(v0.7.1.9100) bug_drug speed, MIC levels

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.1.9098
+Version: 0.7.1.9100
-Date: 2019-10-07
+Date: 2019-10-08
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 0.7.1.9098
+# AMR 0.7.1.9100
-<small>Last updated: 07-Oct-2019</small>
+<small>Last updated: 08-Oct-2019</small>
 
 ### Breaking
 * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
@@ -121,6 +121,7 @@
 * Fix for `key_antibiotics()` on foreign systems
 * Added 80 new LIS codes for microorganisms
 * Relabeled the factor levels of `mdr_tb()`
+* Added more MIC factor levels (`as.mic()`)
 
 #### Other
 * Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors

R/ab_property.R

@@ -181,12 +181,12 @@ ab_validate <- function(x, property, ...) {
     library("AMR")
     # check onLoad() in R/zzz.R: data tables are created there.
   }
-
+  
   # try to catch an error when inputting an invalid parameter
   # so the 'call.' can be set to FALSE
   tryCatch(x[1L] %in% AMR::antibiotics[1, property],
            error = function(e) stop(e$message, call. = FALSE))
-
+  x_bak <- x
   if (!all(x %in% AMR::antibiotics[, property])) {
     x <- data.frame(ab = AMR::as.ab(x, ...), stringsAsFactors = FALSE) %>%
       left_join(AMR::antibiotics, by = "ab") %>%
@@ -199,6 +199,8 @@ ab_validate <- function(x, property, ...) {
   } else if (property %like% "ddd") {
     return(as.double(x))
   } else {
+    # return "(input)" for NAs
+    x[is.na(x) & !is.na(x_bak)] <- paste0("(", x_bak[is.na(x) & !is.na(x_bak)], ")")
     return(x)
   }
 }

R/bug_drug_combinations.R

@@ -39,6 +39,7 @@
 #' The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
 #' @export
 #' @rdname bug_drug_combinations
+#' @return The function \code{bug_drug_combinations} returns a \code{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
 #' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 #' @inheritSection AMR Read more on our website!
 #' @examples 
@@ -58,7 +59,6 @@
 #' }
 bug_drug_combinations <- function(x, 
                                   col_mo = NULL, 
-                                  minimum = 30,
                                   FUN = mo_shortname,
                                   ...) {
   if (!is.data.frame(x)) {
@@ -77,17 +77,17 @@ bug_drug_combinations <- function(x,
   x <- x %>%
     as.data.frame(stringsAsFactors = FALSE) %>% 
     mutate(mo = x %>% pull(col_mo) %>% FUN(...)) %>% 
-    filter(mo %in% (freq(mo) %>%
-                      filter(count >= minimum) %>%
-                      pull(item))) %>% 
     group_by(mo) %>% 
-    AMR::rsi_df(translate_ab = FALSE, combine_SI = FALSE) %>% 
+    select_if(is.rsi) %>% 
-    select(-value) %>%
+    gather("ab", "value", -mo) %>% 
-    spread(interpretation, isolates) %>%
+    group_by(mo, ab) %>% 
+    summarise(S = sum(value == "S", na.rm = TRUE),
+              I = sum(value == "I", na.rm = TRUE),
+              R = sum(value == "R", na.rm = TRUE)) %>%
+    ungroup() %>%
     mutate(total = S + I + R) %>%
-    filter(total >= minimum) %>% 
+    as.data.frame(stringsAsFactors = FALSE)
-    rename(ab = antibiotic)
+
-  
   structure(.Data = x, class = c("bug_drug_combinations", class(x)))
 }
 
@@ -107,6 +107,8 @@ format.bug_drug_combinations <- function(x,
                                          decimal.mark = getOption("OutDec"),
                                          big.mark = ifelse(decimal.mark == ",", ".", ","),
                                          ...) {
+  x <- x %>% filter(total >= minimum)
+  
   if (remove_intrinsic_resistant == TRUE) {
     x <- x %>% filter(R != total)
   }
@@ -133,7 +135,6 @@ format.bug_drug_combinations <- function(x,
   }
 
   y <- x %>%
-    filter(total >= minimum) %>% 
     mutate(ab = as.ab(ab),
            ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>% 
     group_by(ab, ab_txt, mo) %>% 

R/eucast_rules.R

@@ -429,7 +429,7 @@ eucast_rules <- function(x,
             x_original <<- x_original %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
             x <<- x %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
             x_original[rows, cols] <<- to
-            warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = '`, `'), '` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antibiotic columns to guarantee the right structure.', call. = FALSE)
+            warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = '`, `'), '` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antimicrobial columns to guarantee the right structure.', call. = FALSE)
             txt_warning()
             warned <<- FALSE
           } else {

R/guess_ab_col.R

@@ -130,7 +130,7 @@ get_column_abx <- function(x,
   # and that have no more than 50% invalid values
   vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[,c("ab", "atc", "name", "abbreviations", "synonyms")])))
   vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
-  x_columns <- sapply(colnames(x), function(col = x, df = x_bak) {
+  x_columns <- sapply(colnames(x), function(col, df = x_bak) {
     if (toupper(col) %in% vectr_antibiotics | 
         is.rsi(as.data.frame(df)[, col]) |
         is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5)) {
@@ -139,9 +139,9 @@ get_column_abx <- function(x,
       return(NA_character_)
     }
   })
-  x_coluxmns <- x_columns[!is.na(x_columns)]
+  x_columns <- x_columns[!is.na(x_columns)]
-  x <- x[,x_columns[!is.na(x_columns)]]
+  x <- x[, x_columns, drop = FALSE] # without drop = TRUE, x will become a vector when x_columns is length 1
-  
+
   df_trans <- data.frame(colnames = colnames(x),
                          abcode = suppressWarnings(as.ab(colnames(x))))
   df_trans <- df_trans[!is.na(df_trans$abcode),]

R/mic.R

@@ -68,6 +68,9 @@ as.mic <- function(x, na.rm = FALSE) {
     x <- gsub(',', '.', x, fixed = TRUE)
     # remove space between operator and number ("<= 0.002" -> "<=0.002")
     x <- gsub('(<|=|>) +', '\\1', x)
+    # transform => to >= and =< to <=
+    x <- gsub('=>', '>=', x, fixed = TRUE)
+    x <- gsub('=<', '<=', x, fixed = TRUE)
     # starting dots must start with 0
     x <- gsub('^[.]+', '0.', x)
     # <=0.2560.512 should be 0.512
@@ -76,13 +79,19 @@ as.mic <- function(x, na.rm = FALSE) {
     x <- gsub('[.]+0$', '', x)
     # remove all after last digit
     x <- gsub('[^0-9]+$', '', x)
+    # keep only one zero before dot
+    x <- gsub("0+[.]", "0.", x)
+    # starting 00 is probably 0.0 if there's no dot yet
+    x[!x %like% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
     # remove last zeroes
     x <- gsub('([.].?)0+$', '\\1', x)
     x <- gsub('(.*[.])0+$', '\\10', x)
     # remove ending .0 again
-    x <- gsub('[.]+0$', '', x)
+    x[x %like% "[.]"] <- gsub('0+$', '', x[x %like% "[.]"])
     # force to be character
     x <- as.character(x)
+    # trim it
+    x <- trimws(x)
 
     ## previously unempty values now empty - should return a warning later on
     x[x.bak != "" & x == ""] <- "invalid"
@@ -92,15 +101,25 @@ as.mic <- function(x, na.rm = FALSE) {
               "<0.002", "<=0.002", "0.002", ">=0.002", ">0.002",
               "<0.003", "<=0.003", "0.003", ">=0.003", ">0.003",
               "<0.004", "<=0.004", "0.004", ">=0.004", ">0.004",
+              "<0.005", "<=0.005", "0.005", ">=0.005", ">0.005",
               "<0.006", "<=0.006", "0.006", ">=0.006", ">0.006",
+              "<0.007", "<=0.007", "0.007", ">=0.007", ">0.007",
               "<0.008", "<=0.008", "0.008", ">=0.008", ">0.008",
+              "<0.009", "<=0.009", "0.009", ">=0.009", ">0.009",
+              "<0.01", "<=0.01", "0.01", ">=0.01", ">0.01",
               "<0.012", "<=0.012", "0.012", ">=0.012", ">0.012",
               "<0.0125", "<=0.0125", "0.0125", ">=0.0125", ">0.0125",
               "<0.016", "<=0.016", "0.016", ">=0.016", ">0.016",
+              "<0.019", "<=0.019", "0.019", ">=0.019", ">0.019",
+              "<0.02", "<=0.02", "0.02", ">=0.02", ">0.02",
               "<0.023", "<=0.023", "0.023", ">=0.023", ">0.023",
               "<0.025", "<=0.025", "0.025", ">=0.025", ">0.025",
+              "<0.028", "<=0.028", "0.028", ">=0.028", ">0.028",
               "<0.03", "<=0.03", "0.03", ">=0.03", ">0.03",
+              "<0.031", "<=0.031", "0.031", ">=0.031", ">0.031",
               "<0.032", "<=0.032", "0.032", ">=0.032", ">0.032",
+              "<0.038", "<=0.038", "0.038", ">=0.038", ">0.038",
+              "<0.04", "<=0.04", "0.04", ">=0.04", ">0.04",
               "<0.047", "<=0.047", "0.047", ">=0.047", ">0.047",
               "<0.05", "<=0.05", "0.05", ">=0.05", ">0.05",
               "<0.054", "<=0.054", "0.054", ">=0.054", ">0.054",
@@ -108,25 +127,38 @@ as.mic <- function(x, na.rm = FALSE) {
               "<0.0625", "<=0.0625", "0.0625", ">=0.0625", ">0.0625",
               "<0.063", "<=0.063", "0.063", ">=0.063", ">0.063",
               "<0.064", "<=0.064", "0.064", ">=0.064", ">0.064",
+              "<0.075", "<=0.075", "0.075", ">=0.075", ">0.075",
+              "<0.08", "<=0.08", "0.08", ">=0.08", ">0.08",
               "<0.09", "<=0.09", "0.09", ">=0.09", ">0.09",
               "<0.094", "<=0.094", "0.094", ">=0.094", ">0.094",
+              "<0.095", "<=0.095", "0.095", ">=0.095", ">0.095",
+              "<0.1", "<=0.1", "0.1", ">=0.1", ">0.1",
               "<0.12", "<=0.12", "0.12", ">=0.12", ">0.12",
               "<0.125", "<=0.125", "0.125", ">=0.125", ">0.125",
               "<0.128", "<=0.128", "0.128", ">=0.128", ">0.128",
+              "<0.15", "<=0.15", "0.15", ">=0.15", ">0.15",
               "<0.16", "<=0.16", "0.16", ">=0.16", ">0.16",
+              "<0.17", "<=0.17", "0.17", ">=0.17", ">0.17",
+              "<0.18", "<=0.18", "0.18", ">=0.18", ">0.18",
               "<0.19", "<=0.19", "0.19", ">=0.19", ">0.19",
+              "<0.2", "<=0.2", "0.2", ">=0.2", ">0.2",
               "<0.23", "<=0.23", "0.23", ">=0.23", ">0.23",
               "<0.25", "<=0.25", "0.25", ">=0.25", ">0.25",
               "<0.256", "<=0.256", "0.256", ">=0.256", ">0.256",
               "<0.28", "<=0.28", "0.28", ">=0.28", ">0.28",
               "<0.3", "<=0.3", "0.3", ">=0.3", ">0.3",
               "<0.32", "<=0.32", "0.32", ">=0.32", ">0.32",
+              "<0.35", "<=0.35", "0.35", ">=0.35", ">0.35",
               "<0.36", "<=0.36", "0.36", ">=0.36", ">0.36",
               "<0.38", "<=0.38", "0.38", ">=0.38", ">0.38",
+              "<0.47", "<=0.47", "0.47", ">=0.47", ">0.47",
               "<0.5", "<=0.5", "0.5", ">=0.5", ">0.5",
               "<0.512", "<=0.512", "0.512", ">=0.512", ">0.512",
               "<0.64", "<=0.64", "0.64", ">=0.64", ">0.64",
+              "<0.73", "<=0.73", "0.73", ">=0.73", ">0.73",
               "<0.75", "<=0.75", "0.75", ">=0.75", ">0.75",
+              "<0.8", "<=0.8", "0.8", ">=0.8", ">0.8",
+              "<0.94", "<=0.94", "0.94", ">=0.94", ">0.94",
               "<1", "<=1", "1", ">=1", ">1",
               "<1.5", "<=1.5", "1.5", ">=1.5", ">1.5",
               "<2", "<=2", "2", ">=2", ">2",

R/mo.R

@@ -412,13 +412,13 @@ exec_as.mo <- function(x,
     y <- reference_data_to_use[prevalence == 1][data.table(mo = x), on = "mo", ..property][[1]]
     if (any(is.na(y))) {
       y[is.na(y)] <- reference_data_to_use[prevalence == 2][data.table(mo = x[is.na(y)]),
-                                                       on = "mo",
+                                                            on = "mo",
-                                                       ..property][[1]]
+                                                            ..property][[1]]
     }
     if (any(is.na(y))) {
       y[is.na(y)] <- reference_data_to_use[prevalence == 3][data.table(mo = x[is.na(y)]),
-                                                       on = "mo",
+                                                            on = "mo",
-                                                       ..property][[1]]
+                                                            ..property][[1]]
     }
     x <- y
     
@@ -441,13 +441,13 @@ exec_as.mo <- function(x,
     y <- reference_data_to_use[prevalence == 1][data.table(fullname_lower = tolower(x)), on = "fullname_lower", ..property][[1]]
     if (any(is.na(y))) {
       y[is.na(y)] <- reference_data_to_use[prevalence == 2][data.table(fullname_lower = tolower(x[is.na(y)])),
-                                                       on = "fullname_lower",
+                                                            on = "fullname_lower",
-                                                       ..property][[1]]
+                                                            ..property][[1]]
     }
     if (any(is.na(y))) {
       y[is.na(y)] <- reference_data_to_use[prevalence == 3][data.table(fullname_lower = tolower(x[is.na(y)])),
-                                                       on = "fullname_lower",
+                                                            on = "fullname_lower",
-                                                       ..property][[1]]
+                                                            ..property][[1]]
     }
     x <- y
     
@@ -548,7 +548,7 @@ exec_as.mo <- function(x,
       x[nchar(x_backup_without_spp) > 10] <- gsub("[+]", paste0("+[", constants, "]?"), x[nchar(x_backup_without_spp) > 10])
     }
     x <- strip_whitespace(x, dyslexia_mode)
-
+    
     x_trimmed <- x
     x_trimmed_species <- paste(x_trimmed, "species")
     x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed)
@@ -1067,9 +1067,9 @@ exec_as.mo <- function(x,
                       ref_old = found[1, ref],
                       ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
                       mo = microorganismsDT[col_id == found[1, col_id_new], mo])
-          if (initial_search == TRUE) {
+          # if (initial_search == TRUE) {
-            set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
+          #   set_mo_history(a.x_backup, get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
-          }
+          # }
           return(x[i])
         }
         
@@ -1099,7 +1099,7 @@ exec_as.mo <- function(x,
               message("Running '", d.x_withspaces_start_end, "' and '", e.x_withspaces_start_only, "'")
             }
             found <- data.old_to_check[fullname_lower %like_case% d.x_withspaces_start_end
-                                          | fullname_lower %like_case% e.x_withspaces_start_only]
+                                       | fullname_lower %like_case% e.x_withspaces_start_only]
             if (NROW(found) > 0 & nchar(g.x_backup_without_spp) >= 6) {
               if (property == "ref") {
                 # when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
@@ -1119,9 +1119,9 @@ exec_as.mo <- function(x,
                                       format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
                                                                input = a.x_backup,
                                                                result_mo = microorganismsDT[col_id == found[1, col_id_new], mo]))
-              if (initial_search == TRUE) {
+              # if (initial_search == TRUE) {
-                set_mo_history(a.x_backup, get_mo_code(x, property), 1, force = force_mo_history, disable = disable_mo_history)
+              #   set_mo_history(a.x_backup, get_mo_code(x, property), 1, force = force_mo_history, disable = disable_mo_history)
-              }
+              # }
               return(x)
             }
             
@@ -1520,7 +1520,7 @@ exec_as.mo <- function(x,
       # THEN TRY PREVALENT IN HUMAN INFECTIONS ----
       x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 2],
                                    data.old_to_check = microorganisms.oldDT[prevalence %in% c(2, 3)], # run all other old MOs the second time,
-                                                                                                      # otherwise e.g. mo_ref("Chlamydia psittaci") doesn't work correctly
+                                   # otherwise e.g. mo_ref("Chlamydia psittaci") doesn't work correctly
                                    a.x_backup = x_backup[i],
                                    b.x_trimmed = x_trimmed[i],
                                    c.x_trimmed_without_group = x_trimmed_without_group[i],
@@ -1931,12 +1931,12 @@ print.mo_renamed <- function(x, ...) {
   }
   for (i in 1:nrow(x)) {
     message(blue(paste0("NOTE: ", 
-                    italic(x$old_name[i]), ifelse(x$old_ref[i] %in% c("", NA), "", 
+                        italic(x$old_name[i]), ifelse(x$old_ref[i] %in% c("", NA), "", 
-                                                  paste0(" (",  gsub("et al.", italic("et al."), x$old_ref[i]), ")")),
+                                                      paste0(" (",  gsub("et al.", italic("et al."), x$old_ref[i]), ")")),
-                    " was renamed ", 
+                        " was renamed ", 
-                    italic(x$new_name[i]), ifelse(x$new_ref[i] %in% c("", NA), "", 
+                        italic(x$new_name[i]), ifelse(x$new_ref[i] %in% c("", NA), "", 
-                                                  paste0(" (",  gsub("et al.", italic("et al."), x$new_ref[i]), ")")),
+                                                      paste0(" (",  gsub("et al.", italic("et al."), x$new_ref[i]), ")")),
-                    " [", x$mo[i], "]")))
+                        " [", x$mo[i], "]")))
   }
 }
 

data-raw/reproduction_of_antibiotics.R

@@ -279,6 +279,7 @@ antibiotics <- abx2 %>%
 antibiotics[which(antibiotics$ab == "DOX"), "abbreviations"][[1]] <- list(c("dox", "doxy"))
 antibiotics[which(antibiotics$ab == "FLC"), "abbreviations"][[1]] <- list(c("clox"))
 antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CEC"), "abbreviations"][[1]], "CFC")) # cefaclor old WHONET4 code
+antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "AMX"), "synonyms"][[1]], "Amoxy")))
 # 'Polymixin B' (POL) and 'Polymyxin B' (PLB) both exist, so:
 antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "PLB"), "abbreviations"][[1]], "POL", "Polymixin", "Polymixin B"))
 antibiotics <- filter(antibiotics, ab != "POL")
@@ -303,6 +304,10 @@ antibiotics[which(antibiotics$ab == "CPC"), "abbreviations"][[1]] <- list(c("xpm
 antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]], "xpm"))
 antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
 antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct"))
+# High level Gentamcin and Streptomycin
+antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl"))
+antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl"))
+
 
 antibiotics <- antibiotics %>% arrange(name)
 

docs/404.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 

docs/authors.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</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">0.7.1.9098</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 

docs/news/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 
@@ -231,11 +231,11 @@
       
     </div>
 
-    <div id="amr-0-7-1-9098" class="section level1">
+    <div id="amr-0-7-1-9100" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0-7-1-9098" class="anchor"></a>AMR 0.7.1.9098<small> Unreleased </small>
+<a href="#amr-0-7-1-9100" class="anchor"></a>AMR 0.7.1.9100<small> Unreleased </small>
 </h1>
-<p><small>Last updated: 07-Oct-2019</small></p>
+<p><small>Last updated: 08-Oct-2019</small></p>
 <div id="breaking" class="section level3">
 <h3 class="hasAnchor">
 <a href="#breaking" class="anchor"></a>Breaking</h3>
@@ -370,6 +370,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
 <li>Added 80 new LIS codes for microorganisms</li>
 <li>Relabeled the factor levels of <code><a href="../reference/mdro.html">mdr_tb()</a></code>
 </li>
+<li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
 </ul>
 <div id="other" class="section level4">
 <h4 class="hasAnchor">
@@ -1289,7 +1290,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
     <div id="tocnav">
       <h2>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
-        <li><a href="#amr-0-7-1-9098">0.7.1.9098</a></li>
+        <li><a href="#amr-0-7-1-9100">0.7.1.9100</a></li>
         <li><a href="#amr-0-7-1">0.7.1</a></li>
         <li><a href="#amr-0-7-0">0.7.0</a></li>
         <li><a href="#amr-0-6-1">0.6.1</a></li>

docs/reference/bug_drug_combinations.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9089</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 
@@ -237,8 +237,7 @@
     <p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code>format</code> on the result to prettify it to a publicable/printable format, see Examples.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
+    <pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_shortname</span>, <span class='no'>...</span>)
-  <span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_shortname</span>, <span class='no'>...</span>)
 
 <span class='co'># S3 method for bug_drug_combinations</span>
 <span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>,
@@ -259,10 +258,6 @@
       <th>col_mo</th>
       <td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
     </tr>
-    <tr>
-      <th>minimum</th>
-      <td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
-    </tr>
     <tr>
       <th>FUN</th>
       <td><p>the function to call on the <code>mo</code> column to transform the microorganism IDs, defaults to <code><a href='mo_property.html'>mo_shortname</a></code></p></td>
@@ -279,6 +274,10 @@
       <th>language</th>
       <td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
     </tr>
+    <tr>
+      <th>minimum</th>
+      <td><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.</p></td>
+    </tr>
     <tr>
       <th>combine_SI</th>
       <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 section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
@@ -311,6 +310,9 @@
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The function <code>bug_drug_combinations</code> returns a <code>data.frame</code> with columns "mo", "ab", "S", "I", "R" and "total".</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
     <p>The function <code>format</code> calculates the resistance per bug-drug combination. Use <code>combine_IR = FALSE</code> (default) to test R vs. S+I and <code>combine_IR = TRUE</code> to test R+I vs. S.</p>
@@ -342,6 +344,7 @@
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
       <li><a href="#source">Source</a></li>
+      <li><a href="#value">Value</a></li>
       <li><a href="#details">Details</a></li>
       <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
       <li><a href="#examples">Examples</a></li>

docs/reference/eucast_rules.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9098</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 

docs/reference/mdro.html

@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9100</span>
       </span>
     </div>
 

man/bug_drug_combinations.Rd

@@ -8,8 +8,7 @@
 \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
 }
 \usage{
-bug_drug_combinations(x, col_mo = NULL, minimum = 30,
+bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
-  FUN = mo_shortname, ...)
 
 \method{format}{bug_drug_combinations}(x,
   translate_ab = "name (ab, atc)", language = get_locale(),
@@ -23,8 +22,6 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
 
 \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
 
-\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
-
 \item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}}}
 
 \item{...}{arguments passed on to \code{FUN}}
@@ -33,6 +30,8 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
 
 \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{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
+
 \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 section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
 
 \item{combine_IR}{logical to indicate whether values R and I should be summed}
@@ -48,6 +47,9 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
     \code{big.interval} decimals \emph{before} (hence \code{big}) the
     decimal point.}
 }
+\value{
+The function \code{bug_drug_combinations} returns a \code{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
+}
 \description{
 Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a publicable/printable format, see Examples.
 }