Merge pull request #407 from massimoaria/develop

CRAN Release 4.1.4

Author: massimoaria

.Rbuildignore

@@ -22,3 +22,5 @@ Rubbish
 ^inst/biblioshiny/rsconnect
 ^rsconnect
 
+^CRAN-SUBMISSION$
+^cran-comments\.md$

NAMESPACE

@@ -81,7 +81,6 @@ importFrom(Matrix,Matrix)
 importFrom(Matrix,MatrixClass)
 importFrom(Matrix,Ops)
 importFrom(Matrix,Summary)
-importFrom(Matrix,T2graph)
 importFrom(Matrix,abIseq)
 importFrom(Matrix,abIseq1)
 importFrom(Matrix,all.equal)
@@ -115,7 +114,6 @@ importFrom(Matrix,forceSymmetric)
 importFrom(Matrix,format)
 importFrom(Matrix,formatSpMatrix)
 importFrom(Matrix,formatSparseM)
-importFrom(Matrix,graph2T)
 importFrom(Matrix,head)
 importFrom(Matrix,image)
 importFrom(Matrix,invPerm)
@@ -186,15 +184,18 @@ importFrom(dplyr,bind_rows)
 importFrom(dplyr,count)
 importFrom(dplyr,cummean)
 importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
 importFrom(dplyr,do)
 importFrom(dplyr,group_by)
 importFrom(dplyr,if_all)
 importFrom(dplyr,inner_join)
+importFrom(dplyr,join_by)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_at)
 importFrom(dplyr,mutate_if)
 importFrom(dplyr,n)
+importFrom(dplyr,reframe)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)

NEWS

@@ -1,13 +1,16 @@
-bibliometrix v4.1.4 (Release date: )
+bibliometrix v4.1.4 (Release date: 2023-11-29)
 
 Changes:
+* Biblioshiny: After the data quality check, the menus of the analyses that cannot be performed are hidden
 * Start to adding support to OpenAlex data
 * Improvements in historiograph: 
    - Improved Scopus algorithm to match local citations
    - Added OpenAlex algorithm to match local citations
    - Added Lens.org algorithm to match local citations
 * Improved pajek export in biblioshiny
 * Computational speed improvements
+* Solved issue with igraph 1.6.0 release canddate 
+* Solved issue with Matrix package
 
 bibliometrix v4.1.2 (Release date: 2023-03-06)
 

R/Hindex.R

@@ -85,7 +85,7 @@ Hindex <- function(M, field="author", elements=NULL, sep = ";",years=Inf){
 
   H <- df %>% 
     group_by(.data$AUs) %>% 
-    summarize(#Element = .data$AUs[1],
+    reframe(#Element = .data$AUs[1],
       h_index = h_calc(.data$TC),
       g_index = g_calc(.data$TC),
       PY_start = min(.data$PY),

R/couplingMap.R

@@ -22,7 +22,7 @@
 #' @param impact.measure is a character. It indicates the impact measure used to rank cluster elements (documents, authors or sources).
 #' It can be \code{impact.measure = c("local", "global")}.\\
 #' With \code{impact.measure = "local"}, \link{couplingMap} calculates elements impact using the Normalized Local Citation Score while 
-#' using code{impact.measure = "global"}, the function uses the Normalized Global Citation Score to measure elements impact. 
+#' using \code{impact.measure = "global"}, the function uses the Normalized Global Citation Score to measure elements impact. 
 #' @param minfreq is a integer. It indicates the minimum frequency (per thousand) of a cluster. It is a number in the range (0,1000).
 #' @param community.repulsion is a real. It indicates the repulsion force among network communities. It is a real number between 0 and 1. Default is \code{community.repulsion = 0.1}.
 #' @param stemming is logical. If it is TRUE the word (from titles or abstracts) will be stemmed (using the Porter's algorithm).

R/csvScopus2df.R

@@ -29,6 +29,10 @@ csvScopus2df <- function(file){
   DATA$AU=gsub("\\.", "", DATA$AU)
   DATA$AU=gsub(",", ";", DATA$AU)
 
+  ### store raw affiliation format to extract link among authors and affiliations
+  DATA$C1raw <- DATA$C1
+  ###
+  
   # Affiliation
   if (!("C1" %in% names(DATA))){DATA$C1 <- NA}else{
     DATA$C1 <- unlist(lapply(strsplit(DATA$C1,";"), function(l){

R/histNetwork.R

@@ -324,7 +324,7 @@ scopus <- function(M, min.citations, sep, network, verbose){
     dplyr::filter(.data$toRemove != TRUE)
 
   LCS <- CR %>% 
-    group_by(SR_cited) %>% 
+    group_by(.data$SR_cited) %>% 
     count(name="LCS")
 
 
@@ -353,7 +353,7 @@ scopus <- function(M, min.citations, sep, network, verbose){
     CRadd <- data.frame(SR_citing=unique(M$SR), SR_cited=unique(M$SR), value=1)
 
     WLCR <- CR %>%
-      select(SR_citing, SR_cited) %>% 
+      select(.data$SR_citing, .data$SR_cited) %>% 
       mutate(value = 1) %>% 
       bind_rows(CRadd) %>% 
       distinct() %>% 

R/isi2df.R

@@ -64,6 +64,10 @@ Please, take a look at the vignettes:
   df <- cbind(df1,df2)
   rm(df1,df2)
 
+  ### store raw affiliation format to extract link among authors and affiliations
+  df$C1raw <- df$C1
+  ###
+  
   df$DB <- "ISI"
 
   # Authors

R/normalizeCItationScore.R

@@ -18,7 +18,7 @@
 #' @param impact.measure is a character. It indicates the impact measure used to rank cluster elements (documents, authors or sources).
 #' It can be \code{impact.measure = c("local", "global")}.\\
 #' With \code{impact.measure = "local"}, \link{normalizeCitationScore} calculates elements impact using the Normalized Local Citation Score while 
-#' using code{impact.measure = "global"}, the function uses the Normalized Global Citation Score to measure elements impact. 
+#' using \code{impact.measure = "global"}, the function uses the Normalized Global Citation Score to measure elements impact. 
 #' @return a dataframe.
 #'
 #' 

R/zzz.R

@@ -25,6 +25,8 @@
 ## @importFrom dplyr filter
 #' @importFrom dplyr arrange
 #' @importFrom dplyr do
+#' @importFrom dplyr distinct
+#' @importFrom dplyr join_by
 #' @importFrom dplyr n
 #' @importFrom dplyr slice
 #' @importFrom dplyr slice_max
@@ -53,6 +55,7 @@
 #' @importFrom dplyr relocate
 #' @importFrom dplyr slice_head
 #' @importFrom dplyr slice_tail
+#' @importFrom dplyr reframe
 #' @importFrom plotly add_annotations
 #' @importFrom plotly add_lines
 #' @importFrom plotly config
@@ -196,7 +199,6 @@
 #' @importFrom Matrix format
 #' @importFrom Matrix formatSparseM
 #' @importFrom Matrix formatSpMatrix
-#' @importFrom Matrix graph2T
 #' @importFrom Matrix head
 #' @importFrom Matrix image
 #' @importFrom Matrix invPerm
@@ -250,7 +252,6 @@
 #' @importFrom Matrix Summary
 #' @importFrom Matrix symmpart
 #' @importFrom Matrix t
-#' @importFrom Matrix T2graph
 #' @importFrom Matrix tail
 #' @importFrom Matrix tcrossprod
 #' @importFrom Matrix tril

README.md

@@ -120,23 +120,23 @@ Load `bibliometrix`
 
 ``` r
 library('bibliometrix')
-#> To cite bibliometrix in publications, please use:
+#> Please note that our software is open source and available for use, distributed under the MIT license.
+#> When it is used in a publication, we ask that authors properly cite the following reference:
 #> 
 #> Aria, M. & Cuccurullo, C. (2017) bibliometrix: An R-tool for comprehensive science mapping analysis, 
-#>                                  Journal of Informetrics, 11(4), pp 959-975, Elsevier.
-#>                         
-#> 
-#> https://www.bibliometrix.org
+#>                         Journal of Informetrics, 11(4), pp 959-975, Elsevier.
 #> 
+#> Failure to properly cite the software is considered a violation of the license.
 #>                         
 #> For information and bug reports:
+#>                         - Take a look at https://www.bibliometrix.org
 #>                         - Send an email to [email protected]   
 #>                         - Write a post on https://github.com/massimoaria/bibliometrix/issues
 #>                         
-#> Help us to keep Bibliometrix free to download and use by contributing with a small donation to support our research team (https://bibliometrix.org/donate.html)
+#> Help us to keep Bibliometrix and Biblioshiny free to download and use by contributing with a small donation to support our research team (https://bibliometrix.org/donate.html)
 #> 
 #>                         
-#> To start with the shiny web-interface, please digit:
+#> To start with the Biblioshiny app, please digit:
 #> biblioshiny()
 ```
 
@@ -197,23 +197,22 @@ The argument *M* is a bibliographic data frame obtained by
 com <- missingData(M)
 
 com$mandatoryTags
-#>    tag                description missing_counts missing_pct     status
-#> 1   AU                     Author              0        0.00  Excellent
-#> 2   DT              Document Type              0        0.00  Excellent
-#> 3   SO                    Journal              0        0.00  Excellent
-#> 4   LA                   Language              0        0.00  Excellent
-#> 5   NR Number of Cited References              0        0.00  Excellent
-#> 6   WC         Science Categories              0        0.00  Excellent
-#> 7   TI                      Title              0        0.00  Excellent
-#> 8   TC             Total Citation              0        0.00  Excellent
-#> 9   CR           Cited References              2        0.22       Good
-#> 10  AB                   Abstract              7        0.78       Good
-#> 11  PY           Publication Year              9        1.00       Good
-#> 12  RP       Corresponding Author             10        1.11       Good
-#> 13  C1                Affiliation             21        2.34       Good
-#> 14  DI                        DOI             36        4.01       Good
-#> 15  DE                   Keywords             79        8.80       Good
-#> 16  ID              Keywords Plus             97       10.80 Acceptable
+#>    tag          description missing_counts missing_pct     status
+#> 1   AU               Author              0        0.00  Excellent
+#> 2   DT        Document Type              0        0.00  Excellent
+#> 3   SO              Journal              0        0.00  Excellent
+#> 4   LA             Language              0        0.00  Excellent
+#> 5   WC   Science Categories              0        0.00  Excellent
+#> 6   TI                Title              0        0.00  Excellent
+#> 7   TC       Total Citation              0        0.00  Excellent
+#> 8   CR     Cited References              2        0.22       Good
+#> 9   AB             Abstract              7        0.78       Good
+#> 10  PY     Publication Year              9        1.00       Good
+#> 11  RP Corresponding Author             10        1.11       Good
+#> 12  C1          Affiliation             21        2.34       Good
+#> 13  DI                  DOI             36        4.01       Good
+#> 14  DE             Keywords             79        8.80       Good
+#> 15  ID        Keywords Plus             97       10.80 Acceptable
 ```
 
 **missingData** returns a list containing two data frame. The first one,

inst/biblioshiny/libraries.R

@@ -20,6 +20,9 @@ libraries <- function(){
     if (!require(RCurl, quietly=TRUE)){install.packages("RCurl")}
     if (!require(openxlsx, quietly=TRUE)){install.packages("openxlsx"); require(openxlsx, quietly=TRUE)}
     if (!require(shinyWidgets, quietly=TRUE)){install.packages("shinyWidgets"); require(shinyWidgets, quietly=TRUE)}
+    
+    ## Currently "webshot2" 0.1.1 generates empty screenshots on windows 10 for graphics created with visnetwork.
+    ## This workaround installs the previous version 0.1.0 to temporarily fix the problem.
     if (!require(webshot2,quietly=TRUE)){
       install.packages("https://cran.r-project.org/src/contrib/Archive/webshot2/webshot2_0.1.0.tar.gz", repos = NULL, type = "source")
     }else{
@@ -30,11 +33,14 @@ libraries <- function(){
         install.packages("https://cran.r-project.org/src/contrib/Archive/webshot2/webshot2_0.1.0.tar.gz", repos = NULL, type = "source")
       }
     }
+    ##
+    
     if (!(require(chromote, quietly=TRUE))){install.packages("chromote"); require(chromote, quietly=TRUE)}
 
     ### workaround for webshot2 on shinyapps.io
     if (!(require(curl, quietly=TRUE))){install.packages("curl"); require(curl, quietly=TRUE)}
     if (!(require(pagedown, quietly=TRUE))){install.packages("pagedown"); require(pagedown, quietly=TRUE)}
+    ##
     require(Matrix, quietly = TRUE)
     require(dimensionsR, quietly = TRUE)
     require(pubmedR, quietly = TRUE)

inst/biblioshiny/server.R

@@ -30,7 +30,7 @@ server <- function(input, output,session){
       HTML("Chrome or a Chromium-based browser is not installed on your computer.<br>
 If you do not have either of these browsers installed, Biblioshiny will be unable to export graphs.<br>
 To ensure the functionality of Biblioshiny,
-           please download Chrome by <a href='https://www.google.com/intl/it_it/chrome/' target='_blank' > <b>clicking here</b></a>."),
+           please download Chrome by <a href='https://www.google.com/chrome/' target='_blank' > <b>clicking here</b></a>."),
       footer = modalButton("Dismiss"),
       easyClose = TRUE
     ))