Merge pull request #52 from Jean-Baptiste-Camps/cranFix2

fixing non ASCII characters in Namespace comments for CRAN

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: stemmatology
 Type: Package
 Title: Stemmatological Analysis of Textual Traditions
-Version: 0.3.1
-Date: 2018-05-25
+Version: 0.3.2
+Date: 2019-03-28
 Author: Jean-Baptiste Camps ; Florian Cafiero
 Maintainer: Jean-Baptiste Camps <[email protected]>
 Description: Explore and analyse the genealogy of textual or musical traditions, from their variants, with various stemmatological methods, mainly the disagreement-based algorithms suggested by Camps and Cafiero (2015) <doi:10.1484/M.LECTIO-EB.5.102565>.

NAMESPACE

@@ -1,8 +1,5 @@
-exportPattern("^[^\\.]") # This exports everything from stemmatology
-# namespace that does not start with a dot. If at some point we
-# want a more explicit listing, we might use export(PCC, PCC.Exploratory…)
+exportPattern("^[^\\.]")
 importFrom("graphics", "axis", "barplot", "plot","title")
-# It would be possible to remove stats import with a few modifications (only 2 uses)
 importFrom("stats", "fisher.test", "na.omit")
 importFrom("cluster", "pam")
 importFrom("igraph", "graph_from_edgelist", "layout_as_tree", "layout_with_fr", "plot.igraph", "E", "union", "topo_sort","V","neighbors", "as_adjacency_matrix")

R/PCC.conflicts.R

@@ -6,7 +6,7 @@ PCC.conflicts <-
     # TODO: perhaps better, for alternateReadings, to create as many
     # new rows as necessary, at the start, and avoid code redundancy
     # as well as many small inflexions to the code due to the fact
-    # that we need to cross VL with themselves if alternate…
+    # that we need to cross VL with themselves if alternate.
     # it could also make the network more legible.
     # This could even be ported into a different function, 
     # for separate use.

R/PCC.equipollent.R

@@ -61,7 +61,7 @@ PCC.equipollent <-
     # configurations in which some members are in conflict between
     # themselves, in which case we will remove them.
     # In order for that to work, we need to deduplicate problematic
-    # configurations into unproblematic ones… Harder than it looks
+    # configurations into unproblematic ones... Harder than it looks
     toBeRemovedAsWell = as.vector(NULL)
     #If there is more than two members
     for (l in seq_len(length(notInConflict))) {

R/import.TEIApparatus.R

@@ -39,7 +39,7 @@ import.TEIApparatus <-
       myRdgWits = sub("^\\s+|\\s+$", "", myRdgWits)
       myRdgWits = strsplit(myRdgWits, "\\s+")
       myRdgVars = NULL
-      # 0 for omission, 1…n for readings
+      # 0 for omission, 1...n for readings
       for (j in seq_len(length(myRdgs))) {
         if (xml2::xml_text(myRdgs[j], "normalize-space(.)") == "") {
           myRdgVars = c(myRdgVars, 0)

README.md

@@ -4,13 +4,15 @@
 [![Coverage Status](https://img.shields.io/codecov/c/github/Jean-Baptiste-Camps/stemmatology/master.svg)](https://codecov.io/github/Jean-Baptiste-Camps/stemmatology?branch=master) 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/stemmatology)](https://cran.r-project.org/package=stemmatology)
 [![DOI](https://zenodo.org/badge/21941228.svg)](https://zenodo.org/badge/latestdoi/21941228)
+[![metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/stemmatology)](https://cran.r-project.org/package=stemmatology)
+
 
 
     Package: stemmatology
     Type: Package
     Title: Stemmatological Analysis of Textual Traditions
-    Version: 0.3.1
-    Date: 2018-05-25
+    Version: 0.3.2
+    Date: 2019-03-28
     Author: Jean-Baptiste Camps ; Florian Cafiero
     Maintainer: Jean-Baptiste Camps <[email protected]>
     Description: Explore and analyse the genealogy of textual or musical traditions, from their variants, with various stemmatological methods, mainly the disagreement-based algorithms suggested by Camps and Cafiero (2015) <doi:10.1484/M.LECTIO-EB.5.102565>.

tests/testthat/test-PCC.Exploratory.R

@@ -158,3 +158,25 @@ test_that("yields expected output on smaller case", {
 #VL12 1 2  2  2 1   1   2       2
 
 #TODO: extend it to other exploratory functions !
+# 
+# test_that("works on non numeric input", {
+#   x = matrix(data = c(
+#     "1","1","2","2","1,2",
+#     "1","1","2","2","1,2",
+#     "0","0","1","2","1,2",
+#     "1","1","2","2","1",
+#     "1","1","2","2","2",
+#     "1","2","3","4","5"
+#   ), byrow = TRUE,
+#   ncol = 5,
+#   nrow = 6,
+#   dimnames = list(
+#     c("VL1", "VL2", "VL3", "VL4", "VL5", "VL6"),
+#     c("A","B","C","D","E")
+#   )
+#   )
+#   # TODO: create test and debug for very small databases
+#   PCC.Exploratory(x, omissionsAsReadings = FALSE, alternateReadings = TRUE)
+#   
+#   
+# })

tests/testthat/test-PCC.R

@@ -215,3 +215,16 @@ test_that("yields expected output on simple case (with conflicts)", {
   )
 
 })
+
+# test_that("PCC works on non numeric input", {
+#   myData = structure(c("1", "1", "1", "1,3", "1", "1", "1", "1,3", "1", 
+#                        "1", "1", "1,3", "1", "1", "1", "1,3", "2", "2", "1", "1,2", 
+#                        "2", "2", "1", "1,2", "2", "2", "1", "1,2", "2", "2", "1", "1,2", 
+#                        "2", "1,2", "1", "1", "2", "1,2", "1", "1", "2", "1,2", "1", 
+#                        "1", "2", "1,2", "1", "1", "2", "2", "1", "2", "2", "2", "1", 
+#                        "2", "2", "2", "1", "2", "2", "2", "1", "2", "1,2", "1", "2", 
+#                        "3", "1,2", "1", "2", "3", "1,2", "1", "2", "3", "1,2", "1", 
+#                        "2", "3"), .Dim = c(16L, 5L), .Dimnames = list(c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"), c("A", "D", "F", "T", "P")))
+#   PCC(myData, alternateReadings = TRUE)
+#     
+# })