new, automated website

man/pca.Rd

@@ -59,19 +59,6 @@ The \code{\link[=pca]{pca()}} function takes a \link{data.frame} as input and pe
 
 The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object, with an additional attribute \code{non_numeric_cols} which is a vector with the column names of all columns that do not contain \link{numeric} values. These are probably the groups and labels, and will be used by \code{\link[=ggplot_pca]{ggplot_pca()}}.
 }
-\section{Stable Lifecycle}{
-
-\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
-The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
-
-If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
-}
-
-\section{Read more on Our Website!}{
-
-On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
-}
-
 \examples{
 # `example_isolates` is a data set available in the AMR package.
 # See ?example_isolates.
@@ -82,6 +69,7 @@ if (require("dplyr")) {
   resistance_data <- example_isolates \%>\% 
     group_by(order = mo_order(mo),       # group on anything, like order
              genus = mo_genus(mo)) \%>\%   #   and genus as we do here;
+    filter(n() >= 30) \%>\%                # filter on only 30 results per group
     summarise_if(is.rsi, resistance)     # then get resistance of all drugs
     
   # now conduct PCA for certain antimicrobial agents
@@ -90,8 +78,17 @@ if (require("dplyr")) {
     
   pca_result
   summary(pca_result)
+  
+  # old base R plotting method:
   biplot(pca_result)
-  ggplot_pca(pca_result) # a new and convenient plot function
+  # new ggplot2 plotting method using this package:
+  ggplot_pca(pca_result)
+  
+  if (require("ggplot2")) {
+    ggplot_pca(pca_result) +
+      scale_colour_viridis_d() +
+      labs(title = "Title here")
+  }
 }
 }
 }