mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 06:46:11 +01:00
(v0.7.0.9007) renamed notes fix
This commit is contained in:
parent
44ab53128e
commit
699e87ab4a
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 0.7.0.9006
|
||||
Date: 2019-06-11
|
||||
Version: 0.7.0.9007
|
||||
Date: 2019-06-12
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
person(
|
||||
|
||||
3
NEWS.md
3
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
|
||||
|
||||
@ -89,6 +89,7 @@ globalVariables(c(".",
|
||||
"package_v",
|
||||
"Pasted",
|
||||
"patient_id",
|
||||
"pattern",
|
||||
"phylum",
|
||||
"plural",
|
||||
"prevalence",
|
||||
|
||||
10
R/mo.R
10
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
|
||||
|
||||
17
R/zzz.R
17
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!",
|
||||
"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)
|
||||
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, ". ",
|
||||
"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",
|
||||
F_CANDD_GUI = "F_MYRZY_GUI",
|
||||
F_CANDD_LUS = "F_CLVSP_LUS", B_STRPT_TUS = "B_STRPT",
|
||||
# putting full names here will throw notes with new taxonomic names
|
||||
F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "Candida krusei",
|
||||
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")
|
||||
}
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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>
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user