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(v1.4.0.9004) bugfix

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dr. M.S. (Matthijs) Berends
2020-10-21 11:50:43 +02:00
parent 2ef7dfc8a3
commit ade9f8bafd
15 changed files with 32 additions and 32 deletions
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4
R/ggplot_rsi.R
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@ -273,7 +273,7 @@ geom_rsi <- function(position = NULL,
combine_SI = TRUE,
combine_IR = FALSE,
...) {
x <- x[1]
stop_ifnot_installed("ggplot2")
stop_if(is.data.frame(position), "`position` is invalid. Did you accidentally use '%>%' instead of '+'?")
meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
@ -294,8 +294,6 @@ geom_rsi <- function(position = NULL,
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
}
x <- x[1]
# we work with aes_string later on
x_deparse <- deparse(substitute(x))
if (x_deparse != "x") {

10
R/rsi.R
View File

@ -100,14 +100,14 @@
#' summary(example_isolates) # see all R/SI results at a glance
#'
#' if (require("skimr")) {
#' # support for skim() too:
#' # class <rsi> supported in skim() too:
#' skim(example_isolates)
#' }
#'
#' # For INTERPRETING disk diffusion and MIC values -----------------------
#'
#' # a whole data set, even with combined MIC values and disk zones
#' df <- data.frame(microorganism = "E. coli",
#' df <- data.frame(microorganism = "Escherichia coli",
#' AMP = as.mic(8),
#' CIP = as.mic(0.256),
#' GEN = as.disk(18),
@ -136,7 +136,7 @@
#' df %>% mutate(across(AMP:TOB, as.rsi))
#'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
#' mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
#'
#' # to include information about urinary tract infections (UTI)
#' data.frame(mo = "E. coli",
@ -457,7 +457,7 @@ as.rsi.data.frame <- function(x,
meet_criteria(x, allow_class = "data.frame") # will also check for dimensions > 0
meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(uti, allow_class = "logical", has_length = c(1, nrow(x)), allow_NULL = TRUE)
meet_criteria(uti, allow_class = c("logical", "character"), allow_NULL = TRUE)
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
@ -482,6 +482,8 @@ as.rsi.data.frame <- function(x,
}
} else {
# column found, transform to logical
stop_if(length(col_uti) != 1 | !col_uti %in% colnames(x),
"argument `uti` must be a logical vector, of must be a single column name of `x`")
uti <- as.logical(x[, col_uti, drop = TRUE])
}
} else {