Solved the compatibility issue with the new version of rscopus package

NEWS

@@ -11,6 +11,7 @@ New functionality:
 * Added the argument aff.disamb in metaTagExtraction()
 
 Changes:
+* Solved the compatibility issue with the new version of rscopus package
 * Minor changes in argument list of histNetwork() and histPlot()
 * Improved plot layout and colors in networkPlot()
 * Solved the issue regarding the older versions of utils::promptPackage()

R/biblioAnalysis.R

@@ -142,17 +142,6 @@ if (("C1" %in% Tags) & (sum(!is.na(M$C1))>0)){
   names(Affiliation_frac)=c("Affiliation","Frequency")
   Affiliation_frac=Affiliation_frac[order(-Affiliation_frac$Frequency),]
 
-  # AFF=gsub("\\[.*?\\] ", "", M$C1)
-  # listAFF=strsplit(AFF,sep,fixed=TRUE)
-  # nAFF=unlist(lapply(listAFF,length))  
-  # listAFF[nAFF==0]="NA"
-  # fracAFF=unlist(sapply(nAFF,function(x){rep(1/x,x)}))  # fractional frequencies
-  # AFF=trim.leading(unlist(listAFF))  # delete spaces
-  # Affiliation=sort(table(AFF),decreasing=TRUE)
-  # Affiliation_frac=aggregate(fracAFF,by=list(AFF),'sum')
-  # names(Affiliation_frac)=c("Affiliation","Frequency")
-  # Affiliation_frac=Affiliation_frac[order(-Affiliation_frac$Frequency),]
-
   # First Affiliation
   FAffiliation=lapply(listAFF,function(l) l[1])
 
@@ -224,4 +213,4 @@ countryCollaboration<-function(M,Country,k,sep){
   }
   df$MCP=as.numeric(tableTag(M,"AU1_CO")[1:k])-df$SCP
   return(df)
-}
+}

R/convert2df.R

@@ -59,6 +59,7 @@
 #' @import ggrepel
 #' @import ggraph
 #' @importFrom stringdist stringdistmatrix
+#' @importFrom rscopus author_df_orig
 #' @importFrom rscopus author_search
 #' @importFrom rscopus get_complete_author_info
 #' @importFrom RColorBrewer brewer.pal

R/metaTagExtraction.R

@@ -426,4 +426,4 @@ ND<-function(affL,indd){
   cond=length(ind)<1
   r=list(affL=aff[ind[1]],cond=cond)
   return(r)
-}
+}

R/retrievalByAuthorID.R

@@ -51,7 +51,7 @@
 #' 
 #' ## create the bibliographic collection
 #' # 
-#' # res <- retrievalByAuthor(id, api_key)
+#' # res <- retrievalByAuthorID(id, api_key)
 #' #
 #' # M <- res$M  # the entire bibliographic data frame
 #' # M <- res$authorDocuments # the list containing a bibliographic data frame for each author
@@ -65,60 +65,23 @@ retrievalByAuthorID<-function(id, api_key, remove.duplicated=TRUE){
   id=id[!is.na(id)]
   M_list=list()
   n=length(id)
-  M=data.frame(AU=NA,TI=NA,AB=NA,SO=NA,JI=NA,DOI=NA,DT=NA,DE=NA,PY=NA,TC=NA,C1=NA,RP=NA,UT=NA,AU_CO=NA)
+  M=data.frame(AU_ID=NA,AU=NA,C1_ID=NA,C1=NA,nAU=NA,nC1=NA,TC=NA,SO=NA,DT=NA,TI=NA,PII=NA,DI=NA,EID=NA,PY=NA,CDD=NA, URL=NA,UT=NA,AU1=NA,ISSN=NA,EISSN=NA,PAG=NA,AB=NA,PT=NA,SUBTYPE=NA,DE=NA,SO_ID=NA)
   for (j in 1:n){
     AU_ID=id[j]
     cat("\n Query n. ",j,"   Author ID: ",AU_ID)
     ### documents of an author
-    AU_S=author_search(au_id = AU_ID, api_key=api_key)
-    AU_count=length(AU_S[[1]])
+    AU_S=author_df_orig(au_id = AU_ID, api_key=api_key, all_author_info=TRUE,verbose=FALSE)
+    AU_S$cover_date=substr(as.character(AU_S$cover_date),1,4)
 
-    ### first document information
-    AU=NA
-    TI=NA
-    AB=NA
-    SO=NA
-    JI=NA
-    DOI=NA
-    PY=NA
-    TC=NA
-    C1=NA
-    RP=NA
-    UT=NA
-    DT=NA
-    DE=NA
-    AU_CO=NA
-
-    ### documents retrieval
-    for (i in 1:AU_count){
-      D=AU_S[[1]][[i]]
-      AU[i]=paste(unlist(lapply(D$author,function(l){a=l$authname})),collapse=";")
-
-      AU[i]=paste(unique(trim(unlist(strsplit(AU[i],";")))),collapse =";")
-
-      if (!is.null(D$`dc:title`)){TI[i]=D$`dc:title`}else{TI[i]=NA}
-      if (!is.null(D$`dc:description`)){AB[i]=D$`dc:description`}else{AB[i]=NA}
-      if (!is.null(D$subtypeDescription)){DT[i]=D$subtypeDescription}else{DT[i]=NA}
-      if (!is.null(D$`dc:identifier`)){UT[i]=D$`dc:identifier`}else{UT[i]=NA}
-      if (!is.null(D$`prism:publicationName`)){SO[i]=D$`prism:publicationName`}else{SO[i]=NA}
-      JI[i]=SO[i]
-      if (!is.null(D$`prism:doi`)){DOI[i]=D$`prism:doi`}else{DOI[i]=NA}
-      if (!is.null(D$authkeywords)){DE[i]=gsub("\\|",";",D$authkeywords)}else{DE[i]=NA}
-      if (!is.null(D$`prism:coverDate`)){PY[i]=as.numeric(substring(D$`prism:coverDate`,1,4))}else{PY[i]=NA}
-      if (!is.null(D$`citedby-count`)){TC[i]=as.numeric(D$`citedby-count`)}else{TC[i]=NA}
-      if (!is.null(D$affiliation)){
-        aff=D$affiliation
-        C1[i]=paste(unlist(lapply(aff,function(l){
-          a=paste(l$affilname, ", ",l$`affiliation-city`,", ", l$`affiliation-country`,sep="")})),collapse=";")
-        l=aff[[1]]
-        RP[i]=paste(l$affilname, ", ",l$`affiliation-city`,", ", l$`affiliation-country`,sep="")
-        AU_CO[i]=paste(unlist(lapply(aff,function(l){a=l$`affiliation-country`})),collapse=";")
-      }else{
-        C1[i]=NA 
-        RP[i]=NA 
-        AU_CO[i]=NA}
+    for (i in 1:dim(AU_S)[2]){
+      if (is.factor(AU_S[[i]])){
+        AU_S[[i]]=as.character(AU_S[[i]])
+      }
     }
-    M_AU=data.frame(AU,TI,AB,SO,JI,DOI,DT,DE,PY,TC,C1,RP,UT,AU_CO,stringsAsFactors = FALSE)
+
+    M_AU=data.frame(AU_S,stringsAsFactors = FALSE)
+    names(M_AU)=c("AU_ID","AU","C1_ID","C1","nAU","nC1","TC","SO","DT","TI","PII","DI","EID","PY","CDD", "URL","UT","AU1","ISSN","EISSN","PAG","AB","PT","SUBTYPE","DE","SO_ID")
+
     M=rbind(M,M_AU)
     M_list[[j]]=M_AU
     names(M_list)[j]=id[j]
@@ -132,9 +95,52 @@ retrievalByAuthorID<-function(id, api_key, remove.duplicated=TRUE){
   }
   M$CR=NA
   M$DB="SCOPUS"
+  M$DE=gsub("\\| ",";",M$DE)
   M$ID=M$DE
+
+  M$AU_CO=paste(M$C1_ID,";",sep="")
+
+  ### country retrieval
+  cat("\nAuthors' country retrieval\n\n")
+  aff_id=sort(unique(unlist(strsplit(M$C1_ID,";"))))
+  aff_id=aff_id[nchar(aff_id)>1]
+
+  AFF=data.frame(ID=NA,NAME=NA,CO=NA)
+  for (i in 1:length(aff_id)){
+    a=affiliation_retrieval(aff_id[i],api_key=api_key,verbose=FALSE)
+    AFF[i,1]=aff_id[i]
+    AFF[i,2]=a$content$`affiliation-retrieval-response`$`affiliation-name`
+    AFF[i,3]=a$content$`affiliation-retrieval-response`$country
+    cat("\nAffiliation ID: ", AFF[i,1],"   Name: ",AFF[i,2], " ,", AFF[i,3])
+    M$AU_CO=gsub(paste(aff_id[i],";",sep = ""),paste(AFF[i,3],";",sep=""),M$AU_CO)
+  }
+  M$AU_CO=gsub(";;",";",M$AU_CO)
+  M$AU_CO[nchar(M$AU_CO)<3]=NA
+  M$AU1_CO=unlist(lapply(strsplit(M$AU_CO,";"), function(l){
+    l=l[1]
+  }))
+  UN=strsplit(M$C1,";")
+  CO=strsplit(M$AU_CO,";")
+
+  for (i in 1:length(UN)){
+    M$C1[i]=paste(paste(UN[[i]],", ",CO[[i]],sep=""),collapse=";")
+  }
+  #########
+
   M <- data.frame(lapply(M,toupper),stringsAsFactors = FALSE)
-  #M <- mutate_each(M, funs(toupper))
+  M$TC=as.numeric(M$TC)
+  M$PY=as.numeric(M$PY)
+  M$DB="SCOPUS"
+  M$RP=unlist(lapply(strsplit(M$C1,";"), function(l){
+    l=l[1]
+  }))
+  M$CR=NA
+
+
+
+
+
+
   results=list(M=M,authorDocuments=M_list)
   return(results)
 }