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(v0.7.0.9007) renamed notes fix

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dr. M.S. (Matthijs) Berends 2019-06-12 16:08:20 +02:00
parent 44ab53128e
commit 699e87ab4a
11 changed files with 31 additions and 24 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.0.9006 Version: 0.7.0.9007
Date: 2019-06-11 Date: 2019-06-12
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.0.9006 # AMR 0.7.0.9007
#### New #### 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*: * 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 * 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 `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` * 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 #### Other
* Fixed a note thrown by CRAN tests * Fixed a note thrown by CRAN tests

1
R/globals.R
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@ -89,6 +89,7 @@ globalVariables(c(".",
"package_v", "package_v",
"Pasted", "Pasted",
"patient_id", "patient_id",
"pattern",
"phylum", "phylum",
"plural", "plural",
"prevalence", "prevalence",

10
R/mo.R
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@ -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) set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
} }
options(mo_renamed = c(getOption("mo_renamed"), options(mo_renamed = c(getOption("mo_renamed"),
magenta(paste0("Note: ", magenta(paste0("NOTE: ",
italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])), italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
" was considered ", " was considered ",
italic("Salmonella species"), 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) set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
} }
options(mo_renamed = c(getOption("mo_renamed"), options(mo_renamed = c(getOption("mo_renamed"),
magenta(paste0("Note: ", magenta(paste0("NOTE: ",
italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])), italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
" was considered a subspecies of ", " was considered a subspecies of ",
italic("Salmonella enterica"), italic("Salmonella enterica"),
@ -1233,7 +1233,7 @@ exec_as.mo <- function(x,
post_Becker <- c("argensis", "caeli", "cornubiensis", "edaphicus") post_Becker <- c("argensis", "caeli", "cornubiensis", "edaphicus")
if (any(x %in% MOs_staph[species %in% post_Becker, ..property][[1]])) { 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.", italic(paste("S.",
sort(mo_species(unique(x[x %in% MOs_staph[species %in% post_Becker, ..property][[1]]]))), sort(mo_species(unique(x[x %in% MOs_staph[species %in% post_Becker, ..property][[1]]]))),
collapse = ", ")), collapse = ", ")),
@ -1306,7 +1306,7 @@ exec_as.mo <- function(x,
} }
notes <- sort(notes) notes <- sort(notes)
for (i in 1:length(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 <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
msg <- gsub("et al.", italic("et al."), msg) 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 #' @exportMethod print.mo

17
R/zzz.R
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@ -53,12 +53,14 @@
.onAttach <- function(...) { .onAttach <- function(...) {
if (interactive()) { if (interactive() & !isFALSE(getOption("AMR_survey"))) {
options(AMR_survey = FALSE)
console_width <- options()$width - 1 console_width <- options()$width - 1
url <- "https://www.surveymonkey.com/r/AMR_for_R" 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.", "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: # make it honour new lines bases on console width:
txt <- unlist(strsplit(txt, " ")) txt <- unlist(strsplit(txt, " "))
@ -278,9 +280,10 @@ make_trans_tbl <- function() {
B_GRDNR = "B_GRLLA", B_SGMNS = "B_SNGMNS", B_TCLLS = "B_THBCL", B_GRDNR = "B_GRLLA", B_SGMNS = "B_SNGMNS", B_TCLLS = "B_THBCL",
F_CCCCS = "F_CRYPT", F_CCCCS = "F_CRYPT",
# renamings of old genus + species # 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_PRVTL_OLA = "B_PRVTL_OULO", B_FSBCT_RUM = "B_FSBCT",
B_CRYNB_EYI = "B_CRYNB_FRE", B_OLGLL_LIS = "B_OLGLL_URE") B_CRYNB_EYI = "B_CRYNB_FRE", B_OLGLL_LIS = "B_OLGLL_URE")
} }

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

10
docs/news/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>
@ -232,9 +232,9 @@
</div> </div>
<div id="amr-0709006" class="section level1"> <div id="amr-0709007" class="section level1">
<h1 class="page-header"> <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> </h1>
<div id="new" class="section level4"> <div id="new" class="section level4">
<h4 class="hasAnchor"> <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 <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>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
</li> </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> </ul>
</div> </div>
<div id="other" class="section level4"> <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"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <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-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li> <li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li> <li><a href="#amr-060">0.6.0</a></li>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>