Version v3.1.2

NEWS.md

@@ -1,4 +1,19 @@
-# codeface-extraction-r - Changelog
+# codeface-extraction-r – Changelog
+
+
+## 3.1.2
+
+### Changed/Improved
+- Vertex and edge types (attribute `"type"`) are now a character string (e.g., "Author" or "Unipartite") (#110, 3ca6ed99cf377200adb94a4b27ed1ea7d3a6981a)
+- Default plotting layout is now `igraph::layout.kamada.kawai` (#109, 909965453c47c26c902612cb0c9aa16a5b56746a)
+- Remove parameter 'color.attr' from 'motifs.search.in.network' (d33f6863aaf05ae1a8acf7f5667784713796b734)
+- Fix and clean-up of both the plotting and the motif modules (3ca6ed99cf377200adb94a4b27ed1ea7d3a6981a, consequence of #110)
+- Use vectors as vertex attributes instead of lists if there is only one value per vertex (#112, abc0dcbe2aa4ae6ff1c8387c3e961b95e57b2af2)
+- Add a notice that the function `get.date.from.string` does ignore time-zone suffixes (9a51877f32a51850259b323c975182f2155b5302)
+
+### Fixed
+- Probably fixed segfaults during plotting by changing the default layout (see above and issue #109)
+- Fix gray-scale plotting of networks (730cc544edbb30ea3aa89a91e123e74b18a942c6)
 
 
 ## 3.1.1

showcase.R

@@ -11,7 +11,7 @@
 ## with this program; if not, write to the Free Software Foundation, Inc.,
 ## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 ##
-## Copyright 2016-2017 by Claus Hunsen <[email protected]>
+## Copyright 2016-2018 by Claus Hunsen <[email protected]>
 ## Copyright 2017 by Raphael Nömmer <[email protected]>
 ## Copyright 2017 by Christian Hechtl <[email protected]>
 ## Copyright 2017 by Felix Prasse <[email protected]>
@@ -302,8 +302,8 @@ y = NetworkBuilder$new(project.data = y.data, network.conf = net.conf)
 # plot.print.network(g, labels = TRUE, grayscale = FALSE)
 
 # ## set a layout and print directly
-# lay = matrix(c(  20, 179, 552, 693, 956, 1091, 124, 317, 516, 615, 803, 1038,
-#                 245, 175, 185, 255, 253, 225,   73,   8,  75,   0,  96,   86),
+# lay = matrix(c(  20, 179, 693, 552, 956, 1091, 124, 317, 516, 615, 803, 1038,
+#                 245, 175, 255, 185, 253, 225,   73,   8,  75,   0,  96,   86),
 #              nrow = 12, byrow = FALSE) # for sample graph
 # g = igraph::set.graph.attribute(g, "layout", lay)
 # plot.print.network(g, labels = TRUE, grayscale = FALSE)

tests/test-misc.R

@@ -138,6 +138,11 @@ test_that("Parse date from a string.", {
     date.posixct = as.POSIXct(strptime(date.string, format = "%Y-%m-%d"))
     expect_equal(get.date.from.string(date.string), date.posixct, info = "Partial date (no time).")
 
+    ## date string with time zone (which will be ignored as we treat it like UTC anyway)
+    date.string = "2018-02-22 10:02:03 CET"
+    date.posixct = as.POSIXct(strptime("2018-02-22 10:02:03", tz = "UTC", format = "%Y-%m-%d %H:%M:%S"))
+    expect_equal(get.date.from.string(date.string), date.posixct, info = "Date with (ignored) time-zone")
+
 })
 
 ##

tests/test-motifs.R

@@ -32,29 +32,29 @@ test_that("Motifs are found in sample network (remove.duplicates = TRUE).", {
         igraph::V(network)[ c("D3", "D4") ],
         igraph::V(network)[ c("D4", "D5") ]
     )
-    matchings = motifs.search.in.network(network, MOTIFS.LINE, color.attr = "type", remove.duplicates = TRUE)
+    matchings = motifs.search.in.network(network, MOTIFS.LINE, remove.duplicates = TRUE)
     expect_equal(matchings, expected, info = "Line motif")
 
     ## Triangle motif (positive)
     expected = list(
         igraph::V(network)[ c("D1", "D2", "A1") ]
     )
-    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.POSITIVE, color.attr = "type", remove.duplicates = TRUE)
+    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.POSITIVE, remove.duplicates = TRUE)
     expect_equal(matchings, expected, info = "Triangle motif (positive)")
 
     ## Triangle motif (negative)
     expected = list(
         igraph::V(network)[ c("D1", "D2", "A1") ],
         igraph::V(network)[ c("D5", "D6", "A6") ]
     )
-    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.NEGATIVE, color.attr = "type", remove.duplicates = TRUE)
+    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.NEGATIVE, remove.duplicates = TRUE)
     expect_equal(matchings, expected, info = "Triangle motif (negative)")
 
     ## Square motif (positive)
     expected = list(
         igraph::V(network)[ c("D4", "D5", "A5", "A6") ]
     )
-    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.POSITIVE, color.attr = "type", remove.duplicates = TRUE)
+    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.POSITIVE, remove.duplicates = TRUE)
     expect_equal(matchings, expected, info = "Square motif (positive)")
 
     ## Square motif (negative)
@@ -64,7 +64,7 @@ test_that("Motifs are found in sample network (remove.duplicates = TRUE).", {
         igraph::V(network)[ c("D4", "D5", "A5", "A6") ],
         igraph::V(network)[ c("D4", "D6", "A5", "A6") ]
     )
-    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.NEGATIVE, color.attr = "type", remove.duplicates = TRUE)
+    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.NEGATIVE, remove.duplicates = TRUE)
     expect_equal(matchings, expected, info = "Square motif (negative)")
 
 })
@@ -86,15 +86,15 @@ test_that("Motifs are found in sample network (remove.duplicates = FALSE).", {
         igraph::V(network)[ c("D3", "D4") ], # unordered: D4, D3
         igraph::V(network)[ c("D4", "D5") ]  # unordered: D5, D4
     )
-    matchings = motifs.search.in.network(network, MOTIFS.LINE, color.attr = "type", remove.duplicates = FALSE)
+    matchings = motifs.search.in.network(network, MOTIFS.LINE, remove.duplicates = FALSE)
     expect_equal(matchings, expected, info = "Line motif")
 
     ## Triangle motif (positive)
     expected = list(
         igraph::V(network)[ c("D1", "D2", "A1") ],
         igraph::V(network)[ c("D1", "D2", "A1") ]  # unordered: D2, D1, A1
     )
-    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.POSITIVE, color.attr = "type", remove.duplicates = FALSE)
+    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.POSITIVE, remove.duplicates = FALSE)
     expect_equal(matchings, expected, info = "Triangle motif (positive)")
 
     ## Triangle motif (negative)
@@ -104,15 +104,15 @@ test_that("Motifs are found in sample network (remove.duplicates = FALSE).", {
         igraph::V(network)[ c("D5", "D6", "A6") ],
         igraph::V(network)[ c("D5", "D6", "A6") ]  # unordered: D6, D5, A1
     )
-    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.NEGATIVE, color.attr = "type", remove.duplicates = FALSE)
+    matchings = motifs.search.in.network(network, MOTIFS.TRIANGLE.NEGATIVE, remove.duplicates = FALSE)
     expect_equal(matchings, expected, info = "Triangle motif (negative)")
 
     ## Square motif (positive)
     expected = list(
         igraph::V(network)[ c("D4", "D5", "A5", "A6") ],
         igraph::V(network)[ c("D4", "D5", "A5", "A6") ]  # unordered: D5, D4, A5, A6
     )
-    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.POSITIVE, color.attr = "type", remove.duplicates = FALSE)
+    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.POSITIVE, remove.duplicates = FALSE)
     expect_equal(matchings, expected, info = "Square motif (positive)")
 
     ## Square motif (negative)
@@ -126,7 +126,7 @@ test_that("Motifs are found in sample network (remove.duplicates = FALSE).", {
         igraph::V(network)[ c("D4", "D5", "A5", "A6") ], # unordered: D5, D4, A5, A6
         igraph::V(network)[ c("D4", "D6", "A5", "A6") ]  # unordered: D6, D4, A5, A6
     )
-    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.NEGATIVE, color.attr = "type", remove.duplicates = FALSE)
+    matchings = motifs.search.in.network(network, MOTIFS.SQUARE.NEGATIVE, remove.duplicates = FALSE)
     expect_equal(matchings, expected, info = "Square motif (negative)")
 
 })