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v1.5.0

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dr. M.S. (Matthijs) Berends
2021-01-06 11:16:17 +01:00
parent 1563dcd1aa
commit 3b84b8be75
39 changed files with 128 additions and 123 deletions
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15
R/ab_class_selectors.R
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@@ -27,7 +27,7 @@
#'
#' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
#' @inheritParams filter_ab_class
#' @details These functions only work in R 3.2 (2015) and later.
#' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
#'
#' All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#' @rdname antibiotic_class_selectors
@@ -165,7 +165,9 @@ ab_selector <- function(ab_class, function_name) {
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
warning_(function_name, "() can only be used in R >= 3.2", call = FALSE)
warning_("antibiotic class selectors such as ", function_name,
"() require R version 3.2 or later - you have ", R.version.string,
call = FALSE)
return(NULL)
}
@@ -194,10 +196,11 @@ ab_selector <- function(ab_class, function_name) {
if (length(agents) == 0) {
message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
} else {
message_("Selecting ", ab_group, ": ",
paste(paste0("column '", font_bold(agents, collapse = NULL),
"' (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
collapse = ", "),
agents_formatted <- paste0("column '", font_bold(agents, collapse = NULL), "'")
agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
agents_formatted[agents != agents_names] <- paste0(agents_formatted[agents != agents_names],
" (", agents_names[agents != agents_names], ")")
message_("Selecting ", ab_group, ": ", paste(agents_formatted, collapse = ", "),
as_note = FALSE,
extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
}

2
R/catalogue_of_life.R
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@@ -44,7 +44,7 @@ format_included_data_number <- function(data) {
#' This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.
#' @section Catalogue of Life:
#' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
#' This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/Sp2000/colplus) is finished, which we await.
#' This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
#'
#' [Click here][catalogue_of_life] for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with [catalogue_of_life_version()].
#' @section Included taxa:

4
R/data.R
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@@ -120,7 +120,7 @@
#' In February 2020, the DSMZ records were merged with the List of Prokaryotic names with Standing in Nomenclature (LPSN).
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
#'
#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
#'
#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> and <https://lpsn.dsmz.de> (check included version with [catalogue_of_life_version()]).
#' @inheritSection AMR Reference data publicly available
@@ -147,7 +147,7 @@ catalogue_of_life <- list(
#' - `prevalence`\cr Prevalence of the microorganism, see [as.mo()]
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
#'
#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
#' @seealso [as.mo()] [mo_property()] [microorganisms]

4
R/eucast_rules.R
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@@ -83,7 +83,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#'
#' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
#'
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`.
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the option `AMR_eucastrules`, i.e. run `options(AMR_eucastrules = "all")`.
#' @section Antibiotics:
#' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
#'
@@ -96,7 +96,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @return The input of `x`, possibly with edited values of antibiotics. Or, if `verbose = TRUE`, a [data.frame] with all original and new values of the affected bug-drug combinations.
#' @source
#' - EUCAST Expert Rules. Version 2.0, 2012.\cr
#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60. [(link)](https://doi.org/10.1111/j.1469-0691.2011.03703.x)
#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)

6
R/mdro.R
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@@ -59,7 +59,7 @@
#'
#' * `guideline = "MRGN"`
#'
#' The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6
#' The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6}
#'
#' * `guideline = "BRMO"`
#'
@@ -193,7 +193,7 @@ mdro <- function(x,
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
guideline$version <- NA
guideline$source_url <- "Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
guideline$source_url <- "Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x"
guideline$type <- "MDRs/XDRs/PDRs"
} else if (guideline$code == "eucast3.1") {
@@ -222,7 +222,7 @@ mdro <- function(x,
guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
guideline$version <- NA
guideline$source_url <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
guideline$source_url <- "Antimicrobial Resistance and Infection Control 4:7, 2015; doi: 10.1186/s13756-015-0047-6"
guideline$type <- "MRGNs"
} else if (guideline$code == "brmo") {

8
R/mo.R
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@@ -102,10 +102,10 @@
#' @inheritSection catalogue_of_life Catalogue of Life
# (source as a section here, so it can be inherited by other man pages:)
#' @section Source:
#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926. <https://dx.doi.org/10.1128/CMR.00109-13>
#' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect. <https://doi.org/10.1016/j.cmi.2019.02.028>
#' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366. <https://dx.doi.org/10.1080/14787210.2020.1730813>
#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95. <https://dx.doi.org/10.1084/jem.57.4.571>
#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926; \doi{10.1128/CMR.00109-13}
#' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
#' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
#' 5. Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
#' @export
#' @return A [character] [vector] with additional class [`mo`]