mirror of https://github.com/msberends/AMR.git
(v0.7.0.9007) renamed notes fix
This commit is contained in:
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.7.0.9006
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Date: 2019-06-11
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Version: 0.7.0.9007
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Date: 2019-06-12
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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3
NEWS.md
3
NEWS.md
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@ -1,4 +1,4 @@
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# AMR 0.7.0.9006
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# AMR 0.7.0.9007
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#### New
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* 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*:
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@ -22,6 +22,7 @@
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* Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin
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* Removed `latest_annual_release` from the `catalogue_of_life_version()` function
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* Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
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* Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()`
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#### Other
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* Fixed a note thrown by CRAN tests
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@ -89,6 +89,7 @@ globalVariables(c(".",
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"package_v",
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"Pasted",
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"patient_id",
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"pattern",
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"phylum",
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"plural",
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"prevalence",
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10
R/mo.R
10
R/mo.R
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@ -748,7 +748,7 @@ exec_as.mo <- function(x,
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
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}
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options(mo_renamed = c(getOption("mo_renamed"),
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magenta(paste0("Note: ",
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magenta(paste0("NOTE: ",
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italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
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" was considered ",
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italic("Salmonella species"),
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@ -760,7 +760,7 @@ exec_as.mo <- function(x,
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set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
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}
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options(mo_renamed = c(getOption("mo_renamed"),
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magenta(paste0("Note: ",
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magenta(paste0("NOTE: ",
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italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
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" was considered a subspecies of ",
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italic("Salmonella enterica"),
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@ -1233,7 +1233,7 @@ exec_as.mo <- function(x,
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post_Becker <- c("argensis", "caeli", "cornubiensis", "edaphicus")
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if (any(x %in% MOs_staph[species %in% post_Becker, ..property][[1]])) {
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warning("Becker ", italic("et al."), " (2014) does not contain species named after their publication: ",
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warning("Becker ", italic("et al."), " (2014, 2019) does not contain species named after their publication: ",
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italic(paste("S.",
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sort(mo_species(unique(x[x %in% MOs_staph[species %in% post_Becker, ..property][[1]]]))),
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collapse = ", ")),
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@ -1306,7 +1306,7 @@ exec_as.mo <- function(x,
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}
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notes <- sort(notes)
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for (i in 1:length(notes)) {
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base::message(blue(paste("Note:", notes[i])))
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base::message(blue(paste("NOTE:", notes[i])))
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}
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}
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@ -1336,7 +1336,7 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
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}
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msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
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msg <- gsub("et al.", italic("et al."), msg)
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options(mo_renamed = sort(msg))
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options(mo_renamed = c(getOption("mo_renamed"), sort(msg)))
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}
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#' @exportMethod print.mo
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17
R/zzz.R
17
R/zzz.R
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@ -53,12 +53,14 @@
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.onAttach <- function(...) {
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if (interactive()) {
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if (interactive() & !isFALSE(getOption("AMR_survey"))) {
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options(AMR_survey = FALSE)
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console_width <- options()$width - 1
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url <- "https://www.surveymonkey.com/r/AMR_for_R"
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txt <- paste("Thanks for using the AMR package!",
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"As researchers, we are interested in how and why you use this package and if there are things you're missing from it.",
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"Please fill in our 2-minute survey at:", url)
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txt <- paste0("Thanks for using the AMR package! ",
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"As researchers, we are interested in how and why you use this package and if there are things you're missing from it. ",
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"Please fill in our 2-minute survey at: ", url, ". ",
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"This message can be turned off with: options(AMR_survey = FALSE)")
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# make it honour new lines bases on console width:
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txt <- unlist(strsplit(txt, " "))
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@ -278,9 +280,10 @@ make_trans_tbl <- function() {
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B_GRDNR = "B_GRLLA", B_SGMNS = "B_SNGMNS", B_TCLLS = "B_THBCL",
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F_CCCCS = "F_CRYPT",
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# renamings of old genus + species
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F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "F_ISSTC_ORI",
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F_CANDD_GUI = "F_MYRZY_GUI",
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F_CANDD_LUS = "F_CLVSP_LUS", B_STRPT_TUS = "B_STRPT",
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# putting full names here will throw notes with new taxonomic names
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F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "Candida krusei",
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F_CANDD_GUI = "Candida guilliermondii", F_HNSNL_ANO = "Hansenula anomala",
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F_CANDD_LUS = "Candida lusitaniae", B_STRPT_TUS = "B_STRPT",
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B_PRVTL_OLA = "B_PRVTL_OULO", B_FSBCT_RUM = "B_FSBCT",
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B_CRYNB_EYI = "B_CRYNB_FRE", B_OLGLL_LIS = "B_OLGLL_URE")
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}
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
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</span>
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</div>
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@ -232,9 +232,9 @@
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</div>
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<div id="amr-0709006" class="section level1">
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<div id="amr-0709007" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0709006" class="anchor"></a>AMR 0.7.0.9006<small> Unreleased </small>
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<a href="#amr-0709007" class="anchor"></a>AMR 0.7.0.9007<small> Unreleased </small>
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</h1>
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<div id="new" class="section level4">
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<h4 class="hasAnchor">
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@ -268,6 +268,8 @@
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<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>
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<li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
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</li>
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<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>
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</li>
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</ul>
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</div>
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<div id="other" class="section level4">
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@ -1106,7 +1108,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0709006">0.7.0.9006</a></li>
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<li><a href="#amr-0709007">0.7.0.9007</a></li>
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<li><a href="#amr-070">0.7.0</a></li>
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<li><a href="#amr-061">0.6.1</a></li>
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<li><a href="#amr-060">0.6.0</a></li>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
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</span>
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</div>
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