General Upkeep

.Rbuildignore

@@ -1,3 +1,3 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .DS_Store
+inst/doc

DESCRIPTION

@@ -15,15 +15,17 @@ Depends:
 Imports:
     ggplot2,
     gridExtra,
-    plyr,
     utils,
     stats,
     methods,
     grDevices,
-    scales
+    scales,
+    rlang,
+    vctrs
 License: MIT + file LICENSE
-LazyData: true
 VignetteBuilder: knitr
 Suggests:
-    knitr
-RoxygenNote: 7.0.2
+    knitr,
+    rmarkdown
+RoxygenNote: 7.2.3
+Encoding: UTF-8

NAMESPACE

@@ -13,9 +13,14 @@ import(ggplot2)
 import(grDevices)
 import(gridExtra)
 import(methods)
-import(scales)
 import(stats)
 import(utils)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_histogram)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,theme)
 importFrom(grid,gpar)
 importFrom(grid,grid.draw)
 importFrom(grid,grid.layout)
@@ -24,4 +29,5 @@ importFrom(grid,legendGrob)
 importFrom(grid,popViewport)
 importFrom(grid,pushViewport)
 importFrom(grid,viewport)
-importFrom(plyr,count)
+importFrom(rlang,"%||%")
+importFrom(rlang,.data)

NEWS

@@ -1,3 +1,6 @@
+- Fix some warnings from ggplot2 3.0.0.
+- Remove dependency on plyr
+
 Release v1.4.0
 
 - Allow custom y-axis label and scale

R/Boxplot.R

@@ -51,7 +51,7 @@ BoxPlotsPlot <- function(bdat, att, att_color){
                                  panel.grid.minor = element_blank(),
                                  panel.grid.major = element_blank(),
                                  axis.title.x = element_blank())
-                         + geom_boxplot(data = bdat, aes_string(x="x", y="attribute"),
+                         + geom_boxplot(data = bdat, aes(x = .data$x, y = .data$attribute),
                                         fill = att_color, colour = "gray80"))
   return(boxplots)
 }

R/Custom.plots.R

@@ -11,19 +11,19 @@ GenerateCustomPlots <- function(attribute_plots, Set_data, QueryData, att_color,
     if(length(QueryData) != 0){SetAndQueryData[1:nrow(Set_data), ]$color <- "gray23"}
     #      x_att <- attribute_plots$plots[[i]]$x
     #      y_att <- attribute_plots$plots[[i]]$y
-    if(isTRUE(attribute_plots$plots[[i]]$queries) == T){
+    if(isTRUE(attribute_plots$plots[[i]]$queries)){
       if(length(QueryData) == 0){
         warning("To overlay with query data please specify att.x and att.y where applicable.")
-        if(is.null(attribute_plots$plots[[i]]$y) == F){
+        if(!is.null(attribute_plots$plots[[i]]$y)){
           CustomPlot[[i]] <- attribute_plots$plots[[i]]$plot(Set_data, attribute_plots$plots[[i]]$x, attribute_plots$plots[[i]]$y)
         }
         else{
           CustomPlot[[i]] <- attribute_plots$plots[[i]]$plot(Set_data, attribute_plots$plots[[i]]$x)
         }
       }
       else if(length(QueryData) != 0){
-        if(is.null(attribute_plots$plots[[i]]$y) == F){
-          if(is.na(atty[i]) == T){
+        if(!is.null(attribute_plots$plots[[i]]$y)){
+          if(is.na(atty[i])){
             warning("No y attribute provided to overlay with query data.
                         If attempting to display plot that needs both x and y aesthetics please enter att.y parameter.
                         Plots that require just the x aestheitc will not be affected.")
@@ -39,7 +39,7 @@ GenerateCustomPlots <- function(attribute_plots, Set_data, QueryData, att_color,
       }
     }
     else {
-      if(is.null(attribute_plots$plots[[i]]$y) == F){
+      if(!is.null(attribute_plots$plots[[i]]$y)){
         CustomPlot[[i]] <- attribute_plots$plots[[i]]$plot(Set_data, attribute_plots$plots[[i]]$x, attribute_plots$plots[[i]]$y)
       }
       else{

R/Custom.user.queries.R

@@ -27,16 +27,16 @@ customQueriesBar <- function(cust_data, sets,bar_data,custom){
     return(NULL)
   }
   for(i in 1:length(cust_data)){
-    cust_data[[i]] <- count(cust_data[[i]][sets])
+    cust_data[[i]] <- count_compat(cust_data[[i]][sets])
     colnames(cust_data[[i]])[num] <- "freq2"
     cust_data[[i]] <- cust_data[[i]][!(rowSums(cust_data[[i]][ ,1:length(sets)]) == 0), ]
     setup[[i]] <- merge(cust_data[[i]], bar_data, by = sets)
     color2 <- rep(custom[[i]]$color, times = nrow(setup[[i]]))
-    if(isTRUE(custom[[i]]$active) == T){
-      act <- rep(T, nrow(setup[[i]]))
+    if(isTRUE(custom[[i]]$active)){
+      act <- rep(TRUE, nrow(setup[[i]]))
     }
     else{
-      act <- rep(F, nrow(setup[[i]]))
+      act <- rep(FALSE, nrow(setup[[i]]))
     }
     setup[[i]] <- cbind(setup[[i]], color2, act)
   }

R/Element.queries.R

@@ -13,17 +13,17 @@ QuerieElemAtt <- function(q, data, start_col, exp, names, att_x, att_y, palette)
   if(length(q) == 0){
     return(NULL)
   }
-  for(i in 1:length(q)){
+  for(i in seq_along(q)){
     index_q <- unlist(q[[i]]$params)
     elem_color <- unlist(q[[i]]$color)
     test <- as.character(index_q[1])
     check <- match(test, names)
     if(length(check) != 0){
-      if(is.na(att_y[i]) == F){
+      if(!is.na(att_y[i])){
         elems <- GetElements(data, index_q)
         end_col <- ((start_col + as.integer(length(names))) - 1)
         elems <- elems[which(rowSums(elems[ ,start_col:end_col]) != 0), ]
-        if(is.null(exp) == F){
+        if(!is.null(exp)){
           elems <- Subset_att(elems, exp)
         }
         if(nrow(elems) != 0){
@@ -33,11 +33,11 @@ QuerieElemAtt <- function(q, data, start_col, exp, names, att_x, att_y, palette)
           elems <- NULL
         }
       }
-      else if(is.na(att_y[i]) == T){
+      else if(is.na(att_y[i])){
         elems <- GetElements(data, index_q)
         end_col <- ((start_col + as.integer(length(names))) - 1)
         elems <- elems[which(rowSums(elems[ ,start_col:end_col]) != 0), ]
-        if(is.null(exp) == F){
+        if(!is.null(exp)){
           elems <- Subset_att(elems, exp)
         }
         if(nrow(elems) != 0){
@@ -65,39 +65,39 @@ QuerieElemAtt <- function(q, data, start_col, exp, names, att_x, att_y, palette)
 
 
 ElemBarDat <- function(q, data1, first_col, exp, names, palette, mbdata){
-  data1 <- data.frame(data1, check.names = F)
-  bar <- count(data1)
+  data1 <- data.frame(data1, check.names = FALSE)
+  bar <- count_compat(data1)
   bar$x <- 1:nrow(bar)
   rows <- data.frame()
   act <- c()
   if(length(q) == 0){
     return(NULL)
   }
-  for(i in 1:length(q)){
+  for(i in seq_along(q)){
     index_q <- unlist(q[[i]]$params)
     test <- as.character(index_q[1])
     check <- match(test, names)
     elem_color <- q[[i]]$color
-    if(is.na(check) != T){
+    if(!is.na(check)){
       elem_data <- NULL
     }
     else{
       elem_data <- data1[which(as.character(data1[ ,test]) %in% c(index_q[2:length(index_q)])), ]
       if(!is.null(exp)){
       elem_data <- Subset_att(elem_data, exp)
       }
-      elem_data <- as.data.frame(count(elem_data[names]))
+      elem_data <- as.data.frame(count_compat(elem_data[names]))
       names(elem_data) <- c(names, "freq")
       elem_data <- elem_data[which(rowSums(elem_data[names]) != 0), ]
       x <- merge(mbdata, elem_data[names], by = names)
       elem_data <- merge(x[names], elem_data, by = names)
       x <- x$x
       elem_data$x <- x
-      if((isTRUE(q[[i]]$active) == T) && (is.null(elem_data) == F)){
-        act <- T
+      if(isTRUE(q[[i]]$active) && !is.null(elem_data)){
+        act <- TRUE
       }
-      else if((isTRUE(q[[i]]$active) == F || is.null(q[[i]]$active) == T) && (is.null(elem_data) == F)){
-        act <- F
+      else if((!isTRUE(q[[i]]$active) || is.null(q[[i]]$active)) && !is.null(elem_data)){
+        act <- FALSE
       }
       elem_data$color <- elem_color
       elem_data$act <- act

R/General.query.funcs.R

@@ -3,18 +3,18 @@
 SeperateQueries <- function(queries, choice, palette) {
   seperated <- list()
   for (i in 1:length(queries)) {
-    if (is.null(queries[[i]]$color) == T) {
+    if (is.null(queries[[i]]$color)) {
       queries[[i]]$color <- palette[1]
       palette <- palette[-1]
     }
-    else if (is.null(queries[[i]]$color) == F) {
+    else if (!is.null(queries[[i]]$color)) {
       next
     }
   }
   if (choice == 1) {
     for (i in 1:length(queries)) {
-      if (identical(intersects, queries[[i]]$query) == T ||
-          identical(elements, queries[[i]]$query) == T) {
+      if (identical(intersects, queries[[i]]$query) ||
+          identical(elements, queries[[i]]$query)) {
         seperated <- c(seperated, list(queries[[i]]))
       }
       else{
@@ -24,8 +24,8 @@ SeperateQueries <- function(queries, choice, palette) {
   }
   else if (choice == 2) {
     for (i in 1:length(queries)) {
-      if (identical(intersects, queries[[i]]$query) == F &&
-          identical(elements, queries[[i]]$query) == F) {
+      if (!identical(intersects, queries[[i]]$query) &&
+          !identical(elements, queries[[i]]$query)) {
         seperated <- c(seperated, list(queries[[i]]))
       }
       else{
@@ -61,18 +61,18 @@ GuideGenerator <- function(queries, palette) {
     return(NULL)
   }
   for (i in 1:length(queries)) {
-    if (is.null(queries[[i]]$color) == T) {
+    if (is.null(queries[[i]]$color)) {
       queries[[i]]$color <- palette[1]
       palette <- palette[-1]
     }
-    else if (is.null(queries[[i]]$color) == F) {
+    else if (!is.null(queries[[i]]$color)) {
       queries[[i]]$color <- queries[[i]]$color
     }
     colors[i] <- queries[[i]]$color
-    if (is.null(queries[[i]]$query.name) == FALSE) {
+    if (!is.null(queries[[i]]$query.name)) {
       numbers[i] <- queries[[i]]$query.name
     }
-    else if (is.null(queries[[i]]$query.name) == TRUE) {
+    else if (is.null(queries[[i]]$query.name)) {
       numbers[i] <- paste("Query", as.character(i), sep = "")
     }
   }