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mirror of https://github.com/msberends/AMR.git synced 2024-12-24 18:46:14 +01:00

fix for scoped dplyr verbs

This commit is contained in:
dr. M.S. (Matthijs) Berends 2022-10-21 15:13:19 +02:00
parent 3102beb241
commit 4bebba3610
5 changed files with 31 additions and 7 deletions

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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.2.9024
Date: 2022-10-20
Version: 1.8.2.9027
Date: 2022-10-21
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

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@ -1,4 +1,4 @@
# AMR 1.8.2.9024
# AMR 1.8.2.9027
This version will eventually become v2.0! We're happy to reach a new major milestone soon!
@ -27,7 +27,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The `AMR` package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.
* Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info [in this article on our website](https://msberends.github.io/AMR/articles/datasets.html).
* Added confidence intervals in AMR calculation. This is now included in `rsi_df()` and `proportion_df()` and manually available as `rsi_confidence_interval()`
* Support for using antibiotic selectors in `dplyr::vars()`, such as in: `... %>% summarise_at(vars(aminoglycosides()), resistance)`
* Support for using antibiotic selectors in scoped `dplyr` verbs (worh or without `vars()`), such as in: `... %>% summarise_at(aminoglycosides(), resistance)`
### Changed
* Fix for using `as.rsi()` on certain EUCAST breakpoints for MIC values

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@ -882,9 +882,9 @@ get_current_data <- function(arg_name, call) {
return(env$x)
}
} else if (!is.null(names(env)) && all(c(".tbl", ".vars", ".env") %in% names(env), na.rm = TRUE) && valid_df(env$`.tbl`)) {
# an element `.tbl` will be in the environment when using `dplyr::vars()`
# (e.g. in `dplyr::summarise_at()` or `dplyr::mutate_at()`)
} else if (!is.null(names(env)) && all(c(".tbl", ".vars", ".cols") %in% names(env), na.rm = TRUE) && valid_df(env$`.tbl`)) {
# an element `.tbl` will be in the environment when using scoped dplyr variants, with or without `dplyr::vars()`
# (e.g. `dplyr::summarise_at()` or `dplyr::mutate_at()`)
return(env$`.tbl`)
}
}

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@ -143,6 +143,18 @@
#' }
#' if (require("dplyr")) {
#'
#' # scoped dplyr verbs with antibiotic selectors
#' # (you could also use across() of course)
#' example_isolates %>%
#' group_by(ward) %>%
#' summarise_at(
#' c(aminoglycosides(), carbapenems()),
#' resistance
#' )
#'
#' }
#' if (require("dplyr")) {
#'
#' example_isolates %>%
#' group_by(ward) %>%
#' summarise(

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@ -201,6 +201,18 @@ if (require("dplyr")) {
ci_max = rsi_confidence_interval(CIP, side = "max"),
)
}
if (require("dplyr")) {
# scoped dplyr verbs with antibiotic selectors
# (you could also use across() of course)
example_isolates \%>\%
group_by(ward) \%>\%
summarise_at(
c(aminoglycosides(), carbapenems()),
resistance
)
}
if (require("dplyr")) {