From 53bea533decdf592b61b0c31de014b45931408f1 Mon Sep 17 00:00:00 2001
From: Franck SIMON <fsimon.informaticien@wanadoo.fr>
Date: Tue, 27 Aug 2024 18:40:17 +0200
Subject: [PATCH] Rename all.edges.xx and orientations.prob data frames

---
 R/miic.R             | 18 +++++++++---------
 R/miic.plot.R        |  6 +++---
 R/miic.reconstruct.R | 10 +++++-----
 R/tmiic.plot.R       | 18 +++++++++---------
 R/tmiic.wrapper.R    | 10 +++++-----
 R/write.cytoscape.R  |  4 ++--
 man/miic.Rd          |  6 +++---
 src/reconstruct.cpp  |  2 +-
 8 files changed, 37 insertions(+), 37 deletions(-)

diff --git a/R/miic.R b/R/miic.R
index e992210..31ab034 100755
--- a/R/miic.R
+++ b/R/miic.R
@@ -369,7 +369,7 @@
 #'
 #' @return A \emph{miic-like} object that contains:
 #' \itemize{
-#'  \item{\emph{all.edges.summary:} a data frame with information about the
+#'  \item{\emph{summary:} a data frame with information about the
 #'  relationship between relevant pair of variables.
 #'
 #'  As returning the information on all possible pairs of variables could lead
@@ -400,7 +400,7 @@
 #'  retained edges. If the true graph is supplied in the \emph{true_edges}
 #'  parameter, 'P' becomes 'TP' (True Positive) or 'FP' (False Positive),
 #'  while 'N' becomes 'TN' (True Negative) or 'FN' (False Negative).
-#'  Note that, as the \emph{all.edges.summary} does not contain all the
+#'  Note that, as the \emph{summary} does not contain all the
 #'  removed edges, edges not present have to be considered as 'N'
 #'  and, if the true graph is supplied, as 'TN'.}
 #'  \item{ \emph{ai:} the contributing nodes found by the method which
@@ -508,7 +508,7 @@
 #'  the C++ core function. This data frame is used internally by MIIC to
 #'  produce the summary and contains all pairs of variables (\emph{x, y}). }
 #'
-#'  \item{\emph{orientations.prob:} this data frame lists the orientation
+#'  \item{\emph{triples:} this data frame lists the orientation
 #'  probabilities of the two edges of all unshielded triples of the
 #'  reconstructed network with the structure: node1 -- mid-node -- node2:
 #'  \itemize{
@@ -859,7 +859,7 @@ miic <- function(input_data,
   # Post-traitment
   #
   post_start = Sys.time()
-  res$all.edges.summary <- summarizeResults (
+  res$summary <- summarizeResults (
     observations = input_data,
     results = res,
     true_edges = true_edges,
@@ -871,9 +871,9 @@ miic <- function(input_data,
 
   if (!is.null (true_edges))
     {
-    tp = sum (res$all.edges.summary$type == "TP")
-    fp = sum (res$all.edges.summary$type == "FP")
-    fn = sum (res$all.edges.summary$type == "FN")
+    tp = sum (res$summary$type == "TP")
+    fp = sum (res$summary$type == "FP")
+    fn = sum (res$summary$type == "FN")
     precision = tp / (tp + fp)
     recall = tp / (tp + fn)
     fscore = (2 * (precision * recall) ) / (precision + recall)
@@ -907,13 +907,13 @@ miic <- function(input_data,
     # The output of the reconstruction is the "raw" temporal graph, without
     # edges identical by stationarity. To have the "real" temporal graph,
     # we duplicate the edges using the stationary assumption and this "real"
-    # graph is stored the "all.edges.stationarity" data frame.
+    # graph is stored the "stationarity" data frame.
     #
     edges_dup_stat = tmiic_repeat_edges_over_history (res)
     res$tmiic <- list (lagged_state_order = state_order,
                        lagged_black_box = black_box,
                        lagged_true_edges = true_edges,
-                       all.edges.stationarity = edges_dup_stat)
+                       stationarity = edges_dup_stat)
     }
 
   miic_end = Sys.time()
diff --git a/R/miic.plot.R b/R/miic.plot.R
index 0ef7c9b..dd4f76d 100644
--- a/R/miic.plot.R
+++ b/R/miic.plot.R
@@ -139,7 +139,7 @@
 export <- function (miic_res, method="igraph", pcor_palette=NULL,
                     display="compact", show_self_loops=TRUE)
   {
-  if ( is.null(miic_res$all.edges.summary) )
+  if ( is.null(miic_res$summary) )
     stop("The inferred network does not exist")
   if ( (!is.null(method)) && (method != "igraph") )
     stop("Method not supported")
@@ -180,14 +180,14 @@ export <- function (miic_res, method="igraph", pcor_palette=NULL,
 #' plotting parameters and \code{\link[igraph]{layout}} for different layouts.
 #-------------------------------------------------------------------------------
 getIgraph <- function(miic_res, pcor_palette = NULL) {
-  if (is.null(miic_res$all.edges.summary)) {
+  if (is.null(miic_res$summary)) {
     stop("The inferred network does not exist.")
   }
   if (!base::requireNamespace("igraph", quietly = TRUE)) {
     stop("Package 'igraph' is required.")
   }
 
-  summary = miic_res$all.edges.summary[miic_res$all.edges.summary$type %in% c('P', 'TP', 'FP'), ]
+  summary = miic_res$summary[miic_res$summary$type %in% c('P', 'TP', 'FP'), ]
   if (nrow(summary) > 0) {
     # Re-order summary so that all edges go from "x" to "y"
     for(row in 1:nrow(summary)){
diff --git a/R/miic.reconstruct.R b/R/miic.reconstruct.R
index 8750dcf..2f6e093 100755
--- a/R/miic.reconstruct.R
+++ b/R/miic.reconstruct.R
@@ -179,13 +179,13 @@ miic.reconstruct <- function(input_data = NULL,
   )
 
   # create the data frame of the structures after orientation
-  orientations_prob <- res$orientations.prob
+  orientations_prob <- res$triples
 
-  if (length(res$orientations.prob) > 0) {
+  if (length(res$triples) > 0) {
     a <- length(orientations_prob[[1]])
     b <- length(unlist(orientations_prob))
-    tmp <- unlist(res$orientations.prob)[1:a]
-    res1 <- unlist(res$orientations.prob)[(a + 1):b]
+    tmp <- unlist(res$triples)[1:a]
+    res1 <- unlist(res$triples)[(a + 1):b]
     orientations_prob <- data.frame(matrix(
       res1,
       nrow = length(orientations_prob) - 1,
@@ -200,7 +200,7 @@ miic.reconstruct <- function(input_data = NULL,
     orientations_prob[, c(8:9)] <- sapply(orientations_prob[, c(8:9)], as.numeric)
   }
   # update the returned matrix
-  res$orientations.prob <- orientations_prob
+  res$triples <- orientations_prob
 
   res$interrupted <- FALSE
 
diff --git a/R/tmiic.plot.R b/R/tmiic.plot.R
index dfdfbc3..be90488 100644
--- a/R/tmiic.plot.R
+++ b/R/tmiic.plot.R
@@ -71,7 +71,7 @@ tmiic_getIgraph <- function (tmiic_res, display="compact",
                              show_self_loops=TRUE, pcor_palette=NULL)
   {
   if (display == "lagged")
-    tmiic_res$all.edges.summary = tmiic_res$tmiic$all.edges.stationarity
+    tmiic_res$summary = tmiic_res$tmiic$stationarity
   else if (display != "raw")
     tmiic_res <- tmiic_flatten_network (tmiic_res, flatten_mode=display,
                                   keep_edges_on_same_node=show_self_loops)
@@ -86,8 +86,8 @@ tmiic_getIgraph <- function (tmiic_res, display="compact",
   else
     {
     igraph::E(graph)$curved = FALSE
-    if ( "lag" %in% colnames(tmiic_res$all.edges.summary) )
-      igraph::E(graph)$label <- tmiic_res$all.edges.summary$lag
+    if ( "lag" %in% colnames(tmiic_res$summary) )
+      igraph::E(graph)$label <- tmiic_res$summary$lag
     }
   return(graph)
   }
@@ -108,7 +108,7 @@ tmiic_getIgraph <- function (tmiic_res, display="compact",
 #-----------------------------------------------------------------------------
 tmiic_prepare_edges_for_plotting <- function (tmiic_res)
   {
-  df_edges <- tmiic_res$all.edges.summary[tmiic_res$all.edges.summary$type %in% c('P', 'TP', 'FP'), ]
+  df_edges <- tmiic_res$summary[tmiic_res$summary$type %in% c('P', 'TP', 'FP'), ]
   if (nrow(df_edges) <= 0)
     df_edges$xy = character(0)
   else
@@ -145,7 +145,7 @@ tmiic_prepare_edges_for_plotting <- function (tmiic_res)
         }
       }
     }
-  tmiic_res$all.edges.summary <- df_edges
+  tmiic_res$summary <- df_edges
   return (tmiic_res)
   }
 
@@ -165,7 +165,7 @@ tmiic_prepare_edges_for_plotting <- function (tmiic_res)
 #-------------------------------------------------------------------------------
 tmiic_get_multiple_edges_for_plotting <- function (tmiic_res)
   {
-  df_mult <- tmiic_res$all.edges.summary
+  df_mult <- tmiic_res$summary
   if (nrow(df_mult) <= 0)
     df_mult$count <- numeric(0)
   else
@@ -434,7 +434,7 @@ tmiic_compute_row_layout_greedy <- function (tmiic_res)
   # Filter out self edges, count and summarize edges regardless their lags
   #
   tmiic_flat <- tmiic_flatten_network (tmiic_res)
-  df_edges <- tmiic_flat$all.edges.summary
+  df_edges <- tmiic_flat$summary
   df_edges <- df_edges[(df_edges$x != df_edges$y),]
   if (nrow (df_edges) == 0)
     df_edges$count <- integer()
@@ -560,7 +560,7 @@ tmiic_compute_row_layout_sugiyama <- function (tmiic_res)
   # Filter out self edges, count and summarize edges regardless their lags
   #
   tmiic_flat <- tmiic_flatten_network(tmiic_res)
-  df_edges <- tmiic_flat$all.edges.summary
+  df_edges <- tmiic_flat$summary
   df_edges <- df_edges[(df_edges$x != df_edges$y),]
   if (nrow(df_edges) == 0)
     df_edges$count <- integer()
@@ -953,7 +953,7 @@ plot.tmiic = function(x, method='igraph', pcor_palette=NULL,
     # If we have a least on case with multiple edges between the same nodes,
     # draw iteratively
     #
-    df_edges <- x$all.edges.summary
+    df_edges <- x$summary
     edges_colors_iter <- igraph::E(graph)$color
     edges_labels_iter <- igraph::E(graph)$label
     #
diff --git a/R/tmiic.wrapper.R b/R/tmiic.wrapper.R
index 56eb670..29949bc 100644
--- a/R/tmiic.wrapper.R
+++ b/R/tmiic.wrapper.R
@@ -482,12 +482,12 @@ tmiic_flatten_network <- function (tmiic_res, flatten_mode="compact",
   #
   # Keep only edges found by miic
   #
-  df_edges <- tmiic_res$all.edges.summary[tmiic_res$all.edges.summary$type %in% c('P', 'TP', 'FP'), ]
+  df_edges <- tmiic_res$summary[tmiic_res$summary$type %in% c('P', 'TP', 'FP'), ]
   if (nrow(df_edges) <= 0)
     {
     if (flatten_mode != "drop")
       df_edges$lag = numeric(0)
-    tmiic_res$all.edges.summary <- df_edges
+    tmiic_res$summary <- df_edges
     return (tmiic_res)
     }
   #
@@ -539,7 +539,7 @@ tmiic_flatten_network <- function (tmiic_res, flatten_mode="compact",
     {
     if (flatten_mode == "drop")
       df_edges$lag <- NULL
-    tmiic_res$all.edges.summary <- df_edges
+    tmiic_res$summary <- df_edges
     return (tmiic_res)
     }
   #
@@ -645,7 +645,7 @@ tmiic_flatten_network <- function (tmiic_res, flatten_mode="compact",
   #
   # returns the tmiic structure where network summary has been flattened
   #
-  tmiic_res$all.edges.summary <- df_edges
+  tmiic_res$summary <- df_edges
   return (tmiic_res)
   }
 
@@ -668,7 +668,7 @@ tmiic_repeat_edges_over_history <- function (tmiic_res)
   {
   # Consider only edges found by miic  type = "P", "TP", "FP"
   #
-  df_edges <- tmiic_res$all.edges.summary[tmiic_res$all.edges.summary$type %in% c('P', 'TP', 'FP'), ]
+  df_edges <- tmiic_res$summary[tmiic_res$summary$type %in% c('P', 'TP', 'FP'), ]
   if (nrow(df_edges) <= 0)
     return (df_edges)
   #
diff --git a/R/write.cytoscape.R b/R/write.cytoscape.R
index 2bddc70..3fe0e68 100755
--- a/R/write.cytoscape.R
+++ b/R/write.cytoscape.R
@@ -28,11 +28,11 @@ writeCytoscapeNetwork <- function(g, file, layout = NULL) {
     stop("The file path is necessary")
   }
 
-  if (is.null(g$all.edges.summary)) {
+  if (is.null(g$summary)) {
     stop("The result of the miic execution is required")
   }
 
-  summary <- g$all.edges.summary
+  summary <- g$summary
   adj_matrix <- g$adj_matrix
 
   if (is.null(layout)) {
diff --git a/man/miic.Rd b/man/miic.Rd
index 5fd4abe..3dbccf3 100644
--- a/man/miic.Rd
+++ b/man/miic.Rd
@@ -361,7 +361,7 @@ If TRUE, debugging output is printed.}
 \value{
 A \emph{miic-like} object that contains:
 \itemize{
- \item{\emph{all.edges.summary:} a data frame with information about the
+ \item{\emph{summary:} a data frame with information about the
  relationship between relevant pair of variables.
 
  As returning the information on all possible pairs of variables could lead
@@ -392,7 +392,7 @@ A \emph{miic-like} object that contains:
  retained edges. If the true graph is supplied in the \emph{true_edges}
  parameter, 'P' becomes 'TP' (True Positive) or 'FP' (False Positive),
  while 'N' becomes 'TN' (True Negative) or 'FN' (False Negative).
- Note that, as the \emph{all.edges.summary} does not contain all the
+ Note that, as the \emph{summary} does not contain all the
  removed edges, edges not present have to be considered as 'N'
  and, if the true graph is supplied, as 'TN'.}
  \item{ \emph{ai:} the contributing nodes found by the method which
@@ -500,7 +500,7 @@ A \emph{miic-like} object that contains:
  the C++ core function. This data frame is used internally by MIIC to
  produce the summary and contains all pairs of variables (\emph{x, y}). }
 
- \item{\emph{orientations.prob:} this data frame lists the orientation
+ \item{\emph{triples:} this data frame lists the orientation
  probabilities of the two edges of all unshielded triples of the
  reconstructed network with the structure: node1 -- mid-node -- node2:
  \itemize{
diff --git a/src/reconstruct.cpp b/src/reconstruct.cpp
index fd1f9a7..b013b04 100644
--- a/src/reconstruct.cpp
+++ b/src/reconstruct.cpp
@@ -139,7 +139,7 @@ List reconstruct(List input_data, List arg_list) {
       _["proba_adj_matrix"]  = getProbaAdjMatrix(environment.edges),
       _["edges"]             = getEdgesInfoTable(environment.edges,
                                    environment.nodes),
-      _["orientations.prob"] = orientations,
+      _["triples"]           = orientations,
       _["time"]              = vector<double>{time.init, time.iter, time.cut,
                                    time.ori, time.getTotal()},
       _["interrupted"]       = false);