Fixed issue with dplyr and custom class dataframes (#37)

* Removed custom classes from processing dataframes. Additional classes assigned to collect dataframes for S3 routing started causing dplyr and vctrs inheritence issues. * Updated documentation
vosonlab · Jun 14, 2020 · 25b1c99 · 25b1c99
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: vosonSML
-Version: 0.29.11
+Version: 0.29.12
 Title: Collecting Social Media Data and Generating Networks for Analysis
 Description: A suite of tools for collecting and constructing networks from social media data.
     Provides easy-to-use functions for collecting data across popular platforms (Twitter, YouTube

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# vosonSML 0.29.12
+
+## Bug Fixes
+- Fixed an issue with custom classes assigned to dataframes causing an `vctrs` error when using `dplyr` functions. The classes are no longer needed post-method routing so they are simply removed.
+- Replaced an instance of the deprecated `dplyr::funs` function that was generating a warning.
+
+## Minor Changes
+- Minor documentation updates.
+
 # vosonSML 0.29.11
 
 ## Bug Fixes

diff --git a/R/AddText.R b/R/AddText.R
@@ -35,26 +35,29 @@ AddText <- function(net, data, ...) {
 
 #' @noRd
 #' @export
-AddText.default <- function(net, data, ...) {
+AddText.default <- function(net, ...) {
   stop("Unknown network type passed to AddText.", call. = FALSE) 
 }
 
 #' @noRd
 #' @method AddText activity
 #' @export
-AddText.activity <- function(net, data, ...) {
+AddText.activity <- function(net, ...) {
   UseMethod("AddText.activity", net)
 }
 
 #' @noRd
 #' @export
-AddText.activity.default <- function(net, data, ...) {
+AddText.activity.default <- function(net, ...) {
   stop("Unknown social media type passed to AddText.", call. = FALSE)
 }
 
 #' @noRd
 #' @export
 AddText.activity.twitter <- function(net, data, ...) {
+  # data <- tibble::as_tibble(data)
+  class(data) <- rmCustCls(class(data))
+
   net$nodes <- dplyr::left_join(net$nodes, dplyr::select(data, .data$status_id, .data$text), by = "status_id")
   net$nodes <- dplyr::left_join(net$nodes, 
                                 dplyr::select(data, .data$quoted_status_id, .data$quoted_text) %>%
@@ -70,7 +73,7 @@ AddText.activity.twitter <- function(net, data, ...) {
 
   net$nodes$vosonTxt_tweet <- HTMLdecode(net$nodes$vosonTxt_tweet)
 
-  class(net) <- union(class(net), c("voson_text"))
+  class(net) <- union(class(net), c("vosontxt"))
   cat("Done.\n")
 
   net
@@ -79,12 +82,15 @@ AddText.activity.twitter <- function(net, data, ...) {
 #' @noRd
 #' @export
 AddText.activity.youtube <- function(net, data, ...) {
+  # data <- tibble::as_tibble(data)
+  class(data) <- rmCustCls(class(data))
+
   net$nodes <- dplyr::left_join(net$nodes, 
                                 dplyr::select(data, .data$CommentID, .data$Comment) %>%
                                   dplyr::rename(id = .data$CommentID, vosonTxt_comment = .data$Comment), 
                                 by = c("id"))
 
-  class(net) <- union(class(net), c("voson_text"))
+  class(net) <- union(class(net), c("vosontxt"))
   cat("Done.\n")
 
   net
@@ -105,6 +111,9 @@ AddText.activity.youtube <- function(net, data, ...) {
 #' @name vosonSML::AddText.activity.reddit
 #' @export
 AddText.activity.reddit <- function(net, data, cleanText = FALSE, ...) {
+  # data <- tibble::as_tibble(data)
+  class(data) <- rmCustCls(class(data))
+
   net$nodes <- dplyr::left_join(net$nodes, 
                                 dplyr::mutate(data, id = paste0(.data$thread_id, ".", .data$structure)) %>%
                                   dplyr::select(.data$id, .data$subreddit, .data$comment), 
@@ -122,7 +131,7 @@ AddText.activity.reddit <- function(net, data, cleanText = FALSE, ...) {
     net$nodes$title <- CleanRedditText(net$nodes$title)
   }  
 
-  class(net) <- union(class(net), c("voson_text"))
+  class(net) <- union(class(net), c("vosontxt"))
   cat("Done.\n")
 
   net
@@ -132,7 +141,6 @@ AddText.activity.reddit <- function(net, data, cleanText = FALSE, ...) {
 #' @method AddText actor
 #' @export
 AddText.actor <- function(net, ...) {
-
   UseMethod("AddText.actor", net)
 }
 
@@ -145,14 +153,17 @@ AddText.actor.default <- function(net, ...) {
 #' @noRd
 #' @export
 AddText.actor.twitter <- function(net, data, ...) {
+  # data <- tibble::as_tibble(data)
+  class(data) <- rmCustCls(class(data))
+
   net$edges <- dplyr::left_join(net$edges,
                                 dplyr::select(data, .data$status_id, .data$text),
                                 by = c("status_id")) %>%
                dplyr::rename(vosonTxt_tweet = .data$text)
 
   net$edges$vosonTxt_tweet <- HTMLdecode(net$edges$vosonTxt_tweet)
 
-  class(net) <- union(class(net), c("voson_text"))
+  class(net) <- union(class(net), c("vosontxt"))
   cat("Done.\n")
 
   net
@@ -192,6 +203,9 @@ AddText.actor.twitter <- function(net, data, ...) {
 #' @name vosonSML::AddText.actor.youtube
 #' @export
 AddText.actor.youtube <- function(net, data, repliesFromText = FALSE, atRepliesOnly = TRUE, ...) {
+  # data <- tibble::as_tibble(data)
+  class(data) <- rmCustCls(class(data))
+
   net$edges %<>% dplyr::left_join(dplyr::select(data, .data$CommentID, .data$Comment) %>%
                                   dplyr::rename(comment_id = .data$CommentID, vosonTxt_comment = .data$Comment), 
                                   by = c("comment_id"))
@@ -222,7 +236,7 @@ AddText.actor.youtube <- function(net, data, repliesFromText = FALSE, atRepliesO
     # , at_id = NULL # leave in for reference
   }
 
-  class(net) <- union(class(net), c("voson_text"))
+  class(net) <- union(class(net), c("vosontxt"))
   cat("Done.\n")
 
   net
@@ -243,7 +257,9 @@ AddText.actor.youtube <- function(net, data, repliesFromText = FALSE, atRepliesO
 #' @name vosonSML::AddText.actor.reddit
 #' @export
 AddText.actor.reddit <- function(net, data, cleanText = FALSE, ...) {
-
+  # data <- tibble::as_tibble(data)
+  class(data) <- rmCustCls(class(data))
+
   # rename the edge attribute containing the thread comment
   net$edges <- dplyr::left_join(net$edges,
                                 dplyr::select(data, .data$subreddit, .data$thread_id, .data$id, .data$comment),
@@ -264,7 +280,7 @@ AddText.actor.reddit <- function(net, data, cleanText = FALSE, ...) {
     net$edges$title <- CleanRedditText(net$edges$title)
   }
 
-  class(net) <- union(class(net), c("voson_text"))
+  class(net) <- union(class(net), c("vosontxt"))
   cat("Done.\n")
 
   net

diff --git a/R/AddUserData.R b/R/AddUserData.R
@@ -6,6 +6,7 @@
 #' @note Only supports twitter actor networks at this time. Refer to \code{\link{AddUserData.actor.twitter}}.
 #' 
 #' @param net A named list of dataframes \code{nodes} and \code{edges} generated by \code{Create}.
+#' @param data A dataframe generated by \code{Collect}.
 #' @param ... Additional parameters passed to function.
 #'
 #' @return Network as a named list of two dataframes containing \code{$nodes} and \code{$edges}
@@ -14,7 +15,7 @@
 #' @aliases AddUserData
 #' @name vosonSML::AddUserData
 #' @export
-AddUserData <- function(net, ...) {
+AddUserData <- function(net, data, ...) {
   # searches the class list of net for matching method
   UseMethod("AddUserData", net)
 }
@@ -29,7 +30,6 @@ AddUserData.default <- function(net, ...) {
 #' @method AddUserData actor
 #' @export
 AddUserData.actor <- function(net, ...) {
-
   UseMethod("AddUserData.actor", net)
 }
 
@@ -81,6 +81,8 @@ AddUserData.actor.twitter <- function(net, data, lookupUsers = TRUE, twitterAuth
   cat("Adding user profile data to network...")
   if (verbose) { cat("\n") }
 
+  class(data) <- rmCustCls(class(data))
+
   dfUsers <- net$nodes
 
   dfUsers %<>% dplyr::mutate_all(as.character) # changes all col types to character
@@ -126,24 +128,15 @@ AddUserData.actor.twitter <- function(net, data, lookupUsers = TRUE, twitterAuth
   }
 
   df_users_info_all %<>% dplyr::rename("display_name" = .data$name, "name" = .data$user_id)
-
-  # fix type for numeric value columns and also replace na values with zero for convenience
+
   # numeric value column names in rtweet collected data end with "count"
-  df_users_info_all %<>% dplyr::mutate_at(vars(ends_with("count")), funs(ifelse(is.na(.data$.), as.integer(0), 
-                                                                         as.integer(.data$.))))
+  df_users_info_all %<>% dplyr::mutate_at(vars(ends_with("count")), 
+                                          # funs(ifelse(is.na(.data$.), as.integer(0), as.integer(.data$.)))
+                                          list(function(x) ifelse(is.na(x), as.integer(0), as.integer(x))))
 
   net$nodes <- df_users_info_all
 
-  # func_output <- list(
-  #   "nodes" = df_users_info_all,
-  #   "edges" = net$edges
-  # )
-  # 
-  # class(func_output) <- append(class(func_output), c("network", "actor", "twitter"))
-
-  # return(func_output)
-
-  class(net) <- union(class(net), c("voson_user_data"))
+  class(net) <- union(class(net), c("vosonuser"))
   cat("Done.\n")
 
   net

diff --git a/R/AddVideoData.R b/R/AddVideoData.R
@@ -140,7 +140,7 @@ AddVideoData.actor.youtube <- function(net, youtubeAuth = NULL, videoIds = NULL,
                     video_published_at = .data$VideoPublishedAt)
   }
 
-  class(net) <- union(class(net), c("voson_video_data"))
+  class(net) <- union(class(net), c("vosonvideo"))
   cat("Done.\n")
 
   net

diff --git a/R/Authenticate.twitter.R b/R/Authenticate.twitter.R
@@ -1,7 +1,15 @@
 #' @title Twitter API authentication
 #' 
-#' @description Twitter authentication uses OAuth and either requires authorization of the rtweet package rstats2twitter
-#' client app by a registered twitter user or twitter app developer API keys as described here: 
+#' @description Twitter authentication uses OAuth and typically requires four developer API keys
+#' generated when you create a twitter app via the twitter developer web site.
+#' 
+#' There is another method available commonly used by third-party apps in which an app can be
+#' authorized by a user to use the twitter API on their behalf. The implementation
+#' of this method in vosonSML does not require a developer account but does still require
+#' the user to have access to a developers apps two consumer API keys. This allows multiple
+#' users to access the twitter API with vosonSML via a single developer account and app. 
+#' 
+#' The twitter OAuth process is described here: 
 #' \url{https://developer.twitter.com/en/docs/basics/authentication/overview/oauth}.
 #' 
 #' @param socialmedia Character string. Identifier for social media API to authenticate, set to \code{"twitter"}.
@@ -17,23 +25,24 @@
 #' 
 #' @examples
 #' \dontrun{
-#' # twitter authentication via user authorization of app on their account
-#' # will open a web browser to twitter prompting the user to log in and authorize the app
-#' # apiKey and apiSecret are equivalent to a twitter apps consumer key and secret
-#' twitterAuth <- Authenticate("twitter", appName = "An App",
-#'   apiKey = "xxxxxxxxxxxx", apiSecret = "xxxxxxxxxxxx"
-#' )
-#' 
-#' # twitter authentication with developer app api keys
+#' # twitter authentication using developer app API keys
 #' myDevKeys <- list(appName = "My App", apiKey = "xxxxxxxxxxxx",
 #'   apiSecret = "xxxxxxxxxxxx", accessToken = "xxxxxxxxxxxx",
 #'   accessTokenSecret = "xxxxxxxxxxxx")
 #' 
 #' twitterAuth <- Authenticate("twitter", appName = myDevKeys$appName, 
 #'   apiKey = myDevKeys$apiKey, apiSecret = myDevKeys$apiSecret, accessToken = myDevKeys$accessToken, 
 #'   accessTokenSecret = myDevKeys$accessTokenSecret)
-#' }
 #' 
+#' # twitter authentication via authorization of an app to their user account
+#' # requires the apps consumer API keys
+#' # apiKey and apiSecret parameters are equivalent to the apps consumer key and secret
+#' # will open a web browser to twitter prompting the user to log in and authorize the app
+#' twitterAuth <- Authenticate("twitter", appName = "An App",
+#'   apiKey = "xxxxxxxxxxxx", apiSecret = "xxxxxxxxxxxx"
+#' )
+#' }
+#'  
 #' @export
 Authenticate.twitter <- function(socialmedia, appName, apiKey, apiSecret, accessToken, accessTokenSecret, ...) {
 
@@ -70,5 +79,5 @@ Authenticate.twitter <- function(socialmedia, appName, apiKey, apiSecret, access
     access_secret = accessTokenSecret,
     set_renv = FALSE)
 
-  return(credential)
+  credential
 }
diff --git a/R/Collect.reddit.R b/R/Collect.reddit.R
@@ -61,7 +61,7 @@ Collect.reddit <- function(credential, threadUrls, waitTime = c(3, 10), ua = get
   }, error = function(e) {
     stop(gsub("^Error:\\s", "", paste0(e)), call. = FALSE)
   }, finally = {
-    threads_df <- as_tibble(threads_df)
+    threads_df <- tibble::as_tibble(threads_df)
   })
 
   if (!is.null(threads_df)) {
@@ -93,7 +93,7 @@ Collect.reddit <- function(credential, threadUrls, waitTime = c(3, 10), ua = get
   class(threads_df) <- append(class(threads_df), c("datasource", "reddit"))
   cat("Done.\n")
 
-  return(threads_df)
+  threads_df
 }
 
 reddit_build_df <- function(threadUrls, waitTime, ua, verbose) {
@@ -107,7 +107,7 @@ reddit_build_df <- function(threadUrls, waitTime, ua, verbose) {
     # loop protection
     prev_value <- NULL
 
-    extra_threads <- filter(branch_df, grepl("Listing:", .data$comm_id))
+    extra_threads <- dplyr::filter(branch_df, grepl("Listing:", .data$comm_id))
     while (nrow(extra_threads) > 0) {
 
       row_i <- 1 # top row
@@ -128,24 +128,24 @@ reddit_build_df <- function(threadUrls, waitTime, ua, verbose) {
       cont_thread_id <- gsub("Listing:t1_", "", extra_threads[row_i, "comm_id"])
 
       # set continue thread comment rm flag to true
-      branch_df <- mutate(branch_df,
-                          rm = ifelse((.data$comm_id == cont_thread_id | .data$comm_id == extra_threads[row_i, "comm_id"]),
-                                      TRUE, .data$rm))
+      branch_df <- dplyr::mutate(branch_df,
+                    rm = ifelse((.data$comm_id == cont_thread_id | .data$comm_id == extra_threads[row_i, "comm_id"]),
+                                TRUE, .data$rm))
 
       # get continue thread
       cont_json <- reddit_data(paste0(x, cont_thread_id), waitTime, ua, cont = cont_thread_id, verbose = verbose)
       cont_df <- reddit_content_plus(cont_json, x, depth = depth)
 
       # if comments returned
       if (nrow(cont_df)) {
-        cont_df <- cont_df %>% mutate(structure = paste0(struct, "_", .data$structure)) # append structure
+        cont_df <- cont_df %>% dplyr::mutate(structure = paste0(struct, "_", .data$structure)) # append structure
 
         # insert new comments into thread dataframe using position
         if (cont_index == 1) {
-          branch_df <- bind_rows(cont_df, branch_df)
+          branch_df <- dplyr::bind_rows(cont_df, branch_df)
         } else {
-          pre_df <- bind_rows(branch_df[1:cont_index-1, ], cont_df)
-          branch_df <- bind_rows(pre_df, branch_df[cont_index:nrow(branch_df), ])
+          pre_df <- dplyr::bind_rows(branch_df[1:cont_index-1, ], cont_df)
+          branch_df <- dplyr::bind_rows(pre_df, branch_df[cont_index:nrow(branch_df), ])
         }
       }
 
@@ -156,14 +156,14 @@ reddit_build_df <- function(threadUrls, waitTime, ua, verbose) {
     if (!is.null(branch_df) && nrow(branch_df) > 0) {
       branch_df$thread_id <- gsub("^(.*)?/comments/([0-9A-Za-z]{6})?/.*?(/)?$", "\\2", 
                            branch_df$url, ignore.case = TRUE, perl = TRUE, useBytes = TRUE) # extract thread id
-      branch_df <- branch_df %>% filter(.data$rm == FALSE) # remove continue thread entries
-      branch_df <- branch_df %>% arrange(.data$thread_id, .data$id) %>% mutate(id = 1:nrow(branch_df)) # re-index
+      branch_df <- branch_df %>% dplyr::filter(.data$rm == FALSE) # remove continue thread entries
+      branch_df <- branch_df %>% dplyr::arrange(.data$thread_id, .data$id) %>% dplyr::mutate(id = 1:nrow(branch_df)) # re-index
     }
 
     branch_df
   })
 
-  threads_df <- bind_rows(threads)
+  threads_df <- dplyr::bind_rows(threads)
 }
 
 # based on method by @ivan-rivera RedditExtractoR