(v0.7.0.9007) renamed notes fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.7.0.9006
+Version: 0.7.0.9007
-Date: 2019-06-11
+Date: 2019-06-12
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 0.7.0.9006
+# AMR 0.7.0.9007
 
 #### New
 * Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
@@ -22,6 +22,7 @@
 * Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin
 * Removed `latest_annual_release` from the `catalogue_of_life_version()` function
 * Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
+* Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()`
 
 #### Other
 * Fixed a note thrown by CRAN tests

R/globals.R

@@ -89,6 +89,7 @@ globalVariables(c(".",
                   "package_v",
                   "Pasted",
                   "patient_id",
+                  "pattern",
                   "phylum",
                   "plural",
                   "prevalence",

R/mo.R

@@ -748,7 +748,7 @@ exec_as.mo <- function(x,
               set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
             }
             options(mo_renamed = c(getOption("mo_renamed"),
-                                   magenta(paste0("Note: ",
+                                   magenta(paste0("NOTE: ",
                                                   italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
                                                   " was considered ",
                                                   italic("Salmonella species"),
@@ -760,7 +760,7 @@ exec_as.mo <- function(x,
               set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
             }
             options(mo_renamed = c(getOption("mo_renamed"),
-                                   magenta(paste0("Note: ",
+                                   magenta(paste0("NOTE: ",
                                                   italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
                                                   " was considered a subspecies of ",
                                                   italic("Salmonella enterica"),
@@ -1233,7 +1233,7 @@ exec_as.mo <- function(x,
     post_Becker <- c("argensis", "caeli", "cornubiensis", "edaphicus")
     if (any(x %in% MOs_staph[species %in% post_Becker, ..property][[1]])) {
 
-      warning("Becker ", italic("et al."), " (2014) does not contain species named after their publication: ",
+      warning("Becker ", italic("et al."), " (2014, 2019) does not contain species named after their publication: ",
               italic(paste("S.",
                            sort(mo_species(unique(x[x %in% MOs_staph[species %in% post_Becker, ..property][[1]]]))),
                            collapse = ", ")),
@@ -1306,7 +1306,7 @@ exec_as.mo <- function(x,
     }
     notes <- sort(notes)
     for (i in 1:length(notes)) {
-      base::message(blue(paste("Note:", notes[i])))
+      base::message(blue(paste("NOTE:", notes[i])))
     }
   }
 
@@ -1336,7 +1336,7 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
   }
   msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
   msg <- gsub("et al.", italic("et al."), msg)
-  options(mo_renamed = sort(msg))
+  options(mo_renamed = c(getOption("mo_renamed"), sort(msg)))
 }
 
 #' @exportMethod print.mo

R/zzz.R

@@ -53,12 +53,14 @@
 
 
 .onAttach <- function(...) {
-  if (interactive()) {
+  if (interactive() & !isFALSE(getOption("AMR_survey"))) {
+    options(AMR_survey = FALSE)
     console_width <- options()$width - 1
     url <- "https://www.surveymonkey.com/r/AMR_for_R"
-    txt <- paste("Thanks for using the AMR package!",
+    txt <- paste0("Thanks for using the AMR package! ",
                  "As researchers, we are interested in how and why you use this package and if there are things you're missing from it. ",
-                 "Please fill in our 2-minute survey at:", url)
+                 "Please fill in our 2-minute survey at: ", url, ". ",
+                 "This message can be turned off with: options(AMR_survey = FALSE)")
 
     # make it honour new lines bases on console width:
     txt <- unlist(strsplit(txt, " "))
@@ -278,9 +280,10 @@ make_trans_tbl <- function() {
     B_GRDNR = "B_GRLLA", B_SGMNS = "B_SNGMNS", B_TCLLS = "B_THBCL",
     F_CCCCS = "F_CRYPT",
     # renamings of old genus + species
-    F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "F_ISSTC_ORI",
+    # putting full names here will throw notes with new taxonomic names
-    F_CANDD_GUI = "F_MYRZY_GUI",
+    F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "Candida krusei",
-    F_CANDD_LUS = "F_CLVSP_LUS", B_STRPT_TUS = "B_STRPT",
+    F_CANDD_GUI = "Candida guilliermondii", F_HNSNL_ANO = "Hansenula anomala",
+    F_CANDD_LUS = "Candida lusitaniae", B_STRPT_TUS = "B_STRPT",
     B_PRVTL_OLA = "B_PRVTL_OULO", B_FSBCT_RUM = "B_FSBCT",
     B_CRYNB_EYI = "B_CRYNB_FRE", B_OLGLL_LIS = "B_OLGLL_URE")
 }

docs/LICENSE-text.html

@@ -78,7 +78,7 @@
       </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">0.7.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -78,7 +78,7 @@
       </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">0.7.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
       </span>
     </div>
 

docs/authors.html

@@ -78,7 +78,7 @@
       </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">0.7.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </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">0.7.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
       </span>
     </div>
 

docs/news/index.html

@@ -78,7 +78,7 @@
       </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">0.7.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
       </span>
     </div>
 
@@ -232,9 +232,9 @@
       
     </div>
 
-    <div id="amr-0709006" class="section level1">
+    <div id="amr-0709007" class="section level1">
 <h1 class="page-header">
-<a href="#amr-0709006" class="anchor"></a>AMR 0.7.0.9006<small> Unreleased </small>
+<a href="#amr-0709007" class="anchor"></a>AMR 0.7.0.9007<small> Unreleased </small>
 </h1>
 <div id="new" class="section level4">
 <h4 class="hasAnchor">
@@ -268,6 +268,8 @@
 <li>Removed <code>latest_annual_release</code> from the <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
 <li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
 </li>
+<li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
+</li>
 </ul>
 </div>
 <div id="other" class="section level4">
@@ -1106,7 +1108,7 @@ 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-0709006">0.7.0.9006</a></li>
+        <li><a href="#amr-0709007">0.7.0.9007</a></li>
         <li><a href="#amr-070">0.7.0</a></li>
         <li><a href="#amr-061">0.6.1</a></li>
         <li><a href="#amr-060">0.6.0</a></li>

docs/reference/index.html

@@ -78,7 +78,7 @@
       </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">0.7.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
       </span>
     </div>