From a88150ca4ad5527326574cbedde76239a3611e87 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Wed, 24 Jun 2026 19:34:47 +0200 Subject: [PATCH] (v3.0.1.9066) fix documentation --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/data.R | 5 ++--- R/mo_property.R | 32 +++++++++++++++++++------------- index.md | 8 ++++---- man/microorganisms.Rd | 5 ++--- man/mo_property.Rd | 12 +++++++++--- 7 files changed, 38 insertions(+), 28 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7f0aed7b2..90fa94f1c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9065 +Version: 3.0.1.9066 Date: 2026-06-24 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 49ad369ff..942a00893 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9065 +# AMR 3.0.1.9066 Planned as v3.1.0, end of June 2026. diff --git a/R/data.R b/R/data.R index 1a21716dc..279c61556 100755 --- a/R/data.R +++ b/R/data.R @@ -143,11 +143,10 @@ #' ### Manual additions #' For convenience, some entries were added manually: #' +#' - All `r format_included_data_number(length(which(microorganisms$rank == "species group")))` groups and complexes of the [microorganisms.groups] data set, for cross-reference (examples include beta-haemolytic *Streptococcus* groups A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium tuberculosis* complex, etc.) #' - `r format_included_data_number(microorganisms[which(microorganisms$source == "manually added" & microorganisms$genus == "Salmonella"), , drop = FALSE])` entries of *Salmonella*, such as the city-like serovars and groups A to H -#' - `r format_included_data_number(length(which(microorganisms$rank == "species group")))` species groups (such as the beta-haemolytic *Streptococcus* groups A to K, coagulase-negative *Staphylococcus* (CoNS), *Mycobacterium tuberculosis* complex, etc.), of which the group compositions are stored in the [microorganisms.groups] data set #' - 1 entry of *Blastocystis* (*B. hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993) -#' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology -#' - 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria) +#' - `r sum(microorganisms$fullname %like% "unknown")` other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria) #' #' The syntax used to transform the original data to a cleansed \R format, can be [found here](https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R). #' @inheritSection AMR Download Our Reference Data diff --git a/R/mo_property.R b/R/mo_property.R index f16fa7ee5..525f2ebaf 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -83,6 +83,7 @@ #' @examples #' # taxonomic tree ----------------------------------------------------------- #' +#' mo_domain("Klebsiella pneumoniae") #' mo_kingdom("Klebsiella pneumoniae") #' mo_phylum("Klebsiella pneumoniae") #' mo_class("Klebsiella pneumoniae") @@ -92,6 +93,8 @@ #' mo_species("Klebsiella pneumoniae") #' mo_subspecies("Klebsiella pneumoniae") #' +#' # all in one go +#' mo_taxonomy("Klebsiella pneumoniae") #' #' # full names and short names ----------------------------------------------- #' @@ -112,6 +115,7 @@ #' mo_url("Klebsiella pneumoniae") #' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) #' +#' mo_group_members("Streptococcus group A") #' mo_group_members(c( #' "Streptococcus group A", #' "Streptococcus group C", @@ -155,6 +159,7 @@ #' #' mo_fullname("Staph epidermidis") #' mo_fullname("Staph epidermidis", Becker = TRUE) +#' #' mo_shortname("Staph epidermidis") #' mo_shortname("Staph epidermidis", Becker = TRUE) #' @@ -163,6 +168,7 @@ #' #' mo_fullname("Strep agalactiae") #' mo_fullname("Strep agalactiae", Lancefield = TRUE) +#' #' mo_shortname("Strep agalactiae") #' mo_shortname("Strep agalactiae", Lancefield = TRUE) #' @@ -175,10 +181,10 @@ #' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek #' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian #' -#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated -#' mo_kingdom("Klebsiella pneumoniae") +#' # mo_type is equal to mo_domain, but mo_domain will remain untranslated +#' mo_domain("Klebsiella pneumoniae") #' mo_type("Klebsiella pneumoniae") -#' mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect +#' mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect #' mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated #' #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de") @@ -807,19 +813,19 @@ mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) - x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) + x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() out <- list( - domain = mo_domain(x, language = language, keep_synonyms = keep_synonyms), - kingdom = mo_kingdom(x, language = language, keep_synonyms = keep_synonyms), - phylum = mo_phylum(x, language = language, keep_synonyms = keep_synonyms), - class = mo_class(x, language = language, keep_synonyms = keep_synonyms), - order = mo_order(x, language = language, keep_synonyms = keep_synonyms), - family = mo_family(x, language = language, keep_synonyms = keep_synonyms), - genus = mo_genus(x, language = language, keep_synonyms = keep_synonyms), - species = mo_species(x, language = language, keep_synonyms = keep_synonyms), - subspecies = mo_subspecies(x, language = language, keep_synonyms = keep_synonyms) + domain = mo_domain(x.mo, language = language, keep_synonyms = keep_synonyms), + kingdom = suppressMessages(mo_kingdom(x.mo, language = language, keep_synonyms = keep_synonyms)), + phylum = mo_phylum(x.mo, language = language, keep_synonyms = keep_synonyms), + class = mo_class(x.mo, language = language, keep_synonyms = keep_synonyms), + order = mo_order(x.mo, language = language, keep_synonyms = keep_synonyms), + family = mo_family(x.mo, language = language, keep_synonyms = keep_synonyms), + genus = mo_genus(x.mo, language = language, keep_synonyms = keep_synonyms), + species = mo_species(x.mo, language = language, keep_synonyms = keep_synonyms), + subspecies = mo_subspecies(x.mo, language = language, keep_synonyms = keep_synonyms) ) load_mo_uncertainties(metadata) diff --git a/index.md b/index.md index 23a87c6f1..45829bd79 100644 --- a/index.md +++ b/index.md @@ -230,7 +230,7 @@ wisca(example_isolates, | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | |:---|:---|:---| -| 70.1% (64.9-75.7%) | 93.6% (92.2-95%) | 89.8% (86.7-92.3%) | +| 69.9% (64.7-75.2%) | 93.7% (92.2-95.1%) | 89.8% (86.8-92.3%) | WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates: @@ -245,9 +245,9 @@ wisca(example_isolates, | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | |:---|:---|:---|:---| -| Clinical | 74.5% (69.3-80.1%) | 93.7% (92-95.1%) | 90.5% (87.1-93.1%) | -| ICU | 56.7% (48-65.5%) | 86.7% (83.4-89.8%) | 82.9% (78.2-87.3%) | -| Outpatient | 57.8% (46.4-69.7%) | 76.5% (70.1-82.2%) | 67.9% (57.9-77.5%) | +| Clinical | 74.6% (69-80.1%) | 93.6% (91.9-95.1%) | 90.5% (86.9-93%) | +| ICU | 57% (48.7-65.8%) | 86.7% (83.7-89.7%) | 82.8% (77.9-87.2%) | +| Outpatient | 57.5% (46.5-68.7%) | 76.7% (70.6-82.4%) | 67.5% (57.2-76.7%) | **For AMR surveillance**, traditional antibiograms remain the right tool for tracking resistance per species over time: diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index d75ad1714..4f96d3997 100644 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -59,11 +59,10 @@ Included taxonomic data from \href{https://lpsn.dsmz.de}{LPSN}, \href{https://ww For convenience, some entries were added manually: \itemize{ +\item All 37 groups and complexes of the \link{microorganisms.groups} data set, for cross-reference (examples include beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.) \item ~1 500 entries of \emph{Salmonella}, such as the city-like serovars and groups A to H -\item 37 species groups (such as the beta-haemolytic \emph{Streptococcus} groups A to K, coagulase-negative \emph{Staphylococcus} (CoNS), \emph{Mycobacterium tuberculosis} complex, etc.), of which the group compositions are stored in the \link{microorganisms.groups} data set \item 1 entry of \emph{Blastocystis} (\emph{B. hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993) -\item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology -\item 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria) +\item 9 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria) } The syntax used to transform the original data to a cleansed \R format, can be \href{https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R}{found here}. diff --git a/man/mo_property.Rd b/man/mo_property.Rd index adebf117e..50394f8fa 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -401,6 +401,7 @@ Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct \examples{ # taxonomic tree ----------------------------------------------------------- +mo_domain("Klebsiella pneumoniae") mo_kingdom("Klebsiella pneumoniae") mo_phylum("Klebsiella pneumoniae") mo_class("Klebsiella pneumoniae") @@ -410,6 +411,8 @@ mo_genus("Klebsiella pneumoniae") mo_species("Klebsiella pneumoniae") mo_subspecies("Klebsiella pneumoniae") +# all in one go +mo_taxonomy("Klebsiella pneumoniae") # full names and short names ----------------------------------------------- @@ -430,6 +433,7 @@ mo_rank("Klebsiella pneumoniae") mo_url("Klebsiella pneumoniae") mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) +mo_group_members("Streptococcus group A") mo_group_members(c( "Streptococcus group A", "Streptococcus group C", @@ -473,6 +477,7 @@ mo_shortname("K. pneu rh") mo_fullname("Staph epidermidis") mo_fullname("Staph epidermidis", Becker = TRUE) + mo_shortname("Staph epidermidis") mo_shortname("Staph epidermidis", Becker = TRUE) @@ -481,6 +486,7 @@ mo_shortname("Staph epidermidis", Becker = TRUE) mo_fullname("Strep agalactiae") mo_fullname("Strep agalactiae", Lancefield = TRUE) + mo_shortname("Strep agalactiae") mo_shortname("Strep agalactiae", Lancefield = TRUE) @@ -493,10 +499,10 @@ mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian -# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated -mo_kingdom("Klebsiella pneumoniae") +# mo_type is equal to mo_domain, but mo_domain will remain untranslated +mo_domain("Klebsiella pneumoniae") mo_type("Klebsiella pneumoniae") -mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect +mo_domain("Klebsiella pneumoniae", language = "zh") # Chinese, no effect mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")