diff --git a/NEWS.md b/NEWS.md index 1bca0175..e913b50b 100755 --- a/NEWS.md +++ b/NEWS.md @@ -15,6 +15,7 @@ * Function `first_isolate`: * Will now use a column named like "patid" for the patient ID (parameter `col_patientid`), when this parameter was left blank * Will now use a column named like "key(...)ab" or "key(...)antibiotics" for the key antibiotics (parameter `col_keyantibiotics`), when this parameter was left blank +* Function `mo_taxonomy` now contains the kingdom too * Function `first_isolate` will now use a column named like "patid" for the patient ID, when this parameter was left blank * Reduce false positives for `is.rsi.eligible` * Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)` diff --git a/R/mo.R b/R/mo.R index ad0208c0..e13e07d7 100644 --- a/R/mo.R +++ b/R/mo.R @@ -76,7 +76,7 @@ #' \code{guess_mo} is an alias of \code{as.mo}. #' @section ITIS: #' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} -#' This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). +#' This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). #' #' All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. #' diff --git a/R/mo_property.R b/R/mo_property.R index 2bc24ac9..fd5da451 100644 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -275,7 +275,8 @@ mo_year <- function(x, ...) { #' @export mo_taxonomy <- function(x, ...) { x <- AMR::as.mo(x, ...) - base::list(subkingdom = mo_subkingdom(x), + base::list(kingdom = mo_kingdom(x), + subkingdom = mo_subkingdom(x), phylum = mo_phylum(x), class = mo_class(x), order = mo_order(x), diff --git a/README.md b/README.md index 956ac9ca..7db13bd9 100755 --- a/README.md +++ b/README.md @@ -81,7 +81,7 @@ The `AMR` package basically does four important things: ### ITIS -This package contains the **complete microbial taxonomic data** (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). +This package contains the **complete microbial taxonomic data** (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). All (sub)species from **the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package**, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 77e5f509..1e98159b 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -83,7 +83,7 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will \section{ITIS}{ \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} -This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). +This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index 9e40eec4..f5495bdd 100755 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -34,7 +34,7 @@ A data set containing the complete microbial taxonomy of the kingdoms Bacteria, \section{ITIS}{ \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} -This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). +This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. diff --git a/man/microorganisms.old.Rd b/man/microorganisms.old.Rd index 21668920..9558c8c3 100644 --- a/man/microorganisms.old.Rd +++ b/man/microorganisms.old.Rd @@ -23,7 +23,7 @@ A data set containing old (previously valid or accepted) taxonomic names accordi \section{ITIS}{ \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} -This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). +This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. diff --git a/man/mo_property.Rd b/man/mo_property.Rd index f6d221c8..67c3e2f6 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -95,7 +95,7 @@ Supported languages are \code{"en"} (English), \code{"de"} (German), \code{"nl"} \section{ITIS}{ \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr} -This package contains the \strong{complete microbial taxonomic data} (with all eight taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). +This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). All (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria. diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R index 92b6a18f..ee96e5a9 100644 --- a/tests/testthat/test-mo_property.R +++ b/tests/testthat/test-mo_property.R @@ -15,10 +15,12 @@ test_that("mo_property works", { expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative") expect_equal(mo_TSN("E. coli"), 285) expect_equal(class(mo_taxonomy("E. coli")), "list") - expect_equal(names(mo_taxonomy("E. coli")), c("subkingdom", "phylum", "class", "order", + expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "subkingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies")) expect_equal(mo_ref("E. coli"), "Castellani and Chalmers, 1919") + expect_equal(mo_authors("E. coli"), "Castellani and Chalmers") + expect_equal(mo_year("E. coli"), 1919) expect_equal(mo_shortname("MRSA"), "S. aureus") expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")