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mirror of https://github.com/msberends/AMR.git synced 2025-07-10 23:01:58 +02:00

(v0.7.1.9016) deps

This commit is contained in:
2019-07-29 17:34:57 +02:00
parent 240f03a672
commit b7e2d7b9b8
18 changed files with 34 additions and 18 deletions

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@ -70,7 +70,7 @@
#' @keywords isolate isolates first
#' @seealso \code{\link{key_antibiotics}}
#' @export
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange pull
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange pull ungroup
#' @importFrom crayon blue bold silver
#' @return Logical vector
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.

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@ -51,6 +51,8 @@
#'
#' plot(mic_data)
#' barplot(mic_data)
#'
#' library(clean)
#' freq(mic_data)
as.mic <- function(x, na.rm = FALSE) {
if (is.mic(x)) {

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R/mo.R
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@ -1412,6 +1412,7 @@ print.mo <- function(x, ...) {
#' @exportMethod summary.mo
#' @importFrom dplyr n_distinct
#' @importFrom clean freq top_freq
#' @export
#' @noRd
summary.mo <- function(object, ...) {

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@ -58,7 +58,7 @@
#' @rdname resistance_predict
#' @export
#' @importFrom stats predict glm lm
#' @importFrom dplyr %>% pull mutate mutate_at n group_by_at summarise filter filter_at all_vars n_distinct arrange case_when n_groups transmute
#' @importFrom dplyr %>% pull mutate mutate_at n group_by_at summarise filter filter_at all_vars n_distinct arrange case_when n_groups transmute ungroup
#' @inheritSection AMR Read more on our website!
#' @examples
#' x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)

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@ -50,7 +50,7 @@
#' @return Ordered factor with new class \code{rsi}
#' @keywords rsi
#' @export
#' @importFrom dplyr %>%
#' @importFrom dplyr %>% desc arrange filter
#' @seealso \code{\link{as.mic}}
#' @inheritSection AMR Read more on our website!
#' @examples
@ -73,6 +73,8 @@
#'
#' plot(rsi_data) # for percentages
#' barplot(rsi_data) # for frequencies
#'
#' library(clean)
#' freq(rsi_data) # frequency table with informative header
#'
#' # using dplyr's mutate