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(v3.0.1.9066) fix documentation

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dr. M.S. (Matthijs) Berends
2026-06-24 19:34:47 +02:00
parent 39b6a250de
commit a88150ca4a
7 changed files with 38 additions and 28 deletions
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2
DESCRIPTION
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@@ -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)

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9065
# AMR 3.0.1.9066
Planned as v3.1.0, end of June 2026.

5
R/data.R
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@@ -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

32
R/mo_property.R
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@@ -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)

8
index.md
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@@ -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:

5
man/microorganisms.Rd
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@@ -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}.

12
man/mo_property.Rd
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@@ -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")