CI tests

NAMESPACE

@@ -140,6 +140,7 @@ export(mo_fullname)
 export(mo_genus)
 export(mo_gramstain)
 export(mo_kingdom)
+export(mo_name)
 export(mo_order)
 export(mo_phylum)
 export(mo_property)

NEWS.md

@@ -3,6 +3,7 @@
 
 #### New
 * Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
+* Function `mo_name()` as alias of `mo_fullname()`
 
 #### Changed
 * Completely reworked the `antibiotics` data set:

R/mdro.R

@@ -374,42 +374,42 @@ eucast_exceptional_phenotypes <- function(x, country = "EUCAST", ...) {
   mdro(x = x, country = "EUCAST", ...)
 }
 
-is_ESBL <- function(x, col_mo = NULL, ...) {
+# is_ESBL <- function(x, col_mo = NULL, ...) {
-  col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
+#   col_mo <- get_column_mo(tbl = x, col_mo = col_mo)
-  cols_ab <- get_column_abx(tbl = x,
+#   cols_ab <- get_column_abx(tbl = x,
-                            soft_dependencies = c("AMX", "AMP"),
+#                             soft_dependencies = c("AMX", "AMP"),
-                            hard_dependencies = c("CAZ"),
+#                             hard_dependencies = c("CAZ"),
-                            ...)
+#                             ...)
-
+#
-  if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
+#   if (!any(c("AMX", "AMP") %in% names(cols_ab))) {
-    # both ampicillin and amoxicillin are missing
+#     # both ampicillin and amoxicillin are missing
-    generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
+#     generate_warning_abs_missing(c("AMX", "AMP"), any = TRUE)
-    return(rep(NA, nrow(x)))
+#     return(rep(NA, nrow(x)))
-  }
+#   }
-
+#
-  ESBLs <- rep(NA, nrow(x))
+#   ESBLs <- rep(NA, nrow(x))
-
+#
-  # first make all eligible cases FALSE
+#   # first make all eligible cases FALSE
-  ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
+#   ESBLs[which(mo_family(x[, col_mo]) == "Enterobacteriaceae"
-              & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
+#               & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
-              & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
+#               & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
-              & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
+#               & x[, get_ab_col(cols_ab, "AMX")] %in% c("R", "I", "S")
-              )] <- FALSE
+#               )] <- FALSE
-  # now make the positives cases TRUE
+#   # now make the positives cases TRUE
-  ESBLs[which(!is.na(ESBLs)
+#   ESBLs[which(!is.na(ESBLs)
-              & x[, get_ab_col(cols_ab, "AMX")]  == "R"
+#               & x[, get_ab_col(cols_ab, "AMX")]  == "R"
-              & x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
+#               & x[, get_ab_col(cols_ab, "CAZ")] == "R")] <- TRUE
-  ESBLs
+#   ESBLs
-
+#
-}
+# }
-
+#
-is_3MRGN <- function(x, ...) {
+# is_3MRGN <- function(x, ...) {
-
+#
-}
+# }
-
+#
-is_4MRGN <- function(x, ...) {
+# is_4MRGN <- function(x, ...) {
-
+#
-}
+# }
 
 get_column_mo <- function(tbl, col_mo = NULL) {
   # throws a blue note about which column will be used if guessed

R/misc.R

@@ -306,17 +306,17 @@ get_column_abx <- function(tbl,
                          TOB = TOB, TMP = TMP, SXT = SXT, VAN = VAN)
 
   if (!is.null(hard_dependencies)) {
-    if (!all(hard_dependencies %in% names(columns_available))) {
+    if (!all(hard_dependencies %in% names(columns_available[!is.na(columns_available)]))) {
       # missing a hard dependency will return NA and consequently the data will not be analysed
-      missing <- hard_dependencies[!hard_dependencies %in% names(columns_available)]
+      missing <- hard_dependencies[!hard_dependencies %in% names(columns_available[!is.na(columns_available)])]
       generate_warning_abs_missing(missing, any = FALSE)
       return(NA)
     }
   }
   if (!is.null(soft_dependencies)) {
-    if (!all(soft_dependencies %in% names(columns_available))) {
+    if (!all(soft_dependencies %in% names(columns_available[!is.na(columns_available)]))) {
       # missing a soft dependency may lower the reliability
-      missing <- soft_dependencies[!soft_dependencies %in% names(columns_available)]
+      missing <- soft_dependencies[!soft_dependencies %in% names(columns_available[!is.na(columns_available)])]
       missing <- paste0("`", missing, "` (", ab_name(missing, tolower = TRUE), ")")
       warning('Reliability might be improved if these antimicrobial results would be available too: ', paste(missing, collapse = ", "),
               immediate. = TRUE,

R/mo.R

@@ -557,22 +557,22 @@ exec_as.mo <- function(x,
       if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3
           & !x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") {
         # check if search term was like "A. species", then return first genus found with ^A
-        if (x_backup[i] %like% "[a-z]+ species" | x_backup[i] %like% "[a-z] spp[.]?") {
+        # if (x_backup[i] %like% "[a-z]+ species" | x_backup[i] %like% "[a-z] spp[.]?") {
-          # get mo code of first hit
+        #   # get mo code of first hit
-          found <- microorganismsDT[fullname %like% x_withspaces_start_only[i], mo]
+        #   found <- microorganismsDT[fullname %like% x_withspaces_start_only[i], mo]
-          if (length(found) > 0) {
+        #   if (length(found) > 0) {
-            mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
+        #     mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
-            found <- microorganismsDT[mo == mo_code, ..property][[1]]
+        #     found <- microorganismsDT[mo == mo_code, ..property][[1]]
-            # return first genus that begins with x_trimmed, e.g. when "E. spp."
+        #     # return first genus that begins with x_trimmed, e.g. when "E. spp."
-            if (length(found) > 0) {
+        #     if (length(found) > 0) {
-              x[i] <- found[1L]
+        #       x[i] <- found[1L]
-              if (initial_search == TRUE) {
+        #       if (initial_search == TRUE) {
-                set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
+        #         set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
-              }
+        #       }
-              next
+        #       next
-            }
+        #     }
-          }
+        #   }
-        }
+        # }
         # fewer than 3 chars and not looked for species, add as failure
         x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
         if (initial_search == TRUE) {

R/mo_property.R

@@ -64,7 +64,8 @@
 #' mo_subspecies("E. coli")      # ""
 #'
 #' ## colloquial properties
-#' mo_fullname("E. coli")        # "Escherichia coli"
+#' mo_name("E. coli")            # "Escherichia coli"
+#' mo_fullname("E. coli")        # "Escherichia coli", same as mo_name()
 #' mo_shortname("E. coli")       # "E. coli"
 #'
 #' ## other properties
@@ -131,6 +132,12 @@
 #'
 #' # get a list with the complete taxonomy (from kingdom to subspecies)
 #' mo_taxonomy("E. coli")
+mo_name <- function(x, language = get_locale(), ...) {
+  mo_fullname(x = x, language = language, ... = ...)
+}
+
+#' @rdname mo_property
+#' @export
 mo_fullname <- function(x, language = get_locale(), ...) {
   x <- mo_validate(x = x, property = "fullname", ...)
   t(x, language = language)

R/portion.R

@@ -31,7 +31,8 @@
 #' @param data a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})
 #' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}
 #' @inheritParams ab_property
-#' @param combine_SI a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.
+#' @param combine_SI a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.
+#' @param combine_IR a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.
 #' @inheritSection as.rsi Interpretation of S, I and R
 #' @details \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set.
 #'

docs/news/index.html

@@ -242,6 +242,8 @@
 <a href="#new" class="anchor"></a>New</h4>
 <ul>
 <li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
+<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
+</li>
 </ul>
 </div>
 <div id="changed" class="section level4">

docs/reference/count.html

@@ -285,7 +285,11 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
     </tr>
     <tr>
       <th>combine_SI</th>
-      <td><p>a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
+      <td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
+    </tr>
+    <tr>
+      <th>combine_IR</th>
+      <td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
     </tr>
     </table>
     

docs/reference/ggplot_rsi.html

@@ -301,7 +301,11 @@
     </tr>
     <tr>
       <th>combine_SI</th>
-      <td><p>a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
+      <td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
+    </tr>
+    <tr>
+      <th>combine_IR</th>
+      <td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
     </tr>
     <tr>
       <th>language</th>

docs/reference/index.html

@@ -373,7 +373,7 @@
       </tr><tr>
         
         <td>
-          <p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
+          <p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
         </td>
         <td><p>Property of a microorganism</p></td>
       </tr><tr>

docs/reference/mo_property.html

@@ -241,7 +241,9 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
+    <pre class="usage"><span class='fu'>mo_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
+
+<span class='fu'>mo_fullname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
 
 <span class='fu'>mo_shortname</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
 
@@ -364,7 +366,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 <span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>)      <span class='co'># ""</span>
 
 <span class='co'>## colloquial properties</span>
-<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>)        <span class='co'># "Escherichia coli"</span>
+<span class='fu'>mo_name</span>(<span class='st'>"E. coli"</span>)            <span class='co'># "Escherichia coli"</span>
+<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>)        <span class='co'># "Escherichia coli", same as mo_name()</span>
 <span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>)       <span class='co'># "E. coli"</span>
 
 <span class='co'>## other properties</span>

docs/reference/portion.html

@@ -295,7 +295,11 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
     </tr>
     <tr>
       <th>combine_SI</th>
-      <td><p>a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
+      <td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now <code>TRUE</code>.</p></td>
+    </tr>
+    <tr>
+      <th>combine_IR</th>
+      <td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter <code>combine_SI</code>.</p></td>
     </tr>
     </table>
     

man/count.Rd

@@ -43,7 +43,9 @@ count_df(data, translate_ab = "name", language = get_locale(),
 
 \item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
-\item{combine_SI}{a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
+\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
+
+\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
 }
 \value{
 Integer

man/ggplot_rsi.Rd

@@ -50,7 +50,9 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
 
 \item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}}
 
-\item{combine_SI}{a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
+\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
+
+\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
 
 \item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 

man/mo_property.Rd

@@ -2,6 +2,7 @@
 % Please edit documentation in R/mo_property.R
 \name{mo_property}
 \alias{mo_property}
+\alias{mo_name}
 \alias{mo_fullname}
 \alias{mo_shortname}
 \alias{mo_subspecies}
@@ -22,6 +23,8 @@
 \alias{mo_url}
 \title{Property of a microorganism}
 \usage{
+mo_name(x, language = get_locale(), ...)
+
 mo_fullname(x, language = get_locale(), ...)
 
 mo_shortname(x, language = get_locale(), ...)
@@ -132,7 +135,8 @@ mo_species("E. coli")         # "coli"
 mo_subspecies("E. coli")      # ""
 
 ## colloquial properties
-mo_fullname("E. coli")        # "Escherichia coli"
+mo_name("E. coli")            # "Escherichia coli"
+mo_fullname("E. coli")        # "Escherichia coli", same as mo_name()
 mo_shortname("E. coli")       # "E. coli"
 
 ## other properties

man/portion.Rd

@@ -49,7 +49,9 @@ portion_df(data, translate_ab = "name", language = get_locale(),
 
 \item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
-\item{combine_SI}{a logical to indicate whether all values of I and S must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
+\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see below. Default is now \code{TRUE}.}
+
+\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter \code{combine_SI}.}
 }
 \value{
 Double or, when \code{as_percent = TRUE}, a character.

tests/testthat/test-eucast_rules.R

@@ -33,6 +33,9 @@ test_that("EUCAST rules work", {
                  "reference.rule", "reference.rule_group"))
 
   expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
+  expect_error(eucast_rules(x = "text"))
+  expect_error(eucast_rules(data.frame(a = "test")))
+  expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
 
   expect_identical(colnames(septic_patients),
                    colnames(suppressWarnings(eucast_rules(septic_patients))))

tests/testthat/test-misc.R

@@ -42,3 +42,10 @@ test_that("functions missing in older R versions work", {
   expect_equal(trimws(" test ", "l"), "test ")
   expect_equal(trimws(" test ", "r"), " test")
 })
+
+test_that("looking up ab columns works", {
+  expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
+  expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
+  expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS"))
+  expect_warning(get_column_abx(septic_patients, soft_dependencies = "FUS"))
+})

tests/testthat/test-mo.R

@@ -200,6 +200,9 @@ test_that("as.mo works", {
   expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), "UNKNOWN")
   expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
   expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
+  expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
+  expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
+  expect_equal(suppressWarnings(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY")
 
   # predefined reference_df
   expect_equal(as.character(as.mo("TestingOwnID",
@@ -244,4 +247,20 @@ test_that("as.mo works", {
   # summary
   expect_equal(length(summary(septic_patients$mo)), 6)
 
+  # other
+  expect_equal(as.character(as.mo(c("xxx", "con", "na", "nan"), debug = TRUE)),
+               rep(NA_character_, 4))
+
+  expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
+               rep("UNKNOWN", 3))
+
+  expect_null(mo_failures())
+  expect_true(septic_patients %>% pull(mo) %>% is.mo())
+
+  expect_equal(get_mo_code("test", "mo"), "test")
+  expect_equal(length(get_mo_code("Escherichia", "genus")),
+               nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
+
+  expect_error(translate_allow_uncertain(5))
+
 })

tests/testthat/test-mo_property.R

@@ -31,6 +31,7 @@ test_that("mo_property works", {
   expect_equal(mo_species("E. coli"), "coli")
   expect_equal(mo_subspecies("E. coli"), "")
   expect_equal(mo_fullname("E. coli"), "Escherichia coli")
+  expect_equal(mo_name("E. coli"), "Escherichia coli")
   expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
   expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
   expect_equal(class(mo_taxonomy("E. coli")), "list")
@@ -47,6 +48,8 @@ test_that("mo_property works", {
   expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
   expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
 
+  expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
+
   # test integrity
   MOs <- AMR::microorganisms
   expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))