implement recs from package 'goodpractice'

specifically move from c(1:x) to seq_len(x), and add BugReports to DESCRIPTION
mjwestgate · Nov 29, 2018 · 523a286 · 523a286
1 parent 7ec6b6c
commit 523a286
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Showing 5 changed files with 13 additions and 12 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -8,4 +8,5 @@ Depends: R (>= 3.5.0)
 Imports: ade4, plotly, shiny, shinydashboard, SnowballC, stringdist, tm, topicmodels, viridisLite, modeltools
 License: GPL-3
 URL: https://revtools.net
-LazyData: true
+BugReports: https://github.com/mjwestgate/revtools/issues
+LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
@@ -39,7 +39,7 @@ renderPrint, renderPlot, renderUI, splitLayout,
 validate, need,
 showModal, modalDialog, removeModal, modalButton,
 insertUI, removeUI,
-shinyApp)
+shinyApp, stopApp)
 importFrom(shinydashboard,
 sidebarMenu, menuItem, sidebarMenuOutput, renderMenu)
 importFrom(stats, xtabs)

diff --git a/R/bibliography-methods.R b/R/bibliography-methods.R
@@ -18,7 +18,7 @@ summary.bibliography <- function(object, ...){
 		source_freq <- sort(
       xtabs(~ sources),
       decreasing = TRUE
-    )[c(1:min(5, n_sources))]
+    )[seq_len(min(c(5, n_sources)))]
 		# put text together
 		result <- paste(
 			paste0(
@@ -75,14 +75,14 @@ print.bibliography <- function(x, n, ...){
       n <- length_tr
     }
 	}
-	text_tr <- format_citation(x[c(1:n)])
+	text_tr <- format_citation(x[seq_len(n)])
 	cat(paste(unlist(text_tr), collapse = "\n\n"))
 }
 
 
 '[.bibliography' <- function(x, n){
   class(x) <- "list"
-  if(all(n %in% c(1:length(x))) == FALSE){
+  if(all(n %in% seq_len(length(x))) == FALSE){
     stop("subset out of bounds")
   }
   z <- x[n]

diff --git a/R/format_citation.R b/R/format_citation.R
@@ -28,7 +28,7 @@ format_citation.list <- function(
           function(a){
     				dot.lookup <- a %in% "."
     				if(any(dot.lookup)){
-              a <- a[1:max(which(dot.lookup))]
+              a <- a[seq_len(max(which(dot.lookup)))]
             }
     				return(paste(a, collapse = ""))
     			}
@@ -118,7 +118,7 @@ format_citation.data.frame <- function(
     all(c("author", "year", source, "title") %in% names(data)) &
     (details == TRUE)
   ){
-	data_list <- split(data, c(1:nrow(data)))
+	data_list <- split(data, seq_len(nrow(data)))
   data_out <- unlist(lapply(data_list, function(a){
 		author_vector <- strsplit(a[['author']], " and ")[[1]]
 		if(length(author_vector) == 1){

diff --git a/R/read_bibliography.R b/R/read_bibliography.R
@@ -152,7 +152,7 @@ prep_ris <- function(
 	if(delimiter == "endrow"){
     # work out what most common starting tag is
     z_dframe$ref <- c(0, cumsum(z_dframe$ris == "ER")[
-      c(1:(nrow(z_dframe)-1))]
+      seq_len(nrow(z_dframe)-1)]
     ) # split by reference
 
     start_tags <- unlist(lapply(
@@ -183,7 +183,7 @@ prep_ris <- function(
 
 	# cleaning
 	z_dframe$ref <- c(0, cumsum(z_dframe$ris == "ER")[
-    c(1:(nrow(z_dframe)-1))]
+    seq_len(nrow(z_dframe)-1)]
   ) # split by reference
 	z_dframe <- z_dframe[which(z_dframe$text != ""), ] # remove empty rows
 	z_dframe <- z_dframe[which(z_dframe$ris != "ER"), ] # remove end rows
@@ -294,7 +294,7 @@ generate_bibliographic_names <- function(x){
 			rows <- which(nonunique_names == duplicated_names[i])
 			new_names <- paste(
         nonunique_names[rows],
-        letters[1:length(rows)],
+        letters[seq_len(length(rows))],
         sep = "_")
 			nonunique_names[rows] <- new_names
     }
@@ -547,7 +547,7 @@ read_bib <- function(x){
     entry_dframe <- entry_dframe[order(entry_dframe$row), c("tag", "value")]
 
   	if(any(entry_dframe$value == "}")){
-  		entry_dframe <- entry_dframe[c(1:which(entry_dframe$value == "}")[1]-1), ]
+  		entry_dframe <- entry_dframe[seq_len(which(entry_dframe$value == "}")[1]-1), ]
   	}
     if(any(entry_dframe$value == "")){
   		entry_dframe <- entry_dframe[-which(entry_dframe$value == ""), ]
@@ -588,7 +588,7 @@ read_bib <- function(x){
 
   # add type
   x_final <- lapply(
-    c(1:length(x_final)),
+    seq_len(length(x_final)),
     function(a, type, data){
       c(type = type[a], data[[a]])
     },