(v1.1.0.9007) lose dependencies

R/availability.R

@@ -32,6 +32,7 @@
 #' @examples
 #' availability(example_isolates)
 #'
+#' \dontrun{
 #' library(dplyr)
 #' example_isolates %>% availability()
 #'
@@ -43,6 +44,7 @@
 #'   filter(mo == as.mo("E. coli")) %>%
 #'   select_if(is.rsi) %>%
 #'   availability()
+#' }
 availability <- function(tbl, width = NULL) {
   x <- base::sapply(tbl, function(x) {
     1 - base::sum(base::is.na(x)) / base::length(x) 

R/count.R

@@ -69,7 +69,7 @@
 #' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
 #'
 #' 
-#' if (!require("dplyr")) {
+#' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
 #'     summarise(R  = count_R(CIP),

R/disk.R

@@ -33,6 +33,7 @@
 #' @seealso [as.rsi()]
 #' @inheritSection AMR Read more on our website!
 #' @examples
+#' \dontrun{
 #' # transform existing disk zones to the `disk` class
 #' library(dplyr)
 #' df <- data.frame(microorganism = "E. coli",
@@ -50,6 +51,7 @@
 #'        guideline = "EUCAST")
 #'        
 #' as.rsi(df)
+#' }
 as.disk <- function(x, na.rm = FALSE) {
   if (is.disk(x)) {
     x

R/eucast_rules.R

@@ -206,7 +206,8 @@ eucast_rules <- function(x,
                   "\n\nThis may overwrite your existing data if you use e.g.:",
                   "\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
     if ("rstudioapi" %in% rownames(utils::installed.packages())) {
-      q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with eucast_rules()", txt)
+      showQuestion <- get("showQuestion", envir = asNamespace("rstudioapi"))
+      q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt)
     } else {
       q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
     }

R/ggplot_rsi.R

@@ -62,7 +62,7 @@
 #' @export
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' if (!require("ggplot2") & !require("dplyr")) {
+#' if (require("ggplot2") & require("dplyr")) {
 #'  
 #'   # get antimicrobial results for drugs against a UTI:
 #'   ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) +

R/key_antibiotics.R

@@ -73,6 +73,7 @@
 #' # `example_isolates` is a dataset available in the AMR package.
 #' # See ?example_isolates.
 #'
+#' \dontrun{
 #' library(dplyr)
 #' # set key antibiotics to a new variable
 #' my_patients <- example_isolates %>%
@@ -87,7 +88,7 @@
 #' # Check the difference, in this data set it results in 7% more isolates:
 #' sum(my_patients$first_regular, na.rm = TRUE)
 #' sum(my_patients$first_weighted, na.rm = TRUE)
-#'
+#' }
 #'
 #' # output of the `key_antibiotics` function could be like this:
 #' strainA <- "SSSRR.S.R..S"

R/like.R

@@ -57,10 +57,12 @@
 #' #> TRUE TRUE TRUE
 #'
 #' # get isolates whose name start with 'Ent' or 'ent'
+#' \dontrun{
 #' library(dplyr)
 #' example_isolates %>%
 #'   filter(mo_name(mo) %like% "^ent") %>% 
 #'   freq(mo)
+#' }
 like <- function(x, pattern, ignore.case = TRUE) {
   # set to fixed if no regex found
   fixed <- all(!grepl("[$.^*?+}{|)(]", pattern))

R/mdro.R

@@ -66,7 +66,7 @@
 #' @source
 #' Please see *Details* for the list of publications used for this function.
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' library(dplyr)
 #' 
 #' example_isolates %>%
@@ -94,7 +94,8 @@ mdro <- function(x,
                   "\n\nThis may overwrite your existing data if you use e.g.:",
                   "\ndata <- mdro(data, verbose = TRUE)\n\nDo you want to continue?")
     if ("rstudioapi" %in% rownames(utils::installed.packages())) {
-      q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with mdro()", txt)
+      showQuestion <- get("showQuestion", envir = asNamespace("rstudioapi"))
+      q_continue <- showQuestion("Using verbose = TRUE with mdro()", txt)
     } else {
       q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
     }

R/mo_source.R

@@ -126,7 +126,8 @@ set_mo_source <- function(path) {
   } else if (path %like% "[.]xlsx?$") {
     # is Excel file (old or new)
     stopifnot_installed_package("readxl")
-    df <- readxl::read_excel(path)
+    read_excel <- get("read_excel", envir = asNamespace("readxl"))
+    df <- read_excel(path)
 
   } else if (path %like% "[.]tsv$") {
     df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)

R/proportion.R

@@ -99,8 +99,7 @@
 #' proportion_IR(example_isolates$AMX)
 #' proportion_R(example_isolates$AMX)
 #'
-#' if (!require("dplyr")) {
-#'   library(dplyr)
+#' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     group_by(hospital_id) %>%
 #'     summarise(r = resistance(CIP),
@@ -157,7 +156,9 @@
 #'     select(hospital_id, AMX, CIP) %>%
 #'     group_by(hospital_id) %>%
 #'     proportion_df(translate = FALSE)
-#'  
+#' }
+#' 
+#' \dontrun{  
 #'   # calculate current empiric combination therapy of Helicobacter gastritis:
 #'   my_table %>%
 #'     filter(first_isolate == TRUE,

R/resistance_predict.R

@@ -66,11 +66,12 @@
 #'                         year_min = 2010,
 #'                         model = "binomial")
 #' plot(x)
-#' ggplot_rsi_predict(x)
+#' if (require("ggplot2")) {
+#'   ggplot_rsi_predict(x)
+#' }
 #'
 #' # using dplyr:
-#' if (!require("dplyr")) {
-#'   library(dplyr)
+#' if (require("dplyr")) {
 #'   x <- example_isolates %>%
 #'     filter_first_isolate() %>%
 #'     filter(mo_genus(mo) == "Staphylococcus") %>%
@@ -83,7 +84,7 @@
 #' }
 #'
 #' # create nice plots with ggplot2 yourself
-#' if (!require(ggplot2) & !require("dplyr")) {
+#' if (require(ggplot2) & require("dplyr")) {
 #'
 #'   data <- example_isolates %>%
 #'     filter(mo == as.mo("E. coli")) %>%

R/rsi.R

@@ -70,7 +70,7 @@
 #'                  NIT = as.mic(32))
 #' as.rsi(df)
 #' 
-#' \donttest{
+#' \dontrun{
 #' 
 #' # the dplyr way
 #' library(dplyr)
@@ -117,6 +117,7 @@
 #' plot(rsi_data)    # for percentages
 #' barplot(rsi_data) # for frequencies
 #'
+#' \dontrun{
 #' library(dplyr)
 #' example_isolates %>%
 #'   mutate_at(vars(PEN:RIF), as.rsi)
@@ -132,6 +133,7 @@
 #' # default threshold of `is.rsi.eligible` is 5%.
 #' is.rsi.eligible(WHONET$`First name`) # fails, >80% is invalid
 #' is.rsi.eligible(WHONET$`First name`, threshold = 0.99) # succeeds
+#' }
 as.rsi <- function(x, ...) {
   UseMethod("as.rsi")
 }