From 81af0b001cbf6af50295c14daf2349a41e539eb6 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 26 Aug 2020 16:13:40 +0200 Subject: [PATCH] (v1.3.0.9009) documentation update --- DESCRIPTION | 2 +- NEWS.md | 8 ++++---- R/aa_helper_functions.R | 6 ++++-- R/ab_class_selectors.R | 9 +++++---- R/bug_drug_combinations.R | 2 +- data-raw/antibiotics.dta | Bin 329492 -> 329492 bytes data-raw/antibiotics.sas | Bin 1880064 -> 1880064 bytes data-raw/antibiotics.sav | Bin 1406605 -> 1406605 bytes data-raw/antibiotics.xlsx | Bin 66083 -> 66083 bytes data-raw/antivirals.dta | Bin 68841 -> 68841 bytes data-raw/antivirals.sas | Bin 81920 -> 81920 bytes data-raw/antivirals.sav | Bin 69306 -> 69306 bytes data-raw/antivirals.xlsx | Bin 13935 -> 13935 bytes data-raw/intrinsic_resistant.dta | Bin 3909333 -> 3909333 bytes data-raw/intrinsic_resistant.sas | Bin 3985408 -> 3985408 bytes data-raw/intrinsic_resistant.sav | Bin 4353410 -> 4353410 bytes data-raw/intrinsic_resistant.xlsx | Bin 524510 -> 524510 bytes data-raw/microorganisms.dta | Bin 26468289 -> 26468289 bytes data-raw/microorganisms.old.dta | Bin 1896607 -> 1896607 bytes data-raw/microorganisms.old.sas | Bin 1941504 -> 1941504 bytes data-raw/microorganisms.old.sav | Bin 2034367 -> 2034367 bytes data-raw/microorganisms.old.xlsx | Bin 453024 -> 453024 bytes data-raw/microorganisms.sas | Bin 27521024 -> 27521024 bytes data-raw/microorganisms.sav | Bin 29548953 -> 29548953 bytes data-raw/microorganisms.xlsx | Bin 6401595 -> 6401595 bytes data-raw/rsi_translation.dta | Bin 3121505 -> 3121505 bytes data-raw/rsi_translation.sas | Bin 3334144 -> 3334144 bytes data-raw/rsi_translation.sav | Bin 3582161 -> 3582161 bytes data-raw/rsi_translation.xlsx | Bin 656226 -> 656226 bytes docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 14 +++++++------- docs/pkgdown.yml | 2 +- .../reference/antibiotic_class_selectors.html | 17 +++++++++++------ docs/reference/bug_drug_combinations.html | 4 ++-- docs/reference/index.html | 2 +- docs/survey.html | 2 +- man/antibiotic_class_selectors.Rd | 13 +++++++++---- man/bug_drug_combinations.Rd | 2 +- 42 files changed, 53 insertions(+), 40 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 373efc2a..bf4c251a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.3.0.9008 +Version: 1.3.0.9009 Date: 2020-08-26 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 64fb0469..9325353b 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.3.0.9008 +# AMR 1.3.0.9009 ## Last updated: 26 August 2020 ### New @@ -36,9 +36,9 @@ ``` * Speed improvement for `eucast_rules()` * Overall speed improvement by tweaking joining functions -* Function `mo_shortname()` now return the genus for input where the species is unknown -* BORSA is now recognised as an abbreviation for a *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus" -* Support for coloured `tibble` printing of classes `mo`, `rsi`, `mic` and `disk` +* Function `mo_shortname()` now returns the genus for input where the species is unknown +* BORSA is now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus" +* Support for coloured `tibble` printing of classes `ab`, `mo`, `rsi`, `mic` and `disk` # AMR 1.3.0 diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 0ffb96c0..9c00ce8c 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -224,7 +224,7 @@ stop_ifnot_installed <- function(package) { if (package == "rstudioapi") { stop("This function only works in RStudio.", call. = FALSE) } else if (pkg != "base") { - stop("package '", pkg, "' required but not installed.", + stop("This requires the '", pkg, "' package.", "\nTry to install it with: install.packages(\"", pkg, "\")", call. = FALSE) } @@ -240,7 +240,9 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) { get(name, envir = asNamespace(pkg)), error = function(e) { if (isTRUE(error_on_fail)) { - stop_("function ", name, "() not found in package '", pkg, "'. Please contact the maintainers of the AMR package at https://github.com/msberends/AMR/issues.", call = FALSE) + stop_("function ", name, "() not found in package '", pkg, + "'. Please create an issue at https://github.com/msberends/AMR/issues. Many thanks!", + call = FALSE) } else { return(NULL) } diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R index 0d9b723d..001b0cb3 100644 --- a/R/ab_class_selectors.R +++ b/R/ab_class_selectors.R @@ -21,15 +21,16 @@ #' Antibiotic class selectors #' -#' Use these selection helpers inside any function that allows [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html), like `dplyr::select()` or `tidyr::pivot_longer()`. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. +#' Use these selection helpers inside any function that allows [Tidyverse selection helpers](https://tidyselect.r-lib.org/reference/language.html), like `dplyr::select()` or `tidyr::pivot_longer()`. They 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 All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. +#' @details 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. #' -#' These functions only work if the `tidyselect` package is installed, that comes with the `dplyr` package. An error will be thrown if `tidyselect` package is not installed, or if the functions are used outside a function that allows Tidyverse selections like `select()` or `pivot_longer()`. +#' **N.B. These functions only work if the `tidyselect` package is installed**, that comes with the `dplyr` package. An error will be thrown if the `tidyselect` package is not installed, or if the functions are used outside a function that allows Tidyverse selections like `select()` or `pivot_longer()`. #' @rdname antibiotic_class_selectors #' @seealso [filter_ab_class()] for the `filter()` equivalent. #' @name antibiotic_class_selectors #' @export +#' @inheritSection AMR Reference data publicly available #' @inheritSection AMR Read more on our website! #' @examples #' \dontrun{ @@ -58,7 +59,7 @@ #' #' data.frame(irrelevant = "value", #' J01CA01 = "S") %>% # ATC code of ampicillin -#' select(penicillins()) # so the 'J01CA01' column is selected +#' select(penicillins()) # the 'J01CA01' column will be selected #' #' } ab_class <- function(ab_class) { diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index 9d3a6253..f287bde3 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -51,7 +51,7 @@ #' FUN = mo_gramstain) #' #' x <- bug_drug_combinations(example_isolates, 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AMR (for R) - 1.3.0.9008 + 1.3.0.9009 diff --git a/docs/index.html b/docs/index.html index 8c5cf54e..2793708d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.3.0.9008 + 1.3.0.9009 diff --git a/docs/news/index.html b/docs/news/index.html index 6df18f1a..5ed02570 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9008 + 1.3.0.9009 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.3.0.9008 Unreleased +
+

+AMR 1.3.0.9009 Unreleased

@@ -295,9 +295,9 @@

  • Speed improvement for eucast_rules()

  • Overall speed improvement by tweaking joining functions

    • -

  • Function mo_shortname() now return the genus for input where the species is unknown

    • -

  • BORSA is now recognised as an abbreviation for a Staphylococcus aureus, meaning that e.g. mo_genus("BORSA") will return “Staphylococcus”

    • -

  • Support for coloured tibble printing of classes mo, rsi, mic and disk

    • +

  • Function mo_shortname() now returns the genus for input where the species is unknown

    • +

  • BORSA is now recognised as an abbreviation for Staphylococcus aureus, meaning that e.g. mo_genus("BORSA") will return “Staphylococcus”

    • +

  • Support for coloured tibble printing of classes ab, mo, rsi, mic and disk

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 66658eda..89692fc9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.7.3 pkgdown: 1.5.1.9000 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f articles: [] -last_built: 2020-08-26T13:33Z +last_built: 2020-08-26T14:13Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index 2965a5a0..ee9c1090 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -49,7 +49,7 @@ - + @@ -82,7 +82,7 @@ AMR (for R) - 1.3.0.9007 + 1.3.0.9009

    @@ -239,7 +239,7 @@
    -

    Use these selection helpers inside any function that allows Tidyverse selections, like dplyr::select() or tidyr::pivot_longer(). They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.

    +

    Use these selection helpers inside any function that allows Tidyverse selection helpers, like dplyr::select() or tidyr::pivot_longer(). They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.

    ab_class(ab_class)
@@ -281,8 +281,13 @@
 
     
    Details
    
 
-    
    All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. aminoglycosides() will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
    
-
    These functions only work if the tidyselect package is installed, that comes with the dplyr package. An error will be thrown if tidyselect package is not installed, or if the functions are used outside a function that allows Tidyverse selections like select() or pivot_longer().
    
+    
    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.
    
+
    N.B. These functions only work if the tidyselect package is installed, that comes with the dplyr package. An error will be thrown if the tidyselect package is not installed, or if the functions are used outside a function that allows Tidyverse selections like select() or pivot_longer().
    
+    
    Reference data publicly available
    
+
+    
+
+
    All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.
    
     
    Read more on our website!
    
 
     
@@ -319,7 +324,7 @@
     
   data.frame(irrelevant = "value",
              J01CA01 = "S") %>%   # ATC code of ampicillin
-    select(penicillins())         # so the 'J01CA01' column is selected
+    select(penicillins())         # the 'J01CA01' column will be selected
 
 }
    diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index e100a4d1..90a1a538 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -82,7 +82,7 @@ AMR (for R) - 1.3.0.9006 + 1.3.0.9009 @@ -353,7 +353,7 @@ The lifecycle of this function is stablemo_gramstain) x <- bug_drug_combinations(example_isolates, - FUN = function(x) ifelse(x == "B_ESCHR_COLI", + FUN = function(x) ifelse(x == as.mo("E. coli"), "E. coli", "Others")) # } diff --git a/docs/reference/index.html b/docs/reference/index.html index be755b35..4d15e24c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9008 + 1.3.0.9009 diff --git a/docs/survey.html b/docs/survey.html index 4d912bd7..cccb70a9 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9008 + 1.3.0.9009 diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 49e9c0b9..46aca0a4 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -50,13 +50,18 @@ tetracyclines() \item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.} } \description{ -Use these selection helpers inside any function that allows \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selections}, like \code{dplyr::select()} or \code{tidyr::pivot_longer()}. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. +Use these selection helpers inside any function that allows \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selection helpers}, like \code{dplyr::select()} or \code{tidyr::pivot_longer()}. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. } \details{ -All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. +All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. -These functions only work if the \code{tidyselect} package is installed, that comes with the \code{dplyr} package. An error will be thrown if \code{tidyselect} package is not installed, or if the functions are used outside a function that allows Tidyverse selections like \code{select()} or \code{pivot_longer()}. +\strong{N.B. These functions only work if the \code{tidyselect} package is installed}, that comes with the \code{dplyr} package. An error will be thrown if the \code{tidyselect} package is not installed, or if the functions are used outside a function that allows Tidyverse selections like \code{select()} or \code{pivot_longer()}. } +\section{Reference data publicly available}{ + +All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this \code{AMR} package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find \href{https://msberends.github.io/AMR/articles/datasets.html}{all download links on our website}, which is automatically updated with every code change. +} + \section{Read more on our website!}{ On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}! @@ -89,7 +94,7 @@ On our website \url{https://msberends.github.io/AMR} you can find \href{https:// data.frame(irrelevant = "value", J01CA01 = "S") \%>\% # ATC code of ampicillin - select(penicillins()) # so the 'J01CA01' column is selected + select(penicillins()) # the 'J01CA01' column will be selected } } diff --git a/man/bug_drug_combinations.Rd b/man/bug_drug_combinations.Rd index b88afd16..5026d8a0 100644 --- a/man/bug_drug_combinations.Rd +++ b/man/bug_drug_combinations.Rd @@ -89,7 +89,7 @@ x <- bug_drug_combinations(example_isolates, FUN = mo_gramstain) x <- bug_drug_combinations(example_isolates, - FUN = function(x) ifelse(x == "B_ESCHR_COLI", + FUN = function(x) ifelse(x == as.mo("E. coli"), "E. coli", "Others")) }