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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
committed by GitHub
parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
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21
R/key_antimicrobials.R
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@@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@@ -175,8 +179,8 @@ key_antimicrobials <- function(x = NULL,
values <- cols[names(cols) %in% values]
values_new_length <- length(values)
if (values_new_length < values_old_length &
any(filter, na.rm = TRUE) &
if (values_new_length < values_old_length &&
any(filter, na.rm = TRUE) &&
message_not_thrown_before("key_antimicrobials", name)) {
warning_(
"in `key_antimicrobials()`: ",
@@ -305,7 +309,7 @@ antimicrobials_equal <- function(y,
stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
key2rsi <- function(val) {
val <- strsplit(val, "")[[1L]]
val <- strsplit(val, "", fixed = TRUE)[[1L]]
val.int <- rep(NA_real_, length(val))
val.int[val == "S"] <- 1
val.int[val == "I"] <- 2
@@ -347,8 +351,8 @@ antimicrobials_equal <- function(y,
all(a == b, na.rm = TRUE)
}
}
out <- unlist(mapply(
FUN = determine_equality,
out <- unlist(Map(
f = determine_equality,
y,
z,
MoreArgs = list(
@@ -356,7 +360,6 @@ antimicrobials_equal <- function(y,
points_threshold = points_threshold,
ignore_I = ignore_I
),
SIMPLIFY = FALSE,
USE.NAMES = FALSE
))
out[is.na(y) | is.na(z)] <- NA