(v1.6.0.9063) prepare new release

man/antibiotic_class_selectors.Rd

@@ -115,7 +115,7 @@ example_isolates[any(carbapenems() == "R"), penicillins()]
 
 
 # dplyr -------------------------------------------------------------------
-
+\donttest{
 if (require("dplyr")) {
 
   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
@@ -165,3 +165,4 @@ if (require("dplyr")) {
   example_isolates \%>\% filter(across(carbapenems(), ~.x == "R"))
 }
 }
+}

man/as.ab.Rd

@@ -102,13 +102,14 @@ ab_atc("seephthriaaksone") # and even this works
 # they use as.ab() internally:
 ab_name("J01FA01")    # "Erythromycin"
 ab_name("eryt")       # "Erythromycin"
-
+\donttest{
 if (require("dplyr")) {
 
   # you can quickly rename <rsi> columns using dplyr >= 1.0.0:
   example_isolates \%>\%
     rename_with(as.ab, where(is.rsi))
    
+}
 }
 }
 \seealso{

man/as.rsi.Rd

@@ -161,12 +161,12 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 
 \examples{
 summary(example_isolates) # see all R/SI results at a glance
-
+\donttest{
 if (require("skimr")) {
   # 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

man/atc_online.Rd

@@ -80,7 +80,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 }
 
 \examples{
-\donttest{
+\dontrun{
 # oral DDD (Defined Daily Dose) of amoxicillin
 atc_online_property("J01CA04", "DDD", "O")
 

man/availability.Rd

@@ -35,7 +35,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 
 \examples{
 availability(example_isolates)
-
+\donttest{
 if (require("dplyr")) {
   example_isolates \%>\%
     filter(mo == as.mo("E. coli")) \%>\%
@@ -43,3 +43,4 @@ if (require("dplyr")) {
     availability()
 }
 }
+}

man/count.Rd

@@ -157,7 +157,7 @@ n_rsi(example_isolates$AMX)
 count_susceptible(example_isolates$AMX)
 susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
 
-
+\donttest{
 if (require("dplyr")) {
   example_isolates \%>\%
     group_by(hospital_id) \%>\%
@@ -192,6 +192,7 @@ if (require("dplyr")) {
     count_df(translate = FALSE)
 }
 }
+}
 \seealso{
 \code{\link[=proportion]{proportion_*}} to calculate microbial resistance and susceptibility.
 }

man/ggplot_pca.Rd

@@ -121,6 +121,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
 # See ?example_isolates.
 
 # See ?pca for more info about Principal Component Analysis (PCA).
+\donttest{
 if (require("dplyr")) {
   pca_model <- example_isolates \%>\% 
     filter(mo_genus(mo) == "Staphylococcus") \%>\% 
@@ -141,3 +142,4 @@ if (require("dplyr")) {
   }
 }
 }
+}

man/ggplot_rsi.Rd

@@ -154,6 +154,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 }
 
 \examples{
+\donttest{
 if (require("ggplot2") & require("dplyr")) {
  
   # get antimicrobial results for drugs against a UTI:
@@ -203,7 +204,6 @@ if (require("ggplot2") & require("dplyr")) {
     scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R")
 }
   
-\donttest{
 # resistance of ciprofloxacine per age group
 example_isolates \%>\%
   mutate(first_isolate = first_isolate(.)) \%>\%

man/intrinsic_resistant.Rd

@@ -33,6 +33,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 }
 
 \examples{
+\donttest{
 if (require("dplyr")) {
   intrinsic_resistant \%>\%
     filter(antibiotic == "Vancomycin", microorganism \%like\% "Enterococcus") \%>\% 
@@ -40,4 +41,5 @@ if (require("dplyr")) {
   # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
 }
 }
+}
 \keyword{datasets}

man/italicise_taxonomy.Rd

@@ -43,10 +43,11 @@ cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
 
 # since ggplot2 supports no markdown (yet), use
 # italicise_taxonomy() and the `ggtext` pkg for titles:
-
+\donttest{
 if (require("ggplot2") && require("ggtext")) {
   ggplot(example_isolates$AMC,
          title = italicise_taxonomy("Amoxi/clav in E. coli")) +
     theme(plot.title = ggtext::element_markdown())
 }
 }
+}

man/mo_property.Rd

@@ -280,6 +280,7 @@ mo_fullname("S. pyogenes",
 mo_is_yeast(c("Candida", "E. coli"))      # TRUE, FALSE
 
 # gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
+\donttest{
 if (require("dplyr")) {
   example_isolates \%>\%
     filter(mo_is_gram_positive())
@@ -296,6 +297,7 @@ mo_taxonomy("E. coli")
 mo_info("E. coli")
 }
 }
+}
 \seealso{
 \link{microorganisms}
 }

man/pca.Rd

@@ -77,7 +77,6 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 # See ?example_isolates.
 
 \donttest{
-
 if (require("dplyr")) {
   # calculate the resistance per group first 
   resistance_data <- example_isolates \%>\% 

man/plot.Rd

@@ -149,9 +149,11 @@ plot(some_rsi_values)
 plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
 plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
 
+\donttest{
 if (require("ggplot2")) {
   ggplot(some_mic_values)
   ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
   ggplot(some_rsi_values)
 }
 }
+}

man/proportion.Rd

@@ -160,6 +160,7 @@ proportion_I(example_isolates$AMX)
 proportion_IR(example_isolates$AMX)
 proportion_R(example_isolates$AMX)
 
+\donttest{
 if (require("dplyr")) {
   example_isolates \%>\%
     group_by(hospital_id) \%>\%
@@ -219,6 +220,7 @@ if (require("dplyr")) {
     proportion_df(translate = FALSE)
 }
 }
+}
 \seealso{
 \code{\link[=count]{count()}} to count resistant and susceptible isolates.
 }

man/resistance_predict.Rd

@@ -137,6 +137,7 @@ x <- resistance_predict(example_isolates,
                         year_min = 2010,
                         model = "binomial")
 plot(x)
+\donttest{
 if (require("ggplot2")) {
   ggplot_rsi_predict(x)
 }
@@ -182,6 +183,7 @@ if (require("dplyr") & require("ggplot2")) {
     theme_minimal(base_size = 13)
 }
 }
+}
 \seealso{
 The \code{\link[=proportion]{proportion()}} functions to calculate resistance