add missing imports & cosmetic tweaks

* import packages used only in ui.R and server.R
* change import directives so that no functions are masked
  thus avoiding import warnings
* Code now compliant with tidyverse style guide using
  the `styler` package

Author: markheckmann

.Rbuildignore

@@ -15,3 +15,4 @@ dev$
 ^\.dockerignore$
 ^LICENSE\.md$
 ^\.github$
+^inst/extdata/software-animation\.gif$

DESCRIPTION

@@ -22,7 +22,7 @@ Description: Shiny UI to identify cliques of related constructs in repertory gri
     See Burr, King, & Heckmann (2020) <doi:10.1080/14780887.2020.1794088> for a description 
     of the interpretive clustering (IC) method.
 Version: 0.6.1
-Date: 2022-08-27
+Date: 2022-10-25
 Imports:
     graphics,
     grDevices,
@@ -41,7 +41,6 @@ Imports:
     openxlsx,
     DT,
     magrittr,
-    tidyverse,
     dplyr,
     stringr,
     reshape2,
@@ -50,7 +49,8 @@ Imports:
     igraph,
     tidyr,
     withr,
-    RColorBrewer
+    RColorBrewer,
+    tidyverse
 Suggests:
     knitr,
     rmarkdown,

NAMESPACE

@@ -12,12 +12,22 @@ export(ic)
 export(make_names)
 export(make_names_vec)
 export(network_graph_images)
+import(formattable)
 import(grDevices)
 import(graphics, except = box)
-import(igraph, except = compare)
+import(igraph, except = c(compare, normalize))
 import(openxlsx)
 import(reshape2)
+import(rintrojs)
+import(shinyFeedback)
+import(shinyWidgets, except = c(progressBar, alert))
+import(shinydashboard, except = c(dashboardPage, dashboardSidebar, box, dashboardHeader, taskItem, notificationItem, messageItem))
+import(shinydashboardPlus)
+import(shinyjs)
+import(shinythemes)
+import(splines)
 import(stringr)
+import(tidyverse)
 import(utils)
 importFrom(dplyr,case_when)
 importFrom(dplyr,filter)
@@ -26,5 +36,6 @@ importFrom(dplyr,recode)
 importFrom(dplyr,select)
 importFrom(magrittr,"%>%")
 importFrom(shinyBS,tipify)
+importFrom(shinycssloaders,withSpinner)
 importFrom(stats,na.omit)
 importFrom(withr,with_par)

NEWS.Rmd

@@ -5,6 +5,7 @@ output: html_document
 
 ## v0.6.1
 
+-   Code now compliant with tidyverse style guide using the `styler` package
 -   Add animated gif image with short software overview to README
 -   New `Sample output`tab added with extracts from the output for Sylvia's grid
 -   Additional test raising test coverage to over 90%

R/01-utils.R

@@ -1,29 +1,28 @@
-#////////////////////////////////////////////////////////////
+# ////////////////////////////////////////////////////////////
 #
 #                       Helper functions
 #
-#////////////////////////////////////////////////////////////
+# ////////////////////////////////////////////////////////////
 
 
 #' Create empty dataframe while keeping columns names
-#' 
+#'
 #' Also works on lists if dataframes are contained as list elements.
 #' @param x Dataframe or list.
 #' @export
 #' @keywords internal
-#' 
-emptify_object <- function(x) 
-{
+#'
+emptify_object <- function(x) {
   if (is.data.frame(x)) {
     return(x[integer(0), ])
   }
-  
+
   for (nm in names(x)) {
     df <- x[[nm]]
     if (is.data.frame(df)) {
-      df <- df[integer(0), ] 
+      df <- df[integer(0), ]
     } else {
-      df <- list()  
+      df <- list()
     }
     x[[nm]] <- df
   }
@@ -32,65 +31,62 @@ emptify_object <- function(x)
 
 
 #' Default datatable output when loading
-#' 
+#'
 #' @param text Text to be shown
 #' @param header Table header, defaults to an  empty string.
 #' @export
 #' @keywords internal
-dt_default <- function(text = "Waiting for data ...", 
-                       header = "") 
-{
+dt_default <- function(text = "Waiting for data ...",
+                       header = "") {
   df <- data.frame(col1 = text)
   names(df) <- header
-  
+
   # create datatable and format
   df %>%
-    (DT::datatable)(filter = "none", 
-              selection = "none", 
-              colnames = header,
-              class = 'compact', rownames = FALSE, 
-              options = list(
-                dom = 't',  
-                ordering = TRUE,
-                pageLength = 10
-              )
-   )
+    (DT::datatable)(filter = "none",
+      selection = "none",
+      colnames = header,
+      class = "compact", rownames = FALSE,
+      options = list(
+        dom = "t",
+        ordering = TRUE,
+        pageLength = 10
+      )
+    )
 }
 
 
 #' String splitter for comma separated values in Excel cell
-#' 
+#'
 #' @param x String to be split
 #' @export
 #' @keywords internal
 #' @examples
-#' 
-#' cell_text_split("10, 20,30" )
-#' cell_text_split("; ,  10  ,,,  20;30,," ) # very robust
-#' 
-cell_text_split <- function(x)
-{
-  x %>% 
-    stringr::str_replace_all(" +|;+", ",") %>%   # space, semicolon to comma
-    stringr::str_replace_all(",+", ",") %>%      # several commas to one
-    stringr::str_replace_all("^,+|,+$", "") %>%  # remove leading and trainling commas
-    strsplit(",")                       # split string at comma
+#'
+#' cell_text_split("10, 20,30")
+#' cell_text_split("; ,  10  ,,,  20;30,,") # very robust
+#'
+cell_text_split <- function(x) {
+  x %>%
+    stringr::str_replace_all(" +|;+", ",") %>% # space, semicolon to comma
+    stringr::str_replace_all(",+", ",") %>% # several commas to one
+    stringr::str_replace_all("^,+|,+$", "") %>% # remove leading and trainling commas
+    strsplit(",") # split string at comma
 }
 
 
 #' @rdname make-names
 #' @export
-make_names_vec <- function(x) 
-{
+make_names_vec <- function(x) {
   nms <- tolower(x)
-  nms <- stringr::str_replace_all(nms, "[[:blank:]]+", "_")       # replace blanks
-  nms <- stringr::str_replace_all(nms, "\\.|-|/|\\(|\\)|&|\\?", "_")  # replace . - \ ? to _ (underscore)
-  nms <- stringr::str_replace_all(nms, "[_]+", "_")               # replace multiple underscores by one
-  nms <- stringr::str_replace_all(nms, "[_]+$", "")               # remove trailing underscores
-  nms <- stringr::str_replace_all(nms, "\u00DF", "ss")               
-  nms <- stringr::str_replace_all(nms, "\u00E4", "ae")            # replace German umlauts by their two letter ASCII version
-  nms <- stringr::str_replace_all(nms, "\u00FC", "ue") 
-  nms <- stringr::str_replace_all(nms, "\u00F6", "oe") 
+  nms <- stringr::str_replace_all(nms, "[[:blank:]]+", "_") # replace blanks
+  nms <- stringr::str_replace_all(nms, "\\.|-|/|\\(|\\)|&|\\?", "_") # replace . - \ ? to _ (underscore)
+  nms <- stringr::str_replace_all(nms, "[_]+", "_") # replace multiple underscores by one
+  nms <- stringr::str_replace_all(nms, "[_]+$", "") # remove trailing underscores
+  nms <- stringr::str_replace_all(nms, "\u00DF", "ss")
+  nms <- stringr::str_replace_all(nms, "\u00E4", "ae") # replace German umlauts by their two letter ASCII version
+  nms <- stringr::str_replace_all(nms, "\u00FC", "ue")
+  nms <- stringr::str_replace_all(nms, "\u00F6", "oe")
   nms
 }
 
@@ -101,23 +97,22 @@ make_names_vec <- function(x)
 #' @keywords internal
 #' @rdname make-names
 #' @export
-make_names <- function(x) 
-{
-  if (!is.data.frame(x))
+make_names <- function(x) {
+  if (!is.data.frame(x)) {
     stop("x muste be a dataframe")
-  
-  names(x) <- make_names_vec( names(x) )
+  }
+
+  names(x) <- make_names_vec(names(x))
   x
 }
 
 
 #' Format as x digit number
-#' 
+#'
 #' @export
 #' @keywords internal
-#' 
-fnum <- function(x, digits = 2)
-{
+#'
+fnum <- function(x, digits = 2) {
   x <- round(x, digits)
   formatC(x, digits = digits, format = "f")
 }