Make changes for CRAN resubmission

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: DiagrammeR
 Title: Graph/Network Visualization
-Version: 1.0.4
+Version: 1.0.5
 Authors@R:
     person("Richard", "Iannone", , "riannone@me.com", c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3925-190X"))

NEWS.md

@@ -1,4 +1,4 @@
-# DiagrammeR 1.0.4
+# DiagrammeR 1.0.5
 
 * Removes the ability to save a DiagrammeR graph object as a Gephi file (.gexf) since the **rgexf** package is no longer maintained
 

R/add_full_graph.R

@@ -36,7 +36,8 @@
 #' graph <-
 #'   create_graph() %>%
 #'   add_full_graph(
-#'     n = 3, keep_loops = TRUE)
+#'     n = 3, keep_loops = TRUE
+#'   )
 #'
 #' # Get node information
 #' # from this graph
@@ -58,7 +59,8 @@
 #'     n = 3,
 #'     type = "connected",
 #'     label = c("1st", "2nd", "3rd"),
-#'     rel = "connected_to")
+#'     rel = "connected_to"
+#'   )
 #'
 #' # Show the graph's node
 #' # data frame (ndf)
@@ -82,9 +84,10 @@
 #'   sample(9, FALSE) %>%
 #'   round(2) %>%
 #'   matrix(
-#'     nc = 3,
-#'     nr = 3,
-#'     dimnames = list(c("a", "b", "c")))
+#'     ncol = 3,
+#'     nrow = 3,
+#'     dimnames = list(c("a", "b", "c"))
+#'   )
 #'
 #' # Create the fully-connected
 #' # graph (without loops however)
@@ -118,7 +121,8 @@
 #'     label = TRUE,
 #'     rel = "related_to",
 #'     edge_wt_matrix = edge_wt_matrix,
-#'     keep_loops = FALSE) %>%
+#'     keep_loops = FALSE
+#'   ) %>%
 #'   get_edge_df()
 #'
 #' @export

R/display_metagraph.R

@@ -12,7 +12,6 @@
 #'   condition of being a property graph, otherwise the function yields an
 #'   error.
 #' @examples
-#' \dontrun{
 #' # Create a randomized property
 #' # graph with 1000 nodes and 1350 edges
 #' property_graph <-
@@ -73,8 +72,7 @@
 #' # Display this graph's
 #' # metagraph, or, the underlying
 #' # graph model for a property graph
-#' display_metagraph(property_graph)
-#' }
+#' # display_metagraph(property_graph)
 #'
 #' @export
 display_metagraph <- function(graph) {

R/from_adj_matrix.R

@@ -18,10 +18,12 @@
 #' @examples
 #' # Create an adjacency matrix
 #' adj_matrix <-
-#'   sample(0:1, 100,
-#'          replace = TRUE,
-#'          prob = c(0.9,0.1)) %>%
-#'   matrix(nc = 10)
+#'   sample(
+#'     0:1, 100,
+#'     replace = TRUE,
+#'     prob = c(0.9,0.1)
+#'   ) %>%
+#'   matrix(ncol = 10)
 #'
 #' # Create a graph from the adjacency matrix
 #' graph <- from_adj_matrix(adj_matrix)

R/grViz.R

@@ -58,7 +58,9 @@ grViz <- function(diagram = "",
       diagram = diagram,
       config = list(
         engine = engine,
-        options = options))
+        options = options
+      )
+    )
 
   # Only use the Viewer for newer versions of RStudio,
   # but allow other, non-RStudio viewers
@@ -73,7 +75,8 @@ grViz <- function(diagram = "",
     width = width,
     height = height,
     package = "DiagrammeR",
-    htmlwidgets::sizingPolicy(viewer.suppress = viewer.suppress))
+    htmlwidgets::sizingPolicy(viewer.suppress = viewer.suppress)
+  )
 }
 
 #' Widget output function for use in Shiny
@@ -83,45 +86,19 @@ grViz <- function(diagram = "",
 #'   coerced to a string and have `px` appended.
 #' @param height A valid CSS unit for the height or a number, which will be
 #'   coerced to a string and have `px` appended.
-#' @examples
-#' \dontrun{
-#' library(shiny)
-#' library(shinyAce)
-#'
-#' ui = shinyUI(fluidPage(fluidRow(
-#'   column(
-#'     width=4
-#'     , aceEditor("ace", selectionId = "selection", value="digraph {A;}")
-#'   ),
-#'   column(
-#'     width = 6
-#'     , grVizOutput('diagram' )
-#'   )
-#' )))
-#'
-#' server = function(input, output) {
-#'   output$diagram <- renderGrViz({
-#'     grViz(
-#'       input$ace
-#'     )
-#'   })
-#'
-#' }
-#'
-#' shinyApp(ui = ui, server = server)
-#' }
 #'
 #' @export
 grVizOutput <- function(outputId,
-                        width = '100%',
-                        height = '400px') {
+                        width = "100%",
+                        height = "400px") {
 
-  shinyWidgetOutput(
+  htmlwidgets::shinyWidgetOutput(
     outputId = outputId,
-    'grViz',
-    width,
-    height,
-    package = 'DiagrammeR')
+    name = "grViz",
+    width = width,
+    height = height,
+    package = "DiagrammeR"
+  )
 }
 
 #' Widget render function for use in Shiny
@@ -138,11 +115,12 @@ renderGrViz <- function(expr,
 
   if (!quoted) expr <- substitute(expr)
 
-  shinyRenderWidget(
-    expr,
-    grVizOutput,
-    env,
-    quoted = TRUE)
+  htmlwidgets::shinyRenderWidget(
+    expr = expr,
+    outputFunction = grVizOutput,
+    evn = env,
+    quoted = TRUE
+  )
 }
 
 #' Add MathJax-formatted equation text

R/mermaid.R

@@ -19,103 +19,104 @@
 #'   Markdown documents, and within Shiny output bindings.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # Create a simple graph running left to right (note
 #' # that the whitespace is not important)
-#' DiagrammeR("
-#'   graph LR
-#'     A-->B
-#'     A-->C
-#'     C-->E
-#'     B-->D
-#'     C-->D
-#'     D-->F
-#'     E-->F
-#' ")
+#' # DiagrammeR("
+#' #   graph LR
+#' #     A-->B
+#' #     A-->C
+#' #     C-->E
+#' #     B-->D
+#' #     C-->D
+#' #     D-->F
+#' #     E-->F
+#' # ")
+#'
 #' # Create the equivalent graph but have it running
 #' # from top to bottom
-#' DiagrammeR("
-#'    graph TB
-#'    A-->B
-#'    A-->C
-#'    C-->E
-#'    B-->D
-#'    C-->D
-#'    D-->F
-#'    E-->F
-#' ")
+#' # DiagrammeR("
+#' #    graph TB
+#' #    A-->B
+#' #    A-->C
+#' #    C-->E
+#' #    B-->D
+#' #    C-->D
+#' #    D-->F
+#' #    E-->F
+#' # ")
 #'
 #' # Create a graph with different node shapes and
 #' # provide fill styles for each node
-#' DiagrammeR("graph LR;A(Rounded)-->B[Squared];B-->C{A Decision};
-#'  C-->D[Square One];C-->E[Square Two];
-#'  style A fill:#E5E25F;  style B fill:#87AB51; style C fill:#3C8937;
-#'  style D fill:#23772C;  style E fill:#B6E6E6;"
-#' )
+#' # DiagrammeR("graph LR;A(Rounded)-->B[Squared];B-->C{A Decision};
+#' #  C-->D[Square One];C-->E[Square Two];
+#' #  style A fill:#E5E25F;  style B fill:#87AB51; style C fill:#3C8937;
+#' #  style D fill:#23772C;  style E fill:#B6E6E6;"
+#' # )
 #'
 #' # Load in the 'mtcars' dataset
-#' data(mtcars)
-#' connections <- sapply(
-#'  1:ncol(mtcars)
-#'   ,function(i) {
-#'      paste0(
-#'         i
-#'       ,"(",colnames(mtcars)[i],")---"
-#'       ,i,"-stats("
-#'       ,paste0(
-#'         names(summary(mtcars[,i]))
-#'         ,": "
-#'         ,unname(summary(mtcars[,i]))
-#'         ,collapse="<br/>"
-#'       )
-#'       ,")"
-#'    )
-#'  }
-#' )
+#' # data(mtcars)
+#' # connections <- sapply(
+#' #  1:ncol(mtcars)
+#' #   ,function(i) {
+#' #      paste0(
+#' #         i
+#' #       ,"(",colnames(mtcars)[i],")---"
+#' #       ,i,"-stats("
+#' #       ,paste0(
+#' #         names(summary(mtcars[,i]))
+#' #         ,": "
+#' #         ,unname(summary(mtcars[,i]))
+#' #         ,collapse="<br/>"
+#' #       )
+#' #       ,")"
+#' #    )
+#' #  }
+#' # )
 #'
 #' # Create a diagram using the 'connections' object
-#' DiagrammeR(
-#'    paste0(
-#'      "graph TD;", "\n",
-#'      paste(connections, collapse = "\n"),"\n",
-#'      "classDef column fill:#0001CC, stroke:#0D3FF3, stroke-width:1px;" ,"\n",
-#'      "class ", paste0(1:length(connections), collapse = ","), " column;"
-#'    )
-#'  )
+#' # DiagrammeR(
+#' #    paste0(
+#' #      "graph TD;", "\n",
+#' #      paste(connections, collapse = "\n"),"\n",
+#' #      "classDef column fill:#0001CC, stroke:#0D3FF3, stroke-width:1px;" ,"\n",
+#' #      "class ", paste0(1:length(connections), collapse = ","), " column;"
+#' #    )
+#' #  )
 #'
 #' # Also with `DiagrammeR()`, you can use tags
 #' # from `htmltools` (just make sure to use
 #' # `class = "mermaid"`)
 #' library(htmltools)
-#' diagramSpec = "
-#' graph LR;
-#'   id1(Start)-->id2(Stop);
-#'   style id1 fill:#f9f,stroke:#333,stroke-width:4px;
-#'   style id2 fill:#ccf,stroke:#f66,stroke-width:2px,stroke-dasharray: 5, 5;
-#' "
-#' html_print(tagList(
-#'   tags$h1("R + mermaid.js = Something Special")
-#'   ,tags$pre(diagramSpec)
-#'   ,tags$div(class="mermaid",diagramSpec)
-#'   ,DiagrammeR()
-#' ))
+#' # diagramSpec = "
+#' # graph LR;
+#' #   id1(Start)-->id2(Stop);
+#' #   style id1 fill:#f9f,stroke:#333,stroke-width:4px;
+#' #   style id2 fill:#ccf,stroke:#f66,stroke-width:2px,stroke-dasharray: 5, 5;
+#' # "
+#' # html_print(tagList(
+#' #   tags$h1("R + mermaid.js = Something Special")
+#' #   ,tags$pre(diagramSpec)
+#' #   ,tags$div(class="mermaid", diagramSpec)
+#' #   ,DiagrammeR()
+#' # ))
 #'
 #' # Create a sequence diagram
-#' DiagrammeR("
-#' sequenceDiagram;
-#'    customer->>ticket seller: ask for a ticket;
-#'    ticket seller->>database: seats;
-#'    alt tickets available
-#'      database->>ticket seller: ok;
-#'      ticket seller->>customer: confirm;
-#'      customer->>ticket seller: ok;
-#'      ticket seller->>database: book a seat;
-#'      ticket seller->>printer: print a ticket;
-#'    else sold out
-#'      database->>ticket seller: none left;
-#'      ticket seller->>customer: sorry;
-#'    end
-#' ")
+#' # DiagrammeR("
+#' # sequenceDiagram;
+#' #    customer->>ticket seller: ask for a ticket;
+#' #    ticket seller->>database: seats;
+#' #    alt tickets available
+#' #      database->>ticket seller: ok;
+#' #      ticket seller->>customer: confirm;
+#' #      customer->>ticket seller: ok;
+#' #      ticket seller->>database: book a seat;
+#' #      ticket seller->>printer: print a ticket;
+#' #    else sold out
+#' #      database->>ticket seller: none left;
+#' #      ticket seller->>customer: sorry;
+#' #    end
+#' # ")
 #' }
 #'
 #' @import htmlwidgets
@@ -157,5 +158,6 @@ mermaid <- function(diagram = "",
     x = x,
     width = width,
     height = height,
-    package = "DiagrammeR")
+    package = "DiagrammeR"
+  )
 }

R/render_graph.R

@@ -16,7 +16,7 @@
 #' @param height An optional parameter for specifying the height of the
 #'   resulting graphic in pixels.
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # Render a graph that's a
 #' # balanced tree
 #' create_graph() %>%