Trouble at Mill

Author: DrMattG

NAMESPACE

@@ -8,6 +8,7 @@ export(get_citation)
 export(get_refs)
 export(reconstruct_abstract)
 export(repair_refs)
+export(runBibfixApp)
 export(scan_file)
 export(search_openAlex)
 importFrom(MESS,cumsumbinning)

R/build_ris.R

@@ -0,0 +1,93 @@
+#' Build RIS files from other sources
+#' 
+#' @description Builds an RIS file based on a basic input of 
+#' fields corresponding to a minimum information for 
+#' deduplication and record identification from external 
+#' API sources (e.g. CrossRef). 
+#' @param input A dataframe object containing bibliographic 
+#' data. Each item is an independent line in the 
+#' dataframe. The dataframe must contain 
+#' columns named as follows: 'authors', 'year', 'title', 
+#' 'source', 'volume', 'issue', 'start_page', 'end_page', 
+#' and 'doi'.
+#' @param save Logical argument to specify whether the output 
+#' file should be saved as an .ris file.
+#' @param filename Optional name of the output file if 
+#' save = TRUE. Default is 'export'.
+#' @param path Path to which file should be saved.
+#' @return An RIS formatted text file saved to the desired 
+#' path.
+#' @export
+#' @examples 
+#' \dontrun{
+#' data <- read.csv('inst/extdata/data.csv')
+#' ris <- build_ris(data, save=TRUE)
+#' }
+build_ris <- function(data,
+                      save = FALSE,
+                      filename = 'export',
+                      path = NULL){
+  
+  if (is.data.frame(data) == FALSE){
+    stop('Please ensure the input object is a data frame')
+  }
+  
+  #add missing columns where necessary (ensures build below works even if fields not present)
+  if(is.null(data$source_type) == TRUE){data$source_type <- NA}
+  if(is.null(data$author) == TRUE){data$author <- NA}
+  if(is.null(data$year) == TRUE){data$year <- NA}
+  if(is.null(data$title) == TRUE){data$title <- NA}
+  if(is.null(data$journal) == TRUE){data$journal <- NA}
+  if(is.null(data$volume) == TRUE){data$volume <- NA}
+  if(is.null(data$issue) == TRUE){data$issue <- NA}
+  if(is.null(data$start_page) == TRUE){data$start_page <- NA}
+  if(is.null(data$end_page) == TRUE){data$end_page <- NA}
+  if(is.null(data$abstract) == TRUE){data$abstract <- NA}
+  if(is.null(data$doi) == TRUE){data$doi <- NA}
+  if(is.null(data$publisher) == TRUE){data$publisher <- NA}
+  if(is.null(data$url) == TRUE){data$url <- NA}
+  if(is.null(data$notes) == TRUE){data$notes <- NA}
+  if(is.null(data$M1) == TRUE){data$M1 <- NA}
+  if(is.null(data$database) == TRUE){data$database <- NA}
+  if(is.null(data$AN) == TRUE){data$AN <- NA}
+  
+  #replace NAs with ''
+  data[is.na(data)==TRUE]=''
+  
+  #create RIS file
+  ris <- paste(paste0('\n',
+                      'TY  - ', data$source_type, '\n',
+                      'AU  - ', data$author, '\n',
+                      'TI  - ', data$title, '\n',
+                      'PY  - ', data$year, '\n',
+                      'AB  - ', data$abstract, '\n',
+                      'SP  - ', data$start_page, '\n',
+                      'EP  - ', data$end_page, '\n',
+                      'JF  - ', data$journal, '\n',
+                      'VL  - ', data$volume, '\n',
+                      'IS  - ', data$issue, '\n',
+                      'DO  - ', data$doi, '\n',
+                      'UR  - ', data$url, '\n',
+                      'PB  - ', data$publisher, '\n',
+                      'N1  - ', data$notes, '\n',
+                      'M1  - ', data$M1, '\n',
+                      'DB  - ', data$DB, '\n',
+                      'AN  - ', data$AN, '\n',
+                      'ER  - '),
+               collapse = '\n')
+  
+  #generate report if file exported as .ris
+  if (save == TRUE){
+    write.table(ris, file = paste0(path, filename, '.ris'), row.names = FALSE, col.names = FALSE)
+    if (is.null(path) == TRUE){
+      location <- 'your working directory'
+    } else {
+      location <- paste0(path)
+    }
+    report <- paste0('The output file "', filename, '.ris" has been saved to ', location)
+    message(report)
+  }
+  
+  return(ris)
+  
+}

R/repair_refs.R

@@ -19,7 +19,8 @@ repair_refs <- function(refs,
                         repair_incomplete = TRUE,
                         source = 'lens',
                         title_search = TRUE,
-                        token = 'NFxMqRTdXCQRq3uDl8NgduSAXcEf5DAqLIBAPALydHloF0n1n2Xi'){
+                        token = 'NFxMqRTdXCQRq3uDl8NgduSAXcEf5DAqLIBAPALydHloF0n1n2Xi')
+  {
 
   #enter polite pool
   suppressMessages(invisible(capture.output(openalex::openalex_polite("[email protected]"))))
@@ -414,7 +415,7 @@ refs<-refs |>
         }
         )
 
-  }
+  }}
   ####End DOI section####
 
   ####Title section####
@@ -582,10 +583,10 @@ refs<-refs |>
     }}}
 
     ####End title section####
-  }
   } else {
       title_refs <- NULL
-    }
+  }
+  
   #bind doi lookup and title lookup table with original values not missing information
   result <- dplyr::bind_rows(non_missing, doi_refs, title_refs)
 
@@ -606,11 +607,10 @@ refs<-refs |>
   output <- intermediate %>%
     dplyr::group_by(intID) %>%
     dplyr::summarise_all(coalesce_by_column)
-  
+
   return(output)
-  
-    }
   }
+  
 
 
 coalesce_by_column <- function(df) {

R/runBibfixApp.R

@@ -0,0 +1,24 @@
+#' Run Shiny App
+#'
+#' This function launches a Shiny application from the specified directory in an R package.
+#' 
+#' @param app_name bibfix
+#' @return Launches the Shiny application.
+#' @export
+runBibfixApp <- function(app_name="bibfix") {
+  # Ensure the Shiny package is installed
+  if (!requireNamespace("shiny", quietly = TRUE)) {
+    stop("The 'shiny' package is required but not installed.")
+  }
+  
+  # Define the app directory
+  app_dir <- here::here("inst/shiny-examples/bibfix")
+  
+  # Check if the app directory exists
+  if (app_dir == "" || !dir.exists(app_dir)) {
+    stop("App directory not found. Ensure the app is located in inst/shiny/", app_name)
+  }
+  
+  # Launch the app
+  shiny::runApp(app_dir, display.mode = "normal")
+}