " isolates with a microbial ID 'UNKNOWN' (column `", font_bold(col_mo), "`)")))
+                             " isolates with a microbial ID 'UNKNOWN' (column `", font_bold(col_mo), "`)")))
   }
   x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
   
   # exclude all NAs
   if (any(is.na(x$newvar_mo)) & info == TRUE) {
     message(font_blue(paste0("NOTE: Excluded ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
-                                                  decimal.mark = decimal.mark, big.mark = big.mark), 
+                                                       decimal.mark = decimal.mark, big.mark = big.mark), 
-                        " isolates with a microbial ID 'NA' (column `", font_bold(col_mo), "`)")))
+                             " isolates with a microbial ID 'NA' (column `", font_bold(col_mo), "`)")))
   }
   x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
   
@@ -465,7 +465,7 @@ filter_first_weighted_isolate <- function(x,
       col_keyantibiotics <- "keyab"
     }
   }
-
+  
   subset(x, first_isolate(x = y,
                           col_date = col_date,
                           col_patient_id = col_patient_id,

R/like.R

@@ -102,14 +102,19 @@ like <- function(x, pattern, ignore.case = TRUE) {
     as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = FALSE, fixed = fixed)
   } else {
     tryCatch(base::grepl(pattern, x, ignore.case = FALSE, fixed = fixed),
-             error = function(e) ifelse(grepl("Invalid regexp", e$message),
+             error = function(e) {
-                                        # try with perl = TRUE:
+               if (grepl("invalid reg(ular )?exp", e$message, ignore.case = TRUE)) {
-                                        return(base::grepl(pattern = pattern, x = x,
+                 # try with perl = TRUE:
-                                                           ignore.case = FALSE, 
+                 return(base::grepl(pattern = pattern, 
-                                                           fixed = fixed,
+                                    x = x,
-                                                           perl = TRUE)),
+                                    ignore.case = FALSE, 
-                                        # stop otherwise
+                                    fixed = fixed,
-                                        stop(e$message)))
+                                    perl = TRUE))
+               } else {
+                 # stop otherwise
+                 stop(e$message)
+               }
+             })
   }
 }
 

R/rsi_calc.R

@@ -40,6 +40,11 @@ rsi_calc <- function(...,
   data_vars <- dots2vars(...)
 
   dots_df <- switch(1, ...)
+  if (is.data.frame(dots_df)) {
+    # make sure to remove all other classes like tibbles, data.tables, etc
+    dots_df <- as.data.frame(dots_df, stringsAsFactors = FALSE)
+  }
+  
   dots <- base::eval(base::substitute(base::alist(...)))
   stop_if(length(dots) == 0, "no variables selected", call = -2)
 
@@ -50,6 +55,7 @@ rsi_calc <- function(...,
   
   if (is.data.frame(dots_df)) {
     # data.frame passed with other columns, like: example_isolates %>% proportion_S(AMC, GEN)
+  
     dots <- as.character(dots)
     # remove first element, it's the data.frame
     if (length(dots) == 1) {
@@ -62,6 +68,10 @@ rsi_calc <- function(...,
       # and the old rsi function, which has "df" as name of the first parameter
       x <- dots_df
     } else {
+      # get dots that are in column names already, and the ones that will be once evaluated using dots_df or global env
+      # this is to support susceptibility(example_isolates, AMC, dplyr::all_of(some_vector_with_AB_names))
+      dots <- c(dots[dots %in% colnames(dots_df)],
+                eval(parse(text = dots[!dots %in% colnames(dots_df)]), envir = dots_df, enclos = globalenv()))
       dots_not_exist <- dots[!dots %in% colnames(dots_df)]
       stop_if(length(dots_not_exist) > 0, "column(s) not found: ", paste0("'", dots_not_exist, "'", collapse = ", "), call = -2)
       x <- dots_df[, dots, drop = FALSE]
@@ -72,10 +82,10 @@ rsi_calc <- function(...,
   } else {
     # multiple variables passed without pipe, like: proportion_S(example_isolates$AMC, example_isolates$GEN)
     x <- NULL
-    try(x <- as.data.frame(dots), silent = TRUE)
+    try(x <- as.data.frame(dots, stringsAsFactors = FALSE), silent = TRUE)
     if (is.null(x)) {
       # support for example_isolates %>% group_by(hospital_id) %>% summarise(amox = susceptibility(GEN, AMX))
-      x <- as.data.frame(list(...))
+      x <- as.data.frame(list(...), stringsAsFactors = FALSE)
     }
   }
   
@@ -92,9 +102,9 @@ rsi_calc <- function(...,
     rsi_integrity_check <- character(0)
     for (i in seq_len(ncol(x))) {
       # check integrity of columns: force rsi class
-      if (!is.rsi(x %>% pull(i))) {
+      if (!is.rsi(x[, i, drop = TRUE])) {
-        rsi_integrity_check <- c(rsi_integrity_check, x %>% pull(i) %>% as.character())
+        rsi_integrity_check <- c(rsi_integrity_check, as.character(x[, i, drop = TRUE]))
-        x[, i] <- suppressWarnings(x %>% pull(i) %>% as.rsi()) # warning will be given later
+        x[, i] <- suppressWarnings(as.rsi(x[, i, drop = TRUE])) # warning will be given later
         print_warning <- TRUE
       }
     }

docs/404.html

@@ -81,7 +81,7 @@
       </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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/authors.html

@@ -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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/index.html

@@ -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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/news/index.html

@@ -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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 
@@ -229,13 +229,13 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1209022" class="section level1">
+    <div id="amr-1209023" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0.9022">
+<h1 class="page-header" data-toc-text="1.2.0.9023">
-<a href="#amr-1209022" class="anchor"></a>AMR 1.2.0.9022<small> Unreleased </small>
+<a href="#amr-1209023" class="anchor"></a>AMR 1.2.0.9023<small> Unreleased </small>
 </h1>
-<div id="last-updated-01-jul-2020" class="section level2">
+<div id="last-updated-02-jul-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-01-jul-2020" class="anchor"></a><small>Last updated: 01-Jul-2020</small>
+<a href="#last-updated-02-jul-2020" class="anchor"></a><small>Last updated: 02-Jul-2020</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@@ -262,10 +262,10 @@
 <h3 class="hasAnchor">
 <a href="#changed" class="anchor"></a>Changed</h3>
 <ul>
-<li>Using unexisting columns in all <code>count_*()</code>, <code>proportion_*()</code>, <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> functions wil now return an error instead of dropping them silently</li>
+<li>Using unexisting columns in all <code>count_*()</code>, <code>proportion_*()</code>, <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> functions wil now return an error instead of dropping them silently. Using variables for column names (as well as <code><a href="https://dplyr.tidyverse.org/reference/reexports.html">dplyr::all_of()</a></code>) now works again.</li>
 <li>Improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code>:
 <ul>
-<li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable like from digitalised health care records, using too few or too many vowels or consonants and many more</li>
+<li>Dramatic improvement of the algorithm behind <code><a href="../reference/as.ab.html">as.ab()</a></code>, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more</li>
 <li>Added progress bar</li>
 <li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
 <li>The <code><a href="../reference/as.ab.html">as.ab()</a></code> function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.</li>
@@ -279,6 +279,7 @@
 <li>Fixed a bug in <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> for when only one antibiotic was in the input data</li>
 <li>Changed the summary for class <code>&lt;mo&gt;</code>, to highlight the %SI vs. %R</li>
 <li>Improved error handling, giving more useful info when functions return an error</li>
+<li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li>
 </ul>
 </div>
 </div>

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-07-01T14:20Z
+last_built: 2020-07-02T19:12Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/AMR.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/ab_from_text.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 
@@ -240,6 +240,7 @@
   <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"drug"</span>, <span class='st'>"dose"</span>, <span class='st'>"administration"</span>),
   <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>thorough_search</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='no'>...</span>
 )</pre>
 
@@ -262,6 +263,10 @@
       <th>translate_ab</th>
       <td><p>if <code>type = "drug"</code>: a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code>. Defaults to <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></td>
     </tr>
+    <tr>
+      <th>thorough_search</th>
+      <td><p>logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></td>
+    </tr>
     <tr>
       <th>...</th>
       <td><p>parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>

docs/reference/as.ab.html

@@ -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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/eucast_rules.html

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/ggplot_pca.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/ggplot_rsi.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/guess_ab_col.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -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">1.2.0.9022</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/lifecycle.html

@@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
       </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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/mdro.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/pca.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

docs/reference/resistance_predict.html

@@ -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">1.2.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9023</span>
       </span>
     </div>
 

man/ab_from_text.Rd

@@ -9,6 +9,7 @@ ab_from_text(
   type = c("drug", "dose", "administration"),
   collapse = NULL,
   translate_ab = FALSE,
+  thorough_search = NULL,
   ...
 )
 }
@@ -21,6 +22,8 @@ ab_from_text(
 
 \item{translate_ab}{if \code{type = "drug"}: a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}. Defaults to \code{FALSE}. Using \code{TRUE} is equal to using "name".}
 
+\item{thorough_search}{logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to \code{TRUE} will take considerably more time than when using \code{FALSE}. At default, it will turn \code{TRUE} when all input elements contain a maximum of three words.}
+
 \item{...}{parameters passed on to \code{\link[=as.ab]{as.ab()}}}
 }
 \value{

tests/testthat/test-ab_from_text.R

@@ -23,8 +23,14 @@ context("ab_from_text.R")
 
 test_that("ab_from_text works", {
   
+  skip_on_cran()
+  
   expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")[[1]],
                    as.ab("Amoxicillin"))
+  expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = TRUE)[[1]],
+                   as.ab("Amoxicillin"))
+  expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = FALSE)[[1]],
+                   as.ab("Amoxicillin"))
   expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", translate_ab = TRUE)[[1]],
                    "Amoxicillin")
   expect_identical(ab_from_text("administered amoxi/clav and cipro", collapse = ", ")[[1]],