mirror of https://github.com/msberends/AMR.git
`icu_exclude` in `first_isolate()`, fixes #110
This commit is contained in:
parent
5f9769a4f7
commit
3018fb87a9
|
|
@ -1,6 +1,6 @@
|
|||
Package: AMR
|
||||
Version: 2.0.0.9015
|
||||
Date: 2023-05-12
|
||||
Version: 2.0.0.9018
|
||||
Date: 2023-05-17
|
||||
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
|
||||
|
|
|
|||
9
NEWS.md
9
NEWS.md
|
|
@ -1,16 +1,17 @@
|
|||
# AMR 2.0.0.9015
|
||||
# AMR 2.0.0.9018
|
||||
|
||||
## Changed
|
||||
* Added oxygen tolerance to over 25,000 bacteria in the `microorganisms` data set
|
||||
* Added `mo_oxygen_tolerance()` to retrieve the values
|
||||
* Added `mo_is_anaerobic()` to determine which species are obligate anaerobic bacteria
|
||||
* Added LPSN and GBIF identifiers, and oxygen tolerance to `mo_info()`
|
||||
* formatting fix for `sir_interpretation_history()`
|
||||
* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
|
||||
* Added SAS Transport files (file extension `.xpt`) to [our download page](https://msberends.github.io/AMR/articles/datasets.html) to use in SAS software
|
||||
* Added microbial codes for Gram-negative/positive anaerobic bacteria
|
||||
* `mo_rank()` now returns `NA` for 'unknown' microorganisms (`B_ANAER`, `B_ANAER-NEG`, `B_ANAER-POS`, `B_GRAMN`, `B_GRAMP`, `F_FUNGUS`, `F_YEAST`, and `UNKNOWN`)
|
||||
* Fixed formatting for `sir_interpretation_history()`
|
||||
* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
|
||||
* Fixed a bug for `as.mo()` that led to coercion of `NA` values when using custom microorganism codes
|
||||
* Added SAS Transport files (file extension `.xpt`) to [our download page](https://msberends.github.io/AMR/articles/datasets.html) to use in SAS software
|
||||
* Fixed usage of `icu_exclude` in `first_isolates()`
|
||||
|
||||
|
||||
# AMR 2.0.0
|
||||
|
|
|
|||
|
|
@ -191,13 +191,13 @@ first_isolate <- function(x = NULL,
|
|||
}
|
||||
meet_criteria(col_specimen, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
if (is.logical(col_icu)) {
|
||||
meet_criteria(col_icu, allow_class = "logical", has_length = c(1, nrow(x)), allow_NULL = TRUE)
|
||||
if (length(col_icu) == 1) {
|
||||
col_icu <- rep(col_icu, nrow(x))
|
||||
}
|
||||
} else {
|
||||
meet_criteria(col_icu, allow_class = "logical", has_length = c(1, nrow(x)), allow_NA = TRUE)
|
||||
x$newvar_is_icu <- col_icu
|
||||
} else if (!is.null(col_icu)) {
|
||||
meet_criteria(col_icu, allow_class = c("character", "logical"), has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
|
||||
col_icu <- x[, col_icu, drop = TRUE]
|
||||
x$newvar_is_icu <- x[, col_icu, drop = TRUE]
|
||||
} else {
|
||||
x$newvar_is_icu <- NA_real_
|
||||
}
|
||||
# method
|
||||
method <- coerce_method(method)
|
||||
|
|
@ -251,14 +251,13 @@ first_isolate <- function(x = NULL,
|
|||
"Determining first isolates ",
|
||||
ifelse(method %in% c("episode-based", "phenotype-based"),
|
||||
ifelse(is.infinite(episode_days),
|
||||
"without a specified episode length",
|
||||
paste("using an episode length of", episode_days, "days")
|
||||
paste(font_bold("without"), " a specified episode length"),
|
||||
paste("using an episode length of", font_bold(paste(episode_days, "days")))
|
||||
),
|
||||
""
|
||||
)
|
||||
),
|
||||
as_note = FALSE,
|
||||
add_fn = font_black
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
|
||||
|
|
@ -358,8 +357,7 @@ first_isolate <- function(x = NULL,
|
|||
# remove testcodes
|
||||
if (!is.null(testcodes_exclude) && isTRUE(info) && message_not_thrown_before("first_isolate", "excludingtestcodes")) {
|
||||
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
|
||||
|
|
@ -372,8 +370,7 @@ first_isolate <- function(x = NULL,
|
|||
check_columns_existance(col_specimen, x)
|
||||
if (isTRUE(info) && message_not_thrown_before("first_isolate", "excludingspecimen")) {
|
||||
message_("Excluding other than specimen group '", specimen_group, "'",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
}
|
||||
|
|
@ -455,15 +452,13 @@ first_isolate <- function(x = NULL,
|
|||
message_("Basing inclusion on key antimicrobials, ",
|
||||
ifelse(ignore_I == FALSE, "not ", ""),
|
||||
"ignoring I",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
if (type == "points") {
|
||||
message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
|
||||
points_threshold,
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
}
|
||||
|
|
@ -505,34 +500,28 @@ first_isolate <- function(x = NULL,
|
|||
x$newvar_genus_species != "" &
|
||||
(x$other_pat_or_mo | x$more_than_episode_ago)
|
||||
}
|
||||
|
||||
|
||||
decimal.mark <- getOption("OutDec")
|
||||
big.mark <- ifelse(decimal.mark != ",", ",", " ")
|
||||
|
||||
# first one as TRUE
|
||||
x[row.start, "newvar_first_isolate"] <- TRUE
|
||||
# no tests that should be included, or ICU
|
||||
if (!is.null(col_testcode)) {
|
||||
x[which(x[, col_testcode] %in% tolower(testcodes_exclude)), "newvar_first_isolate"] <- FALSE
|
||||
}
|
||||
|
||||
if (!is.null(col_icu)) {
|
||||
if (any(!is.na(x$newvar_is_icu)) && any(x$newvar_is_icu == TRUE, na.rm = TRUE)) {
|
||||
if (icu_exclude == TRUE) {
|
||||
if (isTRUE(info)) {
|
||||
message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = " "), " isolates from ICU.",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
)
|
||||
message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.",
|
||||
add_fn = font_red)
|
||||
}
|
||||
x[which(col_icu), "newvar_first_isolate"] <- FALSE
|
||||
x[which(x$newvar_is_icu), "newvar_first_isolate"] <- FALSE
|
||||
} else if (isTRUE(info)) {
|
||||
message_("Including isolates from ICU.",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
)
|
||||
message_("Including isolates from ICU.")
|
||||
}
|
||||
}
|
||||
|
||||
decimal.mark <- getOption("OutDec")
|
||||
big.mark <- ifelse(decimal.mark != ",", ",", " ")
|
||||
|
||||
if (isTRUE(info)) {
|
||||
# print group name if used in dplyr::group_by()
|
||||
cur_group <- import_fn("cur_group", "dplyr", error_on_fail = FALSE)
|
||||
|
|
@ -560,11 +549,12 @@ first_isolate <- function(x = NULL,
|
|||
# handle empty microorganisms
|
||||
if (any(x$newvar_mo == "UNKNOWN", na.rm = TRUE) && isTRUE(info)) {
|
||||
message_(
|
||||
ifelse(include_unknown == TRUE, "Included ", "Excluded "),
|
||||
ifelse(include_unknown == TRUE, "Including ", "Excluding "),
|
||||
format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
|
||||
decimal.mark = decimal.mark, big.mark = big.mark
|
||||
),
|
||||
" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')"
|
||||
" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')",
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
|
||||
|
|
@ -572,10 +562,11 @@ first_isolate <- function(x = NULL,
|
|||
# exclude all NAs
|
||||
if (anyNA(x$newvar_mo) && isTRUE(info)) {
|
||||
message_(
|
||||
"Excluded ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
|
||||
"Excluding ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
|
||||
decimal.mark = decimal.mark, big.mark = big.mark
|
||||
),
|
||||
" isolates with a microbial ID 'NA' (in column '", font_bold(col_mo), "')"
|
||||
" isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')",
|
||||
add_fn = font_red
|
||||
)
|
||||
}
|
||||
x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
|
||||
|
|
|
|||
Loading…
Reference in New Issue