Merge pull request #233 from ESHackathon/dev

Merge 1.1.0 updates and fixes

Author: TNRiley

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$

.github/workflows/document-and-deploy.yml

@@ -53,7 +53,10 @@ jobs:
           R -e "
             remotes::install_github('ESHackathon/CiteSource', force = TRUE);
             rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}}); 
-            rsconnect::deployApp(appName = 'CiteSource_latest', appDir = './inst/shiny-app/CiteSource', forceUpdate = TRUE)"   
+            rsconnect::deployApp(
+              appName = 'CiteSource_latest',
+              appDir = './inst/shiny-app/CiteSource',
+              forceUpdate = TRUE)"   
 
       - name: Deploy stable version from main
         if: github.ref == 'refs/heads/main'
@@ -63,7 +66,10 @@ jobs:
           R -e "
             remotes::install_github('ESHackathon/CiteSource', force = TRUE);
             rsconnect::setAccountInfo(name=${{secrets.SHINY_LUKAS_ACCOUNT}}, token=${{secrets.SHINY_LUKAS_TOKEN}}, secret=${{secrets.SHINY_LUKAS_SECRET}}); 
-            rsconnect::deployApp(appName = 'CiteSource', appDir = './inst/shiny-app/CiteSource', forceUpdate = TRUE)"   
+            rsconnect::deployApp(
+              appName = 'CiteSource',
+              appDir = './inst/shiny-app/CiteSource',
+              forceUpdate = TRUE)"   
 
       - name: Create pkgdown
         env:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CiteSource
 Title: Analyze the Utility of Information Sources and Retrieval Methodologies for Evidence Synthesis
-Version: 0.0.1
+Version: 0.1.1
 Date: 2023-06-22
 Authors@R: c(
     person("Trevor", "Riley", , "trevor.riley@noaa.gov", role = c("aut", "cre"),

NEWS.md

@@ -8,3 +8,10 @@
 
 - Integrated new dedup function into R shiny app
 
+# CiteSource 0.1.1
+
+- Added new functions which allow creation of tables and plots based on deduplicated (reimported) data. 
+
+- Updated shiny functionality, look and feel, and documentation
+
+- Added new vignettes 

R/dedup.R

@@ -95,8 +95,9 @@ dedup_citations_add_manual <- function(unique_citations, additional_pairs) {
   unique_citations$source = unique_citations$cite_source
   unique_citations$label = unique_citations$cite_label
 
-  dedup_results <- ASySD::dedup_citations_add_manual(unique_citations, additional_pairs = additional_pairs
-                                                     )
+  dedup_results <- ASySD::dedup_citations_add_manual(unique_citations, 
+                                                     additional_pairs = additional_pairs, 
+                                                     extra_merge_fields = "cite_string")
 
   dedup_results$cite_source <- dedup_results$source
   dedup_results$cite_label <- dedup_results$label

R/export.R

@@ -96,7 +96,8 @@ export_ris <- function(citations, filename = "citations.ris", source_field = "DB
       string_field, "cite_string", TRUE,
       label_field, "cite_label", TRUE,
       "C1", "duplicate_id", TRUE,
-      "C2", "record_ids", TRUE
+      "C2", "record_ids", TRUE,
+      "TY", "type", TRUE
     ),
     synthesisr_code_lookup %>% dplyr::filter(.data$ris_synthesisr)
   ) %>% dplyr::distinct(.data$code, .keep_all = TRUE) # Remove fields from synthesisr specification used for CiteSource metadata

R/new_count_and_table.R

@@ -315,15 +315,19 @@ calculate_phase_records <- function(unique_citations, n_unique, db_colname) {
   total_distinct_records <- dplyr::n_distinct(unique_citations$duplicate_id)
 
   # Split the cite_label column and count any occurrence of "screened" and "final"
+  # Updated for edge cases where a citation is duplicated within the screened set
   total_screened <- unique_citations %>%
     tidyr::separate_rows(cite_label, sep = ",\\s*") %>%
     dplyr::filter(cite_label == "screened") %>%
-    nrow()
+    # Count the number of distinct duplicate_ids that remain
+    dplyr::n_distinct(duplicate_id)
 
+  # Updated for edge cases where a citation is duplicated within the screened set (should never happen)
   total_final <- unique_citations %>%
     tidyr::separate_rows(cite_label, sep = ",\\s*") %>%
     dplyr::filter(cite_label == "final") %>%
-    nrow()
+    # Count the number of distinct duplicate_ids that remain
+    dplyr::n_distinct(duplicate_id)
 
   # Step 2: Proceed with the regular calculation for distinct records by source
   distinct_count <- unique_citations %>%

R/plots.R

@@ -260,7 +260,7 @@ cite_source <- cite_label <- type <- NULL
 #'
 plot_contributions <- function(data, facets = cite_source, bars = cite_label, color = type, 
                                center = FALSE, bar_order = "keep", facet_order = "keep", 
-                               color_order = "keep", totals_in_legend = TRUE) {
+                               color_order = "keep", totals_in_legend = FALSE) {
 
   bars <- rlang::enquo(bars)
   color <- rlang::enquo(color)

R/tables.R

@@ -25,32 +25,32 @@
 record_level_table <- function(citations, include = "sources", include_empty = TRUE, return = c("tibble", "DT"), indicator_presence = NULL, indicator_absence = NULL) {
 
   if (!is.data.frame(citations) || nrow(citations) == 0) stop("Citations must be a tibble and cannot have 0 entries")
-
+  
   if (is.null(indicator_absence)) {
     indicator_absence <- switch(return[1],
-      tibble = FALSE,
-      DT = "&#x2717;"
+                                tibble = FALSE,
+                                DT = "&#x2717;"
     )
   }
   if (is.null(indicator_presence)) {
     indicator_presence <- switch(return[1],
-      tibble = TRUE,
-      DT = "&#10004;"
+                                 tibble = TRUE,
+                                 DT = "&#10004;"
     )
   }
 
   sources <- compare_sources(citations, comp_type = include)
-
+  
   if (nrow(sources) == 0) {
     warning("Citations provided contain no information on ", include, ". NA will be displayed, but check whether you intended to do a different comparison")
-  sources <- tibble::tibble(duplicate_id = citations$duplicate_id)
-   sources[[paste0(stringr::str_sub(include, 1, -2), "__NA")]] <- TRUE
+    sources <- tibble::tibble(duplicate_id = citations$duplicate_id)
+    sources[[paste0(stringr::str_sub(include, 1, -2), "__NA")]] <- TRUE
   }
 
   if (!include_empty == TRUE) {
     citations <- citations %>% dplyr::filter(.data$duplicate_id %in% sources$duplicate_id)
   }
-
+  
   if (! "url" %in% colnames(citations)) {
     citations$url <- NA_character_
   }
@@ -65,17 +65,17 @@ record_level_table <- function(citations, include = "sources", include_empty = T
     dplyr::arrange(stringr::str_extract(.data$author, "^.*?,"), .data$citation) %>%
     dplyr::select("duplicate_id", "citation", "reference", "html_reference") %>%
     dplyr::left_join(sources, by = "duplicate_id")
-
+  
   indicator_presence <- as.character(indicator_presence)
   indicator_absence <- as.character(indicator_absence)
-
+  
   to_display <- citations %>%
     dplyr::select(-(1:4)) %>%
     dplyr::mutate(dplyr::across(dplyr::everything(), ~ ifelse(.x, indicator_presence, indicator_absence))) %>%
     dplyr::rename_with(~ paste0(.x, " ")) # Add space to keep column names unique
-
+  
   citations <- dplyr::bind_cols(citations, to_display)
-
+  
   if (return[1] == "DT") {
     if (!rlang::is_installed("DT")) {
       warning('DT can only be returned when the DT package is installed. Please run install.packages("DT")')
@@ -88,7 +88,7 @@ record_level_table <- function(citations, include = "sources", include_empty = T
           stringr::str_remove(glue::glue("^{type}__"))
         list(type = type %>% stringr::str_to_title(), values = values)
       }) %>% purrr::transpose()
-
+      
       sketch <- htmltools::tags$table(
         class = "display",
         htmltools::tags$thead(
@@ -105,24 +105,30 @@ record_level_table <- function(citations, include = "sources", include_empty = T
           htmltools::tags$td(colspan = 4 + length(unlist(headings$values)), htmltools::HTML("Click on the &oplus; to view the full reference"))
         )
       )
-
+      
       citations %>%
         dplyr::select(-"duplicate_id", -"reference") %>%
         cbind(" " = "&oplus;", .) %>%
         DT::datatable(
           escape = FALSE,
           extensions = "Buttons",
           options = list(
+            pageLength = 10,
+            lengthMenu = list(c(10, 25, 50, 100, -1), c('10', '25', '50', '100', 'All')),
             columnDefs = list(
               list(visible = FALSE, targets = c(0, 3:(3 + ncol(to_display)))),
               list(orderable = FALSE, className = "details-control", targets = 1)
             ),
-            dom = "Bfrtip",
+            dom = "lBfrtip",
             buttons =
               list("print", list(
                 extend = "csv", filename = "CiteSource_record_summary",
                 text = "Download csv",
-                exportOptions = list(columns = c(0, 2:(3 + ncol(to_display))))
+                exportOptions = list(
+                  columns = c(0, 2:(3 + ncol(to_display))),
+                  modifier = list(page = "all")
+                )
+                
               ))
           ), container = sketch,
           callback = DT::JS("
@@ -585,8 +591,8 @@ generate_apa_reference <- function(authors, year, title, source, volume, issue,
       dplyr::rowwise() %>%
       dplyr::mutate(
         reference = glue::glue("
-                              {glue::glue_collapse(initialed_names, ', ', last = ' & ')} ({year}). {nNA(title, '.')} {nNA(source, pre = '<i>', '</i>')}{nNA(volume, pre = '<i>, ', '</i>')}{nNA(issue, pre = '(', ')')}. {nNA(link, pre = '<a href = \"', '\">')}{nNA(link, '</a>')}
-                                                     ")
+                               {glue::glue_collapse(initialed_names, ', ', last = ' & ')} ({year}). {nNA(title, '.')} {nNA(source, pre = '<i>', '</i>')}{nNA(volume, pre = '<i>, ', '</i>')}{nNA(issue, pre = '(', ')')}. {nNA(link, pre = '<a href=\"', '\" target=\"_blank\" rel=\"noopener noreferrer\">')}{nNA(link, '</a>')}
+                                     ")
       ) %>%
       dplyr::pull(.data$reference)
   } else {

README.md

@@ -22,7 +22,7 @@ CiteSource was created under [the General Public License (>=v3)](https://www.gnu
 
 **Shiny Web Application**
 
-Whether you know R or not, we want you to be able to use CiteSource! Check out our [CiteSource Shiny App!](https://litrev.shinyapps.io/CiteSource_latest/) 
+Whether you know R or not, we want you to be able to use CiteSource! Check out our [CiteSource Shiny App!](https://litrev.shinyapps.io/CiteSource/) 
 
 ## Features
 **Customizable Metadata Tags**