Update OpenAlexEdges.R

OpenAlexEdges.R

@@ -26,8 +26,91 @@ authorPubEdges <- function(keywords,pub_start_date,pub_end_date){
     
   }
   
-  # import nodes function
-  source("openAlexNodes.R")
+  # define nodes function
+  authorPubNodes <- function(keywords,pub_start_date,pub_end_date){
+  
+  keywords <- keywords
+  pub_start_date <- pub_start_date
+  pub_end_date <- pub_end_date
+  
+  # create search engine function
+  search_engine <- function(keywords,pub_start_date,pub_end_date){
+    suppressPackageStartupMessages(library(openalexR))
+    suppressPackageStartupMessages(library(tidyverse))
+    
+    options(openalexR.mailto = "[email protected]")
+    
+    # search engine
+    works_search <- oa_fetch(
+      entity = "works",
+      title.search = keywords,
+      cited_by_count = ">50",
+      from_publication_date = pub_start_date,
+      to_publication_date = pub_end_date,
+      options = list(sort = "cited_by_count:desc"),
+      verbose = FALSE
+    )
+    
+    return(works_search)
+    
+  }
+  
+  search_data <- search_engine(keywords,pub_start_date,pub_end_date)
+  
+  # grab authors and group them according to collaboration
+  authors_collaboration_groups <- list()
+  for (i in 1:nrow(search_data)){
+    authors_collaboration_groups[[i]] <- search_data$author[[i]][2]
+  }
+  
+  # grab all authors
+  all_authors <- c()
+  for (i in 1:length(authors_collaboration_groups)) {
+    all_authors <- c(all_authors,authors_collaboration_groups[[i]][[1]])
+  }
+  
+  # get length of each authors collaboration
+  authors_length <- c()
+  for(authors in 1:length(authors_collaboration_groups)){
+    authors_length <- c(authors_length,authors_collaboration_groups[[authors]] |> nrow())
+  }
+  
+  # grab all publications
+  publications <- list()
+  for (i in 1:nrow(search_data)){
+    publications[[i]] <- rep(search_data$display_name[i], each = authors_length[i])
+  }
+  
+  # place all publications in a vector
+  all_publications <- c()
+  for(i in 1:length(publications)){
+    all_publications <- c(all_publications,publications[[i]])
+  }
+  
+  # create author_to_publication data frame
+  authors_to_publications <- data.frame(
+    Authors = all_authors,
+    Publications = all_publications
+  )
+  
+  # stack the df so that authors and publications
+  # are together as one column
+  stacked_df <- stack(authors_to_publications)
+  stacked_df <- unique.data.frame(stacked_df) # remove duplicate rows
+  stacked_df <- stacked_df[-2] # delete second column in df
+  
+  # create author_publications_nodes df
+  author_publication_nodes <- data.frame(
+    Id = 1:nrow(stacked_df),
+    Nodes = stacked_df$values,
+    Label = stacked_df$values
+  )
+  
+  
+  return(author_publication_nodes)
+  
+  
+}
   
   # run author nodes function
   author_nodes <- authorPubNodes(keywords,pub_start_date,pub_end_date)