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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 19:26:13 +01:00

support for dplyr 1.1.0

This commit is contained in:
dr. M.S. (Matthijs) Berends 2023-02-15 17:02:10 +01:00
parent fe41fc2e35
commit 6016547f1f
7 changed files with 33 additions and 28 deletions

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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.2.9126 Version: 1.8.2.9127
Date: 2023-02-14 Date: 2023-02-15
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

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@ -1,4 +1,4 @@
# AMR 1.8.2.9126 # 1.8.2.9127
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

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@ -889,34 +889,36 @@ get_current_data <- function(arg_name, call) {
valid_df <- function(x) { valid_df <- function(x) {
!is.null(x) && is.data.frame(x) !is.null(x) && is.data.frame(x)
} }
# try dplyr::cur_data_all() first to support dplyr groups
# only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
# not useful (throws error) with e.g. dplyr::select(), dplyr::across(), or dplyr::vars(),
# but that will be caught later on in this function
cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_data_all)) {
out <- tryCatch(cur_data_all(), error = function(e) NULL)
if (valid_df(out)) {
return(out)
}
}
# try a manual (base R) method, by going over all underlying environments with sys.frames() # try a manual (base R) method, by going over all underlying environments with sys.frames()
for (env in sys.frames()) { for (env in sys.frames()) {
if (!is.null(env$`.Generic`)) {
# dplyr support ----
if (!is.null(env$mask) && is.function(env$mask$current_rows) && (valid_df(env$data) || valid_df(env$`.data`))) {
# an element `.data` or `data` (containing all data) and `mask` (containing functions) will be in the environment when using dplyr verbs
# we use their mask$current_rows() to get the group rows, since dplyr::cur_data_all() is deprecated and will be removed in the future
# e.g. for `example_isolates %>% group_by(ward) %>% mutate(first = first_isolate(.))`
if (valid_df(env$data)) {
# support for dplyr 1.1.x
return(env$data[env$mask$current_rows(), , drop = FALSE])
} else {
# support for dplyr 1.0.x
return(env$`.data`[env$mask$current_rows(), , drop = FALSE])
}
# base R support ----
} else if (!is.null(env$`.Generic`)) {
# don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL # don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
if (valid_df(env$`.data`)) { if (valid_df(env$xx)) {
# an element `.data` will be in the environment when using `dplyr::select()` # an element `xx` will be in the environment for rows + cols in base R, e.g. `example_isolates[c(1:3), carbapenems()]`
# (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
return(env$`.data`)
} else if (valid_df(env$xx)) {
# an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
return(env$xx) return(env$xx)
} else if (valid_df(env$x)) { } else if (valid_df(env$x)) {
# an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]` # an element `x` will be in the environment for only cols in base R, e.g. `example_isolates[, carbapenems()]`
return(env$x) return(env$x)
} }
# scoped dplyr support ----
} else if (!is.null(names(env)) && all(c(".tbl", ".vars", ".cols") %in% names(env), na.rm = TRUE) && valid_df(env$`.tbl`)) { } 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()` # 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()`) # (e.g. `dplyr::summarise_at()` or `dplyr::mutate_at()`)

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@ -177,7 +177,7 @@ first_isolate <- function(x = NULL,
include_untested_sir = TRUE, include_untested_sir = TRUE,
...) { ...) {
if (is_null_or_grouped_tbl(x)) { if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
# is also fix for using a grouped df as input (a dot as first argument) # is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x) x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
} }
@ -634,7 +634,7 @@ filter_first_isolate <- function(x = NULL,
method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"), method = c("phenotype-based", "episode-based", "patient-based", "isolate-based"),
...) { ...) {
if (is_null_or_grouped_tbl(x)) { if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
# is also fix for using a grouped df as input (a dot as first argument) # is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x) x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
} }

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@ -138,7 +138,7 @@ key_antimicrobials <- function(x = NULL,
only_sir_columns = FALSE, only_sir_columns = FALSE,
...) { ...) {
if (is_null_or_grouped_tbl(x)) { if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
# is also fix for using a grouped df as input (a dot as first argument) # is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x) x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
} }
@ -250,7 +250,7 @@ all_antimicrobials <- function(x = NULL,
only_sir_columns = FALSE, only_sir_columns = FALSE,
...) { ...) {
if (is_null_or_grouped_tbl(x)) { if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
# is also fix for using a grouped df as input (a dot as first argument) # is also fix for using a grouped df as input (a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x) x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
} }

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@ -178,7 +178,7 @@ mdro <- function(x = NULL,
only_sir_columns = FALSE, only_sir_columns = FALSE,
...) { ...) {
if (is_null_or_grouped_tbl(x)) { if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all()) # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
# is also a fix for using a grouped df as input (i.e., a dot as first argument) # is also a fix for using a grouped df as input (i.e., a dot as first argument)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x) x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
} }

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@ -54,10 +54,13 @@ mark, .mark {
background: rgba(17, 143, 118, 0.25) !important; background: rgba(17, 143, 118, 0.25) !important;
} }
/* smaller tables */
.table {
font-size: 0.9em !important;
}
/* SYNTAX */ /* SYNTAX */
/* These are simple changes for the syntax highlighting */ /* These are simple changes for the syntax highlighting */
pre { pre {
font-size: 0.8em !important; font-size: 0.8em !important;
} }