code style: add space after comma

stewid · Nov 2, 2019 · 0a2d416 · 0a2d416 · lintr-bot · Nov 2, 2019
1 parent 6c69922
commit 0a2d416
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Showing 8 changed files with 39 additions and 44 deletions.
diff --git a/R/ingoing-contact-chain.R b/R/ingoing-contact-chain.R
@@ -186,7 +186,7 @@ setMethod("IngoingContactChain",
                        "for outgoing contacts")
               }
 
-              return(length(setdiff(x@source,x@root)))
+              return(length(setdiff(x@source, x@root)))
           }
 )
 

diff --git a/R/network-summary.R b/R/network-summary.R
@@ -194,7 +194,7 @@
 ##'
 ##' ## When calculating the network summary for a data.frame of movements
 ##' ## a data.frame for each combination of root, tEnd and days are returned.
-##' root <- c(1,2,3)
+##' root <- c(1, 2, 3)
 ##' tEnd <- c("2005-09-01", "2005-10-01")
 ##' days <- c(30, 45)
 ##'

diff --git a/R/outgoing-contact-chain.R b/R/outgoing-contact-chain.R
@@ -137,7 +137,7 @@ setMethod("OutgoingContactChain",
                   stop("Unable to determine OutgoingContactChain for ingoing contacts")
               }
 
-              return(length(setdiff(x@destination,x@root)))
+              return(length(setdiff(x@destination, x@root)))
           }
 )
 

diff --git a/R/plot.R b/R/plot.R
@@ -104,7 +104,7 @@ setMethod("plot",
               if (is.null(vertices)) {
                   vertices <- tree$outgoing
               } else {
-                  vertices <- rbind(vertices, tree$outgoing[-1,])
+                  vertices <- rbind(vertices, tree$outgoing[-1, ])
               }
           }
 

diff --git a/R/report.R b/R/report.R
@@ -59,7 +59,7 @@ html_detailed_table <- function(contacts, direction) {
         arrow <- "&rarr;"
     }
 
-    contacts <- contacts[order(contacts$t, contacts$id, decreasing = FALSE),]
+    contacts <- contacts[order(contacts$t, contacts$id, decreasing = FALSE), ]
 
     contacts$id <- as.character(contacts$id)
     contacts$id[is.na(contacts$id)] <- "&nbsp;"
@@ -100,8 +100,7 @@ html_detailed_table <- function(contacts, direction) {
     })))
 }
 
-html_report <- function(x)
-{
+html_report <- function(x) {
     lines <- c("<html>",
                "<head>",
                sprintf("<title>%s</title>", x@root),
@@ -174,9 +173,9 @@ html_report <- function(x)
         df$rhs <- df$source
 
         lines <- c(lines,
-                   html_detailed_table(df[df$destination == df$root,], "in"))
+                   html_detailed_table(df[df$destination == df$root, ], "in"))
 
-        df <- df[df$destination != df$root,]
+        df <- df[df$destination != df$root, ]
         if (nrow(df) > 0) {
             lines <- c(lines,
                        "<hr/>",
@@ -196,9 +195,9 @@ html_report <- function(x)
         df$lhs <- df$source
         df$rhs <- df$destination
 
-        html_detailed_table(df[df$source == df$root,], "out")
+        html_detailed_table(df[df$source == df$root, ], "out")
 
-        df <- df[df$source != df$root,]
+        df <- df[df$source != df$root, ]
         if (nrow(df) > 0) {
             lines <- c(lines,
                        "<hr/>",

diff --git a/R/shortest-paths.R b/R/shortest-paths.R
@@ -133,23 +133,22 @@ setGeneric("ShortestPaths",
 ##' @export
 setMethod("ShortestPaths",
           signature(x = "ContactTrace"),
-          function(x)
-      {
+          function(x) {
           ns <- NetworkStructure(x)
-          ns.in <- ns[ns$direction == "in",]
-          ns.out <- ns[ns$direction == "out",]
+          ns.in <- ns[ns$direction == "in", ]
+          ns.out <- ns[ns$direction == "out", ]
 
           result <- NULL
           if (nrow(ns.in)) {
-              ns.in <- ns.in[order(ns.in$distance, ns.in$source),]
-              ns.in <- ns.in[!duplicated(ns.in$source),]
+              ns.in <- ns.in[order(ns.in$distance, ns.in$source), ]
+              ns.in <- ns.in[!duplicated(ns.in$source), ]
               ns.in$destination <- NA_character_
               result <- ns.in
           }
 
           if (nrow(ns.out)) {
-              ns.out <- ns.out[order(ns.out$distance, ns.out$destination),]
-              ns.out <- ns.out[!duplicated(ns.out$destination),]
+              ns.out <- ns.out[order(ns.out$distance, ns.out$destination), ]
+              ns.out <- ns.out[!duplicated(ns.out$destination), ]
               ns.out$source <- NA_character_
               result <- rbind(result, ns.out)
           }
@@ -175,8 +174,7 @@ setMethod("ShortestPaths",
                    inBegin = NULL,
                    inEnd = NULL,
                    outBegin = NULL,
-                   outEnd = NULL)
-      {
+                   outEnd = NULL) {
           ## Check that arguments are ok from various perspectives...
 
           ## Check the data.frame x with movements

diff --git a/R/trace.R b/R/trace.R
@@ -455,10 +455,10 @@ Trace <- function(movements,
 
 
     trace_contacts <- .Call("traceContacts",
-                            as.integer(factor(movements$source, levels=levels(nodes))),
-                            as.integer(factor(movements$destination, levels=levels(nodes))),
+                            as.integer(factor(movements$source, levels = levels(nodes))),
+                            as.integer(factor(movements$destination, levels = levels(nodes))),
                             as.integer(julian(movements$t)),
-                            as.integer(factor(root, levels=levels(nodes))),
+                            as.integer(factor(root, levels = levels(nodes))),
                             as.integer(julian(inBegin)),
                             as.integer(julian(inEnd)),
                             as.integer(julian(outBegin)),
@@ -488,12 +488,12 @@ Trace <- function(movements,
                                root = root[i],
                                tBegin = inBegin[i],
                                tEnd = inEnd[i],
-                               source = contacts[,1],
-                               destination = contacts[,2],
-                               t = contacts[,3],
-                               id = contacts[,4],
-                               n = contacts[,5],
-                               category = contacts[,6],
+                               source = contacts[, 1],
+                               destination = contacts[, 2],
+                               t = contacts[, 3],
+                               id = contacts[, 4],
+                               n = contacts[, 5],
+                               category = contacts[, 6],
                                index = index,
                                distance = distance,
                                direction = "in")
@@ -516,12 +516,12 @@ Trace <- function(movements,
                                 root = root[i],
                                 tBegin = outBegin[i],
                                 tEnd = outEnd[i],
-                                source = contacts[,1],
-                                destination = contacts[,2],
-                                t = contacts[,3],
-                                id = contacts[,4],
-                                n = contacts[,5],
-                                category = contacts[,6],
+                                source = contacts[, 1],
+                                destination = contacts[, 2],
+                                t = contacts[, 3],
+                                id = contacts[, 4],
+                                n = contacts[, 5],
+                                category = contacts[, 6],
                                 index = index,
                                 distance = distance,
                                 direction = "out")

diff --git a/R/tree.R b/R/tree.R
@@ -27,14 +27,13 @@
 ##' \code{data.frame} with the tree. The fields are \code{NULL} if
 ##' there are no in- or outgoing contacts.
 ##' @keywords internal
-build_tree <- function(network_structure)
-{
+build_tree <- function(network_structure) {
     stopifnot(is.data.frame(network_structure))
     root <- unique(network_structure$root)
     stopifnot(identical(length(root), 1L))
 
-    tree.in <- network_structure[network_structure$direction == "in",]
-    tree.out <- network_structure[network_structure$direction == "out",]
+    tree.in <- network_structure[network_structure$direction == "in", ]
+    tree.out <- network_structure[network_structure$direction == "out", ]
 
     result <- list(ingoing=NULL, outgoing=NULL)
 
@@ -46,7 +45,7 @@ build_tree <- function(network_structure)
     if (nrow(tree.in)) {
         i <- order(tree.in$distance, tree.in$source)
         tree.in <- tree.in[i, c("source", "distance")]
-        tree.in <- tree.in[!duplicated(tree.in$source),]
+        tree.in <- tree.in[!duplicated(tree.in$source), ]
         tree.in$parent <- NA_character_
         colnames(tree.in)[1:2] <- c("node", "level")
         tree.in <- tree.in[, colnames(root_node)]
@@ -76,7 +75,7 @@ build_tree <- function(network_structure)
     if (nrow(tree.out)) {
         i <- order(tree.out$distance, tree.out$destination)
         tree.out <- tree.out[i, c("destination", "distance")]
-        tree.out <- tree.out[!duplicated(tree.out$destination),]
+        tree.out <- tree.out[!duplicated(tree.out$destination), ]
         tree.out$parent <- NA_character_
         colnames(tree.out)[1:2] <- c("node", "level")
         tree.out <- tree.out[, colnames(root_node)]
@@ -142,8 +141,7 @@ position_tree <- function(tree,
                           left_size = 1,
                           right_size = 1,
                           top_size = 1,
-                          bottom_size = 1)
-{
+                          bottom_size = 1) {
     ## Clean up the positioning of small sibling subtrees
     apportion <- function(node) {
         left_most <- first_child(node)