diff --git a/DESCRIPTION b/DESCRIPTION index c7bc1f63..bee4363b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.2.0.9000 -Date: 2020-06-02 +Version: 1.2.0.9001 +Date: 2020-06-03 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NAMESPACE b/NAMESPACE index 43f56b96..da462f62 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -114,6 +114,7 @@ export(filter_first_weighted_isolate) export(filter_fluoroquinolones) export(filter_glycopeptides) export(filter_macrolides) +export(filter_penicillins) export(filter_tetracyclines) export(first_isolate) export(full_join_microorganisms) diff --git a/NEWS.md b/NEWS.md index b941d20f..94b06cfa 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,12 @@ -# AMR 1.2.0.9000 -## Last updated: 02-Jun-2020 +# AMR 1.2.0.9001 +## Last updated: 03-Jun-2020 ### Changed * Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded +* All `*_join_microorganisms()` functions now return the original data class (e.g. tibbles and data.tables) * Fixed a bug where `as.ab()` would return an error on invalid input values +* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*) +* Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()` # AMR 1.2.0 @@ -20,7 +23,7 @@ ### Changed * Taxonomy: - * Updated the taxonomy of microorganisms tot May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). **Note:** a taxonomic update may always impact determination of first isolates (using `first_isolate()`), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour. + * Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). **Note:** a taxonomic update may always impact determination of first isolates (using `first_isolate()`), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour. * Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string) * EUCAST rules: * The `eucast_rules()` function no longer applies "other" rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzyme inhibitor = R). The default input value for `rules` is now `c("breakpoints", "expert")` instead of `"all"`, but this can be changed by the user. To return to the old behaviour, set `options(AMR.eucast_rules = "all")`. diff --git a/R/filter_ab_class.R b/R/filter_ab_class.R index aa7a454c..5af90618 100644 --- a/R/filter_ab_class.R +++ b/R/filter_ab_class.R @@ -21,14 +21,14 @@ #' Filter isolates on result in antimicrobial class #' -#' Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside. +#' Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs. #' @inheritSection lifecycle Stable lifecycle #' @param x a data set #' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics] #' @param result an antibiotic result: S, I or R (or a combination of more of them) #' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"` #' @param ... parameters passed on to `filter_at` from the `dplyr` package -#' @details The `group` column in [antibiotics] data set will be searched for `ab_class` (case-insensitive). If no results are found, the `atc_group1` and `atc_group2` columns will be searched. Next, `x` will be checked for column names with a value in any abbreviations, codes or official names found in the [antibiotics] data set. +#' @details The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched for the input given in `ab_class` (case-insensitive). Next, `x` will be checked for column names with a value in any abbreviation, code or official name found in the [antibiotics] data set. #' @rdname filter_ab_class #' @export #' @examples @@ -36,6 +36,7 @@ #' library(dplyr) #' #' # filter on isolates that have any result for any aminoglycoside +#' example_isolates %>% filter_ab_class("aminoglycoside") #' example_isolates %>% filter_aminoglycosides() #' #' # this is essentially the same as (but without determination of column names): @@ -45,7 +46,7 @@ #' #' #' # filter on isolates that show resistance to ANY aminoglycoside -#' example_isolates %>% filter_aminoglycosides("R") +#' example_isolates %>% filter_aminoglycosides("R", "any") #' #' # filter on isolates that show resistance to ALL aminoglycosides #' example_isolates %>% filter_aminoglycosides("R", "all") @@ -76,13 +77,14 @@ filter_ab_class <- function(x, # save to return later x_class <- class(x) + x.bak <- x x <- as.data.frame(x, stringsAsFactors = FALSE) scope <- scope[1L] if (is.null(result)) { result <- c("S", "I", "R") } - # make result = "SI" work too: + # make result = "SI" works too: result <- unlist(strsplit(result, "")) if (!all(result %in% c("S", "I", "R"))) { @@ -92,46 +94,62 @@ filter_ab_class <- function(x, stop("`scope` must be one of: any, all", call. = FALSE) } - # get only columns with class ab, mic or disk - those are AMR results - vars_df <- colnames(x)[sapply(x, function(y) is.rsi(y) | is.mic(y) | is.disk(y))] - vars_df_ab <- suppressWarnings(as.ab(vars_df)) - # get the columns with a group names in the chosen ab class - vars_df <- vars_df[which(ab_group(vars_df_ab) %like% ab_class | - ab_atc_group1(vars_df_ab) %like% ab_class | - ab_atc_group2(vars_df_ab) %like% ab_class)] - ab_group <- find_ab_group(ab_class) - - if (length(vars_df) > 0) { - if (length(result) == 1) { - operator <- " is " - } else { - operator <- " is one of " - } - if (scope == "any") { - scope_txt <- " or " - scope_fn <- any - } else { - scope_txt <- " and " - scope_fn <- all - if (length(vars_df) > 1) { - operator <- gsub("is", "are", operator) - } - } - if (length(vars_df) > 1) { - scope <- paste(scope, "of columns ") - } else { - scope <- "column " - } - message(font_blue(paste0("Filtering on ", ab_group, ": ", scope, - paste0(font_bold(paste0("`", vars_df, "`"), collapse = NULL), collapse = scope_txt), operator, toString(result)))) - filtered <<- as.logical(by(x, seq_len(nrow(x)), - function(row) scope_fn(unlist(row[, vars_df]) %in% result, na.rm = TRUE))) - x <- x[which(filtered), , drop = FALSE] - } else { - message(font_blue(paste0("NOTE: no antimicrobial agents of class ", ab_group, - " (such as ", find_ab_names(ab_group), - ") found, data left unchanged."))) + # get all columns in data with names that resemble antibiotics + ab_in_data <- suppressMessages(get_column_abx(x)) + if (length(ab_in_data) == 0) { + message(font_blue("NOTE: no antimicrobial agents found, data left unchanged.")) + return(x.bak) } + # get reference data + ab_class <- gsub("[^a-zA-Z0-9]+", ".*", ab_class) + ab_class <- gsub("(ph|f)", "(ph|f)", ab_class) + ab_class <- gsub("(t|th)", "(t|th)", ab_class) + ab_reference <- subset(antibiotics, + group %like% ab_class | + atc_group1 %like% ab_class | + atc_group2 %like% ab_class) + ab_group <- find_ab_group(ab_class) + # get the columns with a group names in the chosen ab class + agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab] + if (length(agents) == 0) { + message(font_blue(paste0("NOTE: no antimicrobial agents of class ", ab_group, + " found (such as ", find_ab_names(ab_class, 2), + "), data left unchanged."))) + return(x.bak) + } + + if (length(result) == 1) { + operator <- " is " + } else { + operator <- " is one of " + } + if (scope == "any") { + scope_txt <- " or " + scope_fn <- any + } else { + scope_txt <- " and " + scope_fn <- all + if (length(agents) > 1) { + operator <- gsub("is", "are", operator) + } + } + if (length(agents) > 1) { + scope <- paste(scope, "of columns ") + } else { + scope <- "column " + } + + # sort columns on official name + agents <- agents[order(ab_name(names(agents), language = NULL))] + + message(font_blue(paste0("Filtering on ", ab_group, ": ", scope, + paste(paste0("`", font_bold(agents, collapse = NULL), + "` (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"), + collapse = scope_txt), + operator, toString(result)))) + filtered <- as.logical(by(x, seq_len(nrow(x)), + function(row) scope_fn(unlist(row[, agents]) %in% result, na.rm = TRUE))) + x <- x[which(filtered), , drop = FALSE] class(x) <- x_class x } @@ -279,6 +297,19 @@ filter_macrolides <- function(x, ...) } +#' @rdname filter_ab_class +#' @export +filter_penicillins <- function(x, + result = NULL, + scope = "any", + ...) { + filter_ab_class(x = x, + ab_class = "penicillin", + result = result, + scope = scope, + ...) +} + #' @rdname filter_ab_class #' @export filter_tetracyclines <- function(x, @@ -312,9 +343,9 @@ find_ab_group <- function(ab_class) { ) } -find_ab_names <- function(ab_group) { +find_ab_names <- function(ab_group, n = 3) { drugs <- antibiotics[which(antibiotics$group %like% ab_group), "name"] - paste0(ab_name(sample(drugs, size = min(4, length(drugs)), replace = FALSE), - tolower = TRUE, language = NULL), + paste0(sort(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE), + tolower = TRUE, language = NULL)), collapse = ", ") } diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index fa152014..b31f07eb 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -160,6 +160,11 @@ get_column_abx <- function(x, x <- x[!is.na(x)] } + if (length(x) == 0) { + message(font_blue("No columns found.")) + return(x) + } + # sort on name x <- x[order(names(x), x)] duplicates <- c(x[base::duplicated(x)], x[base::duplicated(names(x))]) @@ -167,7 +172,7 @@ get_column_abx <- function(x, x <- c(x[!names(x) %in% names(duplicates)], duplicates) x <- x[order(names(x), x)] - # succeeded with aut-guessing + # succeeded with auto-guessing message(font_blue("OK.")) for (i in seq_len(length(x))) { diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index e7ec8dd6..f940ae56 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -55,7 +55,9 @@ #' } inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { check_dataset_integrity() + check_groups_before_join(x, "inner_join_microorganisms") checked <- joins_check_df(x, by) + x_class <- class(x) x <- checked$x by <- checked$by join <- suppressWarnings( @@ -64,6 +66,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { if (NROW(join) > NROW(x)) { warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.") } + class(join) <- x_class join } @@ -71,7 +74,9 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { #' @export left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { check_dataset_integrity() + check_groups_before_join(x, "left_join_microorganisms") checked <- joins_check_df(x, by) + x_class <- class(x) x <- checked$x by <- checked$by join <- suppressWarnings( @@ -80,6 +85,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { if (NROW(join) > NROW(x)) { warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.") } + class(join) <- x_class join } @@ -87,7 +93,9 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { #' @export right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { check_dataset_integrity() + check_groups_before_join(x, "right_join_microorganisms") checked <- joins_check_df(x, by) + x_class <- class(x) x <- checked$x by <- checked$by join <- suppressWarnings( @@ -96,6 +104,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { if (NROW(join) > NROW(x)) { warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.") } + class(join) <- x_class join } @@ -103,7 +112,9 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { #' @export full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { check_dataset_integrity() + check_groups_before_join(x, "full_join_microorganisms") checked <- joins_check_df(x, by) + x_class <- class(x) x <- checked$x by <- checked$by join <- suppressWarnings( @@ -112,6 +123,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { if (NROW(join) > NROW(x)) { warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.") } + class(join) <- x_class join } @@ -119,24 +131,32 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) { #' @export semi_join_microorganisms <- function(x, by = NULL, ...) { check_dataset_integrity() + check_groups_before_join(x, "semi_join_microorganisms") + x_class <- class(x) checked <- joins_check_df(x, by) x <- checked$x by <- checked$by - suppressWarnings( + join <- suppressWarnings( semi_join(x = x, y = microorganisms, by = by, ...) ) + class(join) <- x_class + join } #' @rdname join #' @export anti_join_microorganisms <- function(x, by = NULL, ...) { check_dataset_integrity() + check_groups_before_join(x, "anti_join_microorganisms") checked <- joins_check_df(x, by) + x_class <- class(x) x <- checked$x by <- checked$by - suppressWarnings( + join <- suppressWarnings( anti_join(x = x, y = microorganisms, by = by, ...) ) + class(join) <- x_class + join } joins_check_df <- function(x, by) { @@ -146,6 +166,7 @@ joins_check_df <- function(x, by) { by <- "mo" } } + x <- as.data.frame(x, stringsAsFactors = FALSE) if (is.null(by)) { # search for column with class `mo` and return first one found by <- colnames(x)[lapply(x, is.mo) == TRUE][1] @@ -168,3 +189,9 @@ joins_check_df <- function(x, by) { list(x = x, by = joinby) } + +check_groups_before_join <- function(x, fn) { + if (is.data.frame(x) && !is.null(attributes(x)$groups)) { + warning("Groups are dropped, since the ", fn, "() function relies on merge() from base R, not on join() from dplyr.", call. = FALSE) + } +} diff --git a/R/sysdata.rda b/R/sysdata.rda index b8053be4..59422158 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/docs/404.html b/docs/404.html index a142f5ad..59e1de27 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9000 + 1.2.0.9001 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index e5df0e43..c47d9102 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9000 + 1.2.0.9001 diff --git a/docs/articles/index.html b/docs/articles/index.html index 76f9b45b..874f954c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9000 + 1.2.0.9001 diff --git a/docs/authors.html b/docs/authors.html index b878a3e7..5e1062d3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9000 + 1.2.0.9001 diff --git a/docs/index.html b/docs/index.html index 31c5afe2..e8eaa3e9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9000 + 1.2.0.9001 diff --git a/docs/news/index.html b/docs/news/index.html index 25f03586..3fc1b176 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9000 + 1.2.0.9001 @@ -229,20 +229,24 @@ Source: NEWS.md -
-

-AMR 1.2.0.9000 Unreleased +
+

+AMR 1.2.0.9001 Unreleased

-
+

-Last updated: 02-Jun-2020 +Last updated: 03-Jun-2020

Changed

  • Fixed a bug where eucast_rules() would not work on a tibble when the tibble or dplyr package was loaded
    • +
  • All *_join_microorganisms() functions now return the original data class (e.g. tibbles and data.tables)
  • Fixed a bug where as.ab() would return an error on invalid input values
    • +
  • Added function filter_penicillins() to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup Beta-lactam antibacterials, penicillins)
    • +
  • Added official antimicrobial names to all filter_ab_class() functions, such as filter_aminoglycosides() +
@@ -274,7 +278,7 @@
  • Taxonomy:
      -
    • Updated the taxonomy of microorganisms tot May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). Note: a taxonomic update may always impact determination of first isolates (using first_isolate()), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.
      • +
    • Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). Note: a taxonomic update may always impact determination of first isolates (using first_isolate()), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.
    • Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 36962fff..180cf058 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-06-02T14:04Z +last_built: 2020-06-03T09:44Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index 192b0fbd..4ab7b380 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -49,7 +49,7 @@ - + @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0 + 1.2.0.9001
@@ -232,7 +232,7 @@
-

Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.

+

Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.

filter_ab_class(x, ab_class, result = NULL, scope = "any", ...)
@@ -259,6 +259,8 @@
 
 filter_macrolides(x, result = NULL, scope = "any", ...)
 
+filter_penicillins(x, result = NULL, scope = "any", ...)
+
 filter_tetracyclines(x, result = NULL, scope = "any", ...)

Arguments

@@ -288,7 +290,7 @@

Details

-

The group column in antibiotics data set will be searched for ab_class (case-insensitive). If no results are found, the atc_group1 and atc_group2 columns will be searched. Next, x will be checked for column names with a value in any abbreviations, codes or official names found in the antibiotics data set.

+

The columns group, atc_group1 and atc_group2 of the antibiotics data set will be searched for the input given in ab_class (case-insensitive). Next, x will be checked for column names with a value in any abbreviation, code or official name found in the antibiotics data set.

Stable lifecycle

@@ -302,6 +304,7 @@ The lifecycle of this function is stablelibrary(dplyr) # filter on isolates that have any result for any aminoglycoside +example_isolates %>% filter_ab_class("aminoglycoside") example_isolates %>% filter_aminoglycosides() # this is essentially the same as (but without determination of column names): @@ -311,7 +314,7 @@ The lifecycle of this function is stable# filter on isolates that show resistance to ANY aminoglycoside -example_isolates %>% filter_aminoglycosides("R") +example_isolates %>% filter_aminoglycosides("R", "any") # filter on isolates that show resistance to ALL aminoglycosides example_isolates %>% filter_aminoglycosides("R", "all") diff --git a/docs/reference/index.html b/docs/reference/index.html index d7a23262..70319af4 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9000 + 1.2.0.9001
@@ -421,7 +421,7 @@ -

filter_ab_class() filter_aminoglycosides() filter_carbapenems() filter_cephalosporins() filter_1st_cephalosporins() filter_2nd_cephalosporins() filter_3rd_cephalosporins() filter_4th_cephalosporins() filter_5th_cephalosporins() filter_fluoroquinolones() filter_glycopeptides() filter_macrolides() filter_tetracyclines()

+

filter_ab_class() filter_aminoglycosides() filter_carbapenems() filter_cephalosporins() filter_1st_cephalosporins() filter_2nd_cephalosporins() filter_3rd_cephalosporins() filter_4th_cephalosporins() filter_5th_cephalosporins() filter_fluoroquinolones() filter_glycopeptides() filter_macrolides() filter_penicillins() filter_tetracyclines()

Filter isolates on result in antimicrobial class

diff --git a/man/filter_ab_class.Rd b/man/filter_ab_class.Rd index 05b052d1..44e724ef 100644 --- a/man/filter_ab_class.Rd +++ b/man/filter_ab_class.Rd @@ -13,6 +13,7 @@ \alias{filter_fluoroquinolones} \alias{filter_glycopeptides} \alias{filter_macrolides} +\alias{filter_penicillins} \alias{filter_tetracyclines} \title{Filter isolates on result in antimicrobial class} \usage{ @@ -40,6 +41,8 @@ filter_glycopeptides(x, result = NULL, scope = "any", ...) filter_macrolides(x, result = NULL, scope = "any", ...) +filter_penicillins(x, result = NULL, scope = "any", ...) + filter_tetracyclines(x, result = NULL, scope = "any", ...) } \arguments{ @@ -54,10 +57,10 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...) \item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package} } \description{ -Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside. +Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs. } \details{ -The \code{group} column in \link{antibiotics} data set will be searched for \code{ab_class} (case-insensitive). If no results are found, the \code{atc_group1} and \code{atc_group2} columns will be searched. Next, \code{x} will be checked for column names with a value in any abbreviations, codes or official names found in the \link{antibiotics} data set. +The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched for the input given in \code{ab_class} (case-insensitive). Next, \code{x} will be checked for column names with a value in any abbreviation, code or official name found in the \link{antibiotics} data set. } \section{Stable lifecycle}{ @@ -72,6 +75,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp library(dplyr) # filter on isolates that have any result for any aminoglycoside +example_isolates \%>\% filter_ab_class("aminoglycoside") example_isolates \%>\% filter_aminoglycosides() # this is essentially the same as (but without determination of column names): @@ -81,7 +85,7 @@ example_isolates \%>\% # filter on isolates that show resistance to ANY aminoglycoside -example_isolates \%>\% filter_aminoglycosides("R") +example_isolates \%>\% filter_aminoglycosides("R", "any") # filter on isolates that show resistance to ALL aminoglycosides example_isolates \%>\% filter_aminoglycosides("R", "all") diff --git a/tests/testthat/test-join_microorganisms.R b/tests/testthat/test-join_microorganisms.R index f942216d..ab960f84 100755 --- a/tests/testthat/test-join_microorganisms.R +++ b/tests/testthat/test-join_microorganisms.R @@ -55,5 +55,9 @@ test_that("joins work", { expect_warning(right_join_microorganisms("B_ESCHR_COLI")) expect_warning(full_join_microorganisms("B_ESCHR_COLI")) + + library(dplyr) + x <- tibble(bact = as.mo("E.coli")) + expect_warning(left_join_microorganisms(x %>% group_by(bact), "bact")) })