Fixes for R checks

R/miic.R

@@ -408,12 +408,12 @@
 #'  and possibly separate them.}
 #'  \item{ \emph{raw_contributions:} describes the share of total mutual
 #'  information between \emph{x} and \emph{y} explained by each contributor,
-#'  measured by I'(x;y;ai|{aj}) / I'(x;y),
-#'  where {aj} is the separating set before adding ai.}
+#'  measured by I'(x;y;ai|\{aj\}) / I'(x;y),
+#'  where \{aj\} is the separating set before adding ai.}
 #'  \item{ \emph{contributions:} describes the share of remaining mutual
 #'  information between \emph{x} and \emph{y} explained  by each successive
-#'  contributors, measured by I'(x;y;ai|{aj}) / I'(x;y|{aj}),
-#'  where {aj} is the separating set before adding ai. }
+#'  contributors, measured by I'(x;y;ai|\{aj\}) / I'(x;y|\{aj\}),
+#'  where \{aj\} is the separating set before adding ai. }
 #'  \item{ \emph{info:} the mutual information \emph{I(x;y)} times the number
 #'  of complete samples \emph{n_xy} for the pair (\emph{x}, \emph{y}).}
 #'  \item{ \emph{n_xy:} gives the number of complete samples on which the
@@ -651,7 +651,7 @@
 #'
 #' # write graph to graphml format. Note that to correctly visualize
 #' # the network we created the miic style for Cytoscape (http://www.cytoscape.org/).
-#' writeCytoscapeNetwork(g = miic_obj, file = file.path(tempdir(), "temp"))
+#' writeCytoscapeNetwork(miic_obj, file = file.path(tempdir(), "temp"))
 #'
 #' # EXAMPLE OHNOLOGS
 #' data(ohno)

R/parseResults.R

@@ -140,7 +140,7 @@ summarizeResults = function (observations, results,
   # If no edge in the summary, returns directly an empty data frame
   #
   if (nrow (summary) == 0)
-    return (data._frame (x = character(0), y = character(0),
+    return (data.frame (x = character(0), y = character(0),
       type = character(0), ai = character(0),
       raw_contributions = character(0), contributions = character(0),
       info = numeric(0), n_xy = numeric(0), info_cond = numeric(0),