P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 04:02:19 +02:00
Code Releases Activity

(v1.5.0.9017) unit testing

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-08 21:09:36 +01:00
parent 4a84894f79
commit cb404492b2
20 changed files with 47 additions and 36 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
R/aa_helper_functions.R
View File

@ -734,7 +734,7 @@ get_current_column <- function() {
is_null_or_grouped_tbl <- function(x) {
# attribute "grouped_df" might change at one point, so only set in one place; here.
is.null(x) || inherits(x, "grouped_tbl")
is.null(x) || inherits(x, "grouped_df")
}
unique_call_id <- function(entire_session = FALSE) {

3
R/filter_ab_class.R
View File

@ -147,9 +147,6 @@ filter_ab_class <- function(x,
} else {
scope_txt <- " and "
scope_fn <- all
if (length(agents) > 1) {
operator <- gsub("is", "are", operator)
}
}
if (length(agents) > 1) {
operator <- " are"

9
R/first_isolate.R
View File

@ -187,7 +187,8 @@ first_isolate <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- get_current_data(arg_name = "x", call = -2)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
meet_criteria(x, allow_class = "data.frame")
}
# remove data.table, grouping from tibbles, etc.
x <- as.data.frame(x, stringsAsFactors = FALSE)
@ -518,7 +519,8 @@ filter_first_isolate <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- get_current_data(arg_name = "x", call = -2)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
meet_criteria(x, allow_class = "data.frame")
}
subset(x, first_isolate(x = x,
col_date = col_date,
@ -543,7 +545,8 @@ filter_first_weighted_isolate <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- get_current_data(arg_name = "x", call = -2)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
meet_criteria(x, allow_class = "data.frame")
}
y <- x
if (is.null(col_keyantibiotics)) {

3
R/key_antibiotics.R
View File

@ -155,7 +155,8 @@ key_antibiotics <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- get_current_data(arg_name = "x", call = -2)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
meet_criteria(x, allow_class = "data.frame")
}
# force regular data.frame, not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE)

3
R/mdro.R
View File

@ -218,7 +218,8 @@ mdro <- function(x = NULL,
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
# is also fix for using a grouped df as input (a dot as first argument)
x <- get_current_data(arg_name = "x", call = -2)
x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
meet_criteria(x, allow_class = "data.frame")
}
# force regular data.frame, not a tibble or data.table