Merge pull request #40 from nealhaddaway/Make_a_package

Make a package

.Rproj.user/shared/notebooks/paths

@@ -1,16 +1,17 @@
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/R/decode_dois.R="F95AE8CF"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/app.R="16CC443D"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/build_ris.R="6F85CBC8"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/decode_dois.R="94F305F8"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/functions.R="0E38325C"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/google-analytics.html="FF9CB785"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/plot_health.R="B7F16593"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/repair_refs.R="3FACFBA9"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/scan_file.R="13B1F476"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/bibfix/inst/shiny-examples/bibfix/search_openAlex.R="EF8B2266"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/citationchaser private/citationchaser/inst/shiny-examples/citationchaser/app.R="03706E48"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/citationchaser private/citationchaser/inst/shiny-examples/citationchaser/functions.R="032381A8"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/citationchaser private/citationchaser/inst/shiny-examples/citationchaser/mixed_id_wrapper.R="8380540F"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/citationchasertest/inst/shiny-examples/citationchasertest/app.R="A216DC70"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/citationchasertest/inst/shiny-examples/citationchasertest/functions.R="D49257AD"
-/Users/nealhaddaway/OneDrive - SEI/ESHackathon/4.Remote 2020/citationchasertest/inst/shiny-examples/citationchasertest/mixed_id_wrapper.R="F1817740"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/DESCRIPTION="6FA2B510"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/build_ris.R="EC8188C9"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/decode_dois.R="136028EC"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/dev/fill_blanks.R="0C299367"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/fill_blanks.R="1AA9D749"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/functions.R="D6783113"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/plot_health.R="24D8B67D"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/repair_refs.R="81AE1A63"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/runBibfixApp.R="D70915BB"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/scan_file.R="5A66CA1E"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/search_openAlex.R="0AA59F97"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/R/update_retractionwatch_data.R="1A74B192"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/inst/extdata/data.csv="708A568C"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/inst/shiny-examples/bibfix/app.R="CF9E49B4"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/inst/shiny-examples/bibfix/www/Factory_Scholar.ris="25D08583"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/inst/shiny-examples/bibfix/www/Forest_scholar.ris="FA10FDC7"
+C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/inst/shiny-examples/bibfix/www/lookup_table.txt="6CF87D1B"

DESCRIPTION

@@ -31,10 +31,19 @@ Description: bibfix is an R package (with future plans for a Shiny app) that
 Imports:
     magrittr,
     utils,
-    tools
+    tools,
+    MESS, 
+    data.table, 
+    dplyr,
+    httr,
+    jsonlite,
+    maditr,
+    stringi,
+    tibble
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 2.10)
+LazyData: true

NAMESPACE

@@ -1,25 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
 export(build_ris)
-export(getLENSData)
-export(get_abstract)
-export(get_doi)
-export(get_urls)
-export(journal_abbreviation)
-export(remove_abstracts)
-importFrom(dplyr,coalesce)
+export(crawl_url)
+export(crawl_urls)
+export(decode_dois)
+export(get_citation)
+export(get_refs)
+export(reconstruct_abstract)
+export(repair_refs)
+export(runBibfixApp)
+export(scan_file)
+export(search_openAlex)
+importFrom(MESS,cumsumbinning)
+importFrom(data.table,data.table)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,group_split)
 importFrom(dplyr,mutate)
-importFrom(dplyr,rename)
-importFrom(dplyr,select)
-importFrom(expss,vlookup)
 importFrom(httr,POST)
 importFrom(httr,add_headers)
 importFrom(httr,content)
 importFrom(jsonlite,fromJSON)
-importFrom(magrittr,"%>%")
-importFrom(rcrossref,cr_abstract)
-importFrom(rcrossref,cr_works)
-importFrom(roadoi,oadoi_fetch)
-importFrom(stringdist,stringdist)
-importFrom(synthesisr,read_refs)
-importFrom(tidyr,unite)
+importFrom(maditr,vlookup)
+importFrom(stringi,stri_replace_all_fixed)
+importFrom(tibble,tibble)
+importFrom(utils,write.table)

R/decode_dois.R

@@ -36,11 +36,9 @@ decode_dois <- function(dois,
   dois <- data.frame(dois)
 
   #load lookup_table
-  lookup_table <- read.delim('www/lookuptable.txt',
-                             sep = '\t', 
-                             header =  TRUE, 
-                             quote = '')
-
+  # need to replace this with call from bibfix
+  load("C:/Users/matthew.grainger/Documents/Projects_in_development/bibfix/data/lookup_table.rda")
+
   #replace characters using lookup table
   dois <- dois %>% 
     dplyr::mutate(across(c(dois), ~ stringi::stri_replace_all_fixed(

inst/shiny-examples/bibfix/functions.R → R/functions.R

@@ -566,7 +566,7 @@ getLENSData <- function(token, query){
 
 #' Find citation based on identifier
 #' 
-#' @description 
+#' @description Finds a citation based on e.g. DOI
 #' @param article_list List of article identifiers for which the reference 
 #'   lists will be returned. Must be a list/vector of identifiers, e.g. 
 #'   '"10.1186/s13750-018-0126-2" "10.1002/jrsm.1378"'.
@@ -579,7 +579,7 @@ getLENSData <- function(token, query){
 #'   applying for scholarly API access and creating a token once approved. See 
 #'   'https://www.lens.org/lens/user/subscriptions#scholar' for further details.
 #' @return A dataframe containing the matching citation from Lens.org.
-#' @importFrom expss vlookup
+#' @importFrom maditr vlookup
 #' @importFrom httr content
 #' @importFrom jsonlite fromJSON
 #' @importFrom data.table data.table

R/plot_health.R

@@ -1,41 +1,65 @@
 #' Plot RIS file health
 #' remotes::install_git("https://git.rud.is/hrbrmstr/ggchicklet.git")
-#' health_check <- scan_file(refs)
-plot_health <- function(health_check){
+#' report <- scan_file(refs)
+#' health_plot <- plot_health(report)
+#' health_plot
+plot_health <- function(health_check, session=NULL){
 
+
+  health_check<-health_check[-1]
   reportdf <- as.data.frame(health_check)
+
+  # Select relevant fields including n_retracted
   reportdf <- select(reportdf, -c('n_complete', 'n_findable_titles', 'n_total'))
   names(reportdf) <- str_to_sentence(gsub('_', ' ', gsub('n_', '', names(reportdf))))
   names(reportdf) <- gsub('Doi', 'DOI', names(reportdf))
+
+  # Add n_retracted to the report
   reportdf <- data.frame(field = names(reportdf), 
                          value = t(reportdf),
                          row.names = NULL)
+
+  # Include retracted in field levels
+  reportdf$field <- factor(reportdf$field, 
+                           levels = c('DOI', 'End page', 'Start page', 
+                                      'Issue', 'Volume', 'Journal', 
+                                      'Abstract', 'Title', 'Year', 
+                                      'Author', 'Retracted'))
+
+  # Create missing data summary
   reportdf$health <- 'healthy'
-  reportdf$field <- factor(reportdf$field, levels = c('DOI', 'End page', 'Start page', 'Issue', 'Volume', 'Journal', 'Abstract', 'Title', 'Year', 'Author'))
   new <- reportdf
   new$value <- health_check$n_total - reportdf$value
   new$health <- 'missing'
   reportdf <- rbind(reportdf, new)
   reportdf$health <- factor(reportdf$health, levels = c('missing', 'healthy'))
 
-  #correct text size in ratio 14/5: https://stackoverflow.com/questions/25061822/ggplot-geom-text-font-size-control
-  geom.text.size <- 5
-  theme.size <- 20
-
-  plot <- ggplot(data=reportdf, aes(x=value, y=field, fill=health)) +
-    geom_bar(stat="identity", position = 'stack') +
-    #geom_text(aes(label=value), position = position_dodge(width=0.9), hjust=-0.5, size=geom.text.size, color='grey50') + 
-    theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
-          panel.background = element_blank(),
-          axis.title.y=element_blank(),
-          axis.ticks.y = element_blank(),
-          text = element_text(size = theme.size, color="grey50"),
-          axis.text = element_text(color="grey50")) +
-    xlim(0, 1.1*max(reportdf$value)) +
-    labs(x = "Health level of field") +
-    scale_fill_manual(values=c('grey90', '#e43235')) + 
-    theme(legend.position = "none")
+  # Plot setup
+  geom.text.size <- 4
+  theme.size <- 16
 
-  return(plot)
+  plot <- ggplot2::ggplot(data = reportdf, 
+                          ggplot2::aes(x = value, y = field, fill = health)) +
+    ggplot2::geom_bar(stat = "identity", position = 'stack') +
+    ggplot2::theme_minimal(base_size = theme.size) +
+    ggplot2::theme(
+      axis.title.y = ggplot2::element_blank(),
+      axis.ticks.y = ggplot2::element_blank(),
+      text = ggplot2::element_text(size = theme.size, color = "grey50"),
+      axis.text = ggplot2::element_text(color = "grey50"),
+      legend.position = "none"
+    ) +
+    ggplot2::xlim(0, 1.1 * max(reportdf$value)) +
+    ggplot2::labs(x = "Health level of field") +
+    ggplot2::scale_fill_manual(values = c('grey90', '#e43235'))
+  if (shiny::isTruthy(session)) {
+  # Convert to interactive plot
+  plot <- plotly::ggplotly(plot, tooltip = "x")
+  config(plot, displayModeBar = FALSE)
 
+  }else{
+    plot
+   }
+
+  return(plot)
 }