fix for Salmonella group A, unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9114
+Version: 1.8.2.9115
 Date: 2023-02-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9114
+# AMR 1.8.2.9115
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/aa_globals.R

@@ -94,7 +94,9 @@ TAXONOMY_VERSION <- list(
 )
 
 globalVariables(c(
+  ".mo",
   ".rowid",
+  ".syndromic_group",
   "ab",
   "ab_txt",
   "affect_ab_name",
@@ -105,8 +107,10 @@ globalVariables(c(
   "atc_group1",
   "atc_group2",
   "base_ab",
-  "ci_min",
+  "bind_rows",
   "ci_max",
+  "ci_min",
+  "clinical_breakpoints",
   "code",
   "cols",
   "count",
@@ -138,6 +142,7 @@ globalVariables(c(
   "mo",
   "name",
   "new",
+  "numerator",
   "observations",
   "old",
   "old_name",
@@ -149,13 +154,14 @@ globalVariables(c(
   "reference.rule_group",
   "reference.version",
   "rowid",
-  "sir",
-  "clinical_breakpoints",
   "rule_group",
   "rule_name",
   "se_max",
   "se_min",
+  "SI",
+  "sir",
   "species",
+  "syndromic_group",
   "total",
   "txt",
   "type",

R/bug_drug_combinations.R

@@ -165,7 +165,7 @@ bug_drug_combinations <- function(x,
     out <- run_it(x)
   }
   rownames(out) <- NULL
-  out <- out %>% pm_arrange(mo, ab)
+  out <- out %pm>% pm_arrange(mo, ab)
   out <- as_original_data_class(out, class(x.bak)) # will remove tibble groups
   structure(out, class = c("bug_drug_combinations", ifelse(data_has_groups, "grouped", character(0)), class(out)))
 }

R/mo.R

@@ -966,14 +966,14 @@ convert_colloquial_input <- function(x) {
   out[x %like_case% "(viridans.* (strepto|^s).*|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
 
   # Salmonella in different languages, like "Salmonella grupo B"
-  out[x %like_case% "salmonella.* [bcd]$"] <- gsub(".*salmonella.* ([bcd])$",
+  out[x %like_case% "salmonella.* [abcd]$"] <- gsub(".*salmonella.* ([abcd])$",
     "B_SLMNL_GRP\\U\\1",
-    x[x %like_case% "salmonella.* [bcd]$"],
+    x[x %like_case% "salmonella.* [abcd]$"],
     perl = TRUE
   )
-  out[x %like_case% "group [bcd] salmonella"] <- gsub(".*group ([bcd]) salmonella*",
+  out[x %like_case% "group [abcd] salmonella"] <- gsub(".*group ([abcd]) salmonella*",
     "B_SLMNL_GRP\\U\\1",
-    x[x %like_case% "group [bcd] salmonella"],
+    x[x %like_case% "group [abcd] salmonella"],
     perl = TRUE
   )
 

R/mo_property.R

@@ -69,9 +69,8 @@
 #' @return
 #' - An [integer] in case of [mo_year()]
 #' - An [ordered factor][factor] in case of [mo_pathogenicity()]
-#' - A [list] in case of [mo_taxonomy()], [mo_synonyms()] and [mo_info()]
+#' - A [list] in case of [mo_taxonomy()], [mo_synonyms()], [mo_snomed()] and [mo_info()]
 #' - A named [character] in case of [mo_url()]
-#' - A [numeric] in case of [mo_snomed()]
 #' - A [character] in all other cases
 #' @export
 #' @seealso Data set [microorganisms]

inst/tinytest/test-mo_property.R

@@ -163,7 +163,7 @@ expect_identical(mo_current(c("Escherichia blattae", "Escherichia coli")),
 expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
 expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
 
-expect_true(112283007 %in% mo_snomed("Escherichia coli"))
+expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
 # old codes must throw a warning in mo_* family
 expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
 # outcome of mo_fullname must always return the fullname from the data set

man/mo_property.Rd

@@ -284,9 +284,8 @@ mo_property(
 \itemize{
 \item An \link{integer} in case of \code{\link[=mo_year]{mo_year()}}
 \item An \link[=factor]{ordered factor} in case of \code{\link[=mo_pathogenicity]{mo_pathogenicity()}}
-\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}}, \code{\link[=mo_synonyms]{mo_synonyms()}} and \code{\link[=mo_info]{mo_info()}}
+\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}}, \code{\link[=mo_synonyms]{mo_synonyms()}}, \code{\link[=mo_snomed]{mo_snomed()}} and \code{\link[=mo_info]{mo_info()}}
 \item A named \link{character} in case of \code{\link[=mo_url]{mo_url()}}
-\item A \link{numeric} in case of \code{\link[=mo_snomed]{mo_snomed()}}
 \item A \link{character} in all other cases
 }
 }