Change NEWS.md and simple style fixes

Signed-off by: Leo Sendelbach <s8lesend@stud.uni-saarland.de>

NEWS.md

@@ -8,27 +8,28 @@
 
 - Add issue-based artifact-networks (PR #244, 98a93ee721a293410623aafe46890cfba9d81e72, 771bcc8d961d419b53a1e891e9dc536371f1143b)
 - Add a new `split.data.by.bins` function (not to be confused with a previously existing function that had the same name and was renamed in this context), which splits data based on given activity-based bins (PR #244, ece569ceaf557bb38cd0cfad437b69b30fe8a698, ed5feb214a123b605c9513262f187cfd72b9e1f4)
-- Add new `compare.sparse.matrices` function to compare two sparse matrices for equality for testing purposes (PR #248, 9784cdf12d1497ee122e2ae73b768b8c334210d4)
-- Add tests for file `util-networks.misc.R` (PR #248, f3202a6f96723d11c170346556d036cf087521c8, 030574b9d0f3435db4032d0e195a3d407fb7244b, 380b02234275127297fcd508772c69db21c216de, 8b803c50d60fc593e4e527a08fd4c2068d801a48, 7335c3dd4d0302b024a66d18701d9800ed3fe806, 6b600df04bec1fe70c272604f274ec5309840e65)
+- Add new `assert.sparse.matrices.equal` function to compare two sparse matrices for equality for testing purposes (PR #248, 9784cdf12d1497ee122e2ae73b768b8c334210d4, d9f1a8d90e00a634d7caeb5e7f8f262776496838)
+- Add tests for file `util-networks.misc.R` for issue #242 (PR #248, f3202a6f96723d11c170346556d036cf087521c8, 030574b9d0f3435db4032d0e195a3d407fb7244b, 380b02234275127297fcd508772c69db21c216de, 8b803c50d60fc593e4e527a08fd4c2068d801a48, 7335c3dd4d0302b024a66d18701d9800ed3fe806, 6b600df04bec1fe70c272604f274ec5309840e65)
 
 ### Changed/Improved
 
 - Enhance testing data by adding `add_link` and `referenced_by` issue events which connect issues to form edges in issue-based artifact-networks (PR #244, 9f840c040d552e8639aa82c3dd537c189679b348, ea4fe8d3c84f948af6147cf0137e80181ebb7a1e)
 - Add input validation for the `bins` parameter in `split.data.time.based` and `split.data.by.bins` (PR #244, ed0a5302ea8c8934d7200b95be7ac1446305af07, 5e5ecbac44d07927b953ae9d4330a616f8224ba7)
 - Rename `split.data.by.bins` into `split.dataframe.by.bins` as this it what it does (PR #244, ed5feb214a123b605c9513262f187cfd72b9e1f4)
-- Enhance `get.author.names.from.network` and `get.author.names.from.data` to always have the same output format, not depending on the `global` flag (PR #248, d87d32564156f13c83ebe3361c2b68e5d0ac16ac, ddbfe68d3e628e82f34e09b36fffe886646986c5)
-- Changed `util-tensor.R` to correctly use `get.author.names.from.network` function
+- Enhance `get.author.names.from.network` and `get.author.names.from.data` to always have the same output format. Now it doesn't depend on the `global` flag anymore (PR #248, d87d32564156f13c83ebe3361c2b68e5d0ac16ac, ddbfe68d3e628e82f34e09b36fffe886646986c5)
+- Change `util-tensor.R` to correctly use the new output format of `get.author.names.from.network` (PR #248, 72b663ebf7169c0da5c687fe215529f3be0c08c5)
+- Fix `convert.adjacency.matrix.list.to.array` to throw an error if the function is called with wrong parameters (PR #248, ece2d38b4972745af3a83e06f32317a06465a345, 1a3e510df15f5fa4e920e9fce3e0e162c27cd6d1)
+- Rename `compare.networks` to `assert.networks.equal` to better match the purpose of the function (PR #248, d9f1a8d90e00a634d7caeb5e7f8f262776496838)
 
 ### Fixed
 
 - Reformat `event.info.1` column of issue data according to the <issue-%source-%id> format, if the content of the `event.info.1` field references another issue (PR #244, 62ff9d0f31adbefb3381936237dc4ab984e33acb)
 - Fix an issue in activity-based splitting where elements close to the border of bins might be assigned to the wrong bin. The issue was caused by the usage of `split.data.time.based` inside `split.data.activity.based` to split data into the previously derived bins, when elements close to bin borders share the same timestamps. It is fixed by replacing `split.data.time.based` by `split.data.by.bins` (PR #244, ece569ceaf557bb38cd0cfad437b69b30fe8a698)
 - Remove the last range when using a sliding-window approach and the last range's elements are fully contained in the second last range (PR #244, 48ef4fa685adf6e5d85281e5b90a8ed8f6aeb197)
 - Rename vertex attribute `IssueEvent` to `Issue` in multi-networks, to be consistent with bipartite-networks (PR #244, 26d7b7e9fd6d33d1c0a8a08f19c5c2e30346a3d9)
-- Fix `get.expanded.adjacency` to work if provided author list does not contain all authors from network and add a warning when that happens because it causes some authors from the network to be lost in the resulting matrix (PR #248, ff59017e114b10812dcfb1704a19e01fc1586a13)
+- Fix `get.expanded.adjacency` to work if the provided author list does not contain all authors from network and add a warning when that happens since it causes some authors from the network to be lost in the resulting matrix (PR #248, ff59017e114b10812dcfb1704a19e01fc1586a13)
 - Fix `get.expanded.adjacency.matrices` to have correct names for the columns and rows (PR #248, e72eff864a1cb1a4aecd430e450d4a6a5044fdf2)
 - Fix `get.expanded.adjacency.cumulated` so that it works if `weighted` parameter is set to `FALSE` (PR #248, 2fb9a5d446653f6aee808cbfc87c2dafeb9a749a)
-- Fix `convert.adjacency.matrix.list.to.array` to throw an error if the function is called with wrong parameters (PR #248, ece2d38b4972745af3a83e06f32317a06465a345, 1a3e510df15f5fa4e920e9fce3e0e162c27cd6d1)
 
 
 ## 4.3

tests/test-util-networks-misc.R

@@ -112,6 +112,7 @@ test_that("getting all authors of a list of networks, list length 2", {
         to = "Dieter"
         )
     second.network = igraph::graph.data.frame(second.edges, directed = FALSE, vertices = second.vertices)
+
     ## Act
     result = get.author.names.from.networks(networks = list(first.network, second.network))
 
@@ -145,6 +146,7 @@ test_that("getting all authors of a list of networks, list length 2, not global"
         to = "Dieter"
         )
     second.network = igraph::graph.data.frame(second.edges, directed = FALSE, vertices = second.vertices)
+
     ## Act
     result = get.author.names.from.networks(networks = list(first.network, second.network), globally = FALSE)
 

tests/testing-utils.R

@@ -147,7 +147,7 @@ assert.sparse.matrices.equal = function(matrix.expected, matrix.actual) {
     expected.size = length(matrix.expected)
     expect_equal(expected.size, length(matrix.actual))
     # check if contents are the same
-    for(i in 1 : expected.size) {
+    for (i in 1 : expected.size) {
         expect_equal(matrix.expected[i], matrix.actual[i])
     }
 }

util-networks-misc.R

@@ -147,7 +147,7 @@ get.expanded.adjacency = function(network, authors, weighted = FALSE) {
                             order((rownames(matrix.data)[rownames(matrix.data) %in% authors]))]
         }
 
-        if(network.authors.num > nrow(matrix.data)) { 
+        if (network.authors.num > nrow(matrix.data)) { 
             # write a warning with the number of authors from the network that we ignore
             warning.string = sprintf("The network had %d authors that will not be displayed in the matrix!",
                                         network.authors.num - nrow(matrix.data))
@@ -181,7 +181,7 @@ get.expanded.adjacency.matrices = function(networks, weighted = FALSE){
     adjacency.matrices = parallel::mclapply(networks, function(network) {
         active.authors = igraph::V(network)$name
         active.authors = sort(active.authors)
-        return (get.expanded.adjacency(network = network, authors = active.authors, weighted = weighted))
+        return(get.expanded.adjacency(network = network, authors = active.authors, weighted = weighted))
     })
 
     return(adjacency.matrices)
@@ -214,7 +214,7 @@ get.expanded.adjacency.cumulated = function(networks, weighted = FALSE) {
 
                 ## search for a non-zero entry and set them to an arbitray number (e.g., 42)
                 ## to force that all non-zero entries are correctly set to 1 afterwards
-                if(length(matrices.cumulated[[m]]@i) > 0) {
+                if (length(matrices.cumulated[[m]]@i) > 0) {
 
                     row = matrices.cumulated[[m]]@i[[1]] + 1
                     col = matrices.cumulated[[m]]@j[[1]] + 1
@@ -241,14 +241,14 @@ convert.adjacency.matrix.list.to.array = function(adjacency.list){
         logging::logerror("The method convert.adjacency.matrix.list.to.array received an empty list!")
         stop("The method convert.adjacency.matrix.list.to.array received an empty list!")
     }
-    ## Check if all matrices have equal colomn- and rownames
+    ## Check if all matrices have equal column- and rownames
     rownames = rownames(adjacency.list[[1]])
     colnames = colnames(adjacency.list[[1]])
-    
+
     if (length(adjacency.list) > 1) {
-        for(i in 2 : length(adjacency.list)) {
+        for (i in 2 : length(adjacency.list)) {
             if (!identical(rownames, rownames(adjacency.list[[i]])) || !identical(colnames, colnames(adjacency.list[[i]]))) {
-                error.string = sprintf("The matrix at position %d has a different col or rownames from the first!", i)
+                error.string = sprintf("The matrix at position %d has different col or rownames from the first!", i)
                 logging::logerror(error.string)
                 stop(error.string)
             }