Standardization of exported function names

NAMESPACE

@@ -7,11 +7,10 @@ export(computeThreePointInfo)
 export(discretizeMDL)
 export(discretizeMutual)
 export(estimateTemporalDynamic)
+export(export)
 export(miic)
-export(miic.export)
-export(miic.write.network.cytoscape)
-export(miic.write.style.cytoscape)
-export(tmiic.export)
+export(writeCytoscapeNetwork)
+export(writeCytoscapeStyle)
 import(Rcpp)
 importFrom(stats,density)
 importFrom(stats,sd)

NEWS.md

@@ -1,5 +1,18 @@
 # Development version
 
+# v2.0.1
+
+## Fixes and improvements
+
+- Updated version published on CRAN.
+
+- Standardization of exported function names, parameters and return values.
+
+## Known issues
+
+- A (very) large number of contributors can lead to a memory fault.
+  Initial fix has been reverted due to side effects.
+
 # v2.0.0
 
 ## Features
@@ -9,11 +22,6 @@
   [Simon et al., eLife, reviewed preprint]
   (https://www.biorxiv.org/content/10.1101/2024.02.06.579177v1.abstract)
 
-## Known issues
-
-- A (very) large number of contributors can lead to a memory fault.
-  Initial fix has been reverted due to side effects.
-
 # v1.8.1
 
 ## Fixes and improvements

R/miic.R

@@ -619,76 +619,76 @@
 #' data(hematoData)
 #'
 #' # execute MIIC (reconstruct graph)
-#' miic.res <- miic(
+#' miic_res <- miic(
 #'   input_data = hematoData[1:1000,], latent = "yes",
 #'   n_shuffles = 10, conf_threshold = 0.001
 #' )
 #'
 #' # plot graph
 #' if(require(igraph)) {
-#'  plot(miic.res, method="igraph")
+#'  plot(miic_res, method="igraph")
 #' }
 #'
 #' \donttest{
 #' # write graph to graphml format. Note that to correctly visualize
 #' # the network we created the miic style for Cytoscape (http://www.cytoscape.org/).
 #'
-#' miic.write.network.cytoscape(g = miic.res, file = file.path(tempdir(), "temp"))
+#' writeCytoscapeNetwork(g = miic_res, file = file.path(tempdir(), "temp"))
 #'
 #' # EXAMPLE CANCER
 #' data(cosmicCancer)
 #' data(cosmicCancer_stateOrder)
 #' # execute MIIC (reconstruct graph)
-#' miic.res <- miic(
+#' miic_res <- miic(
 #'   input_data = cosmicCancer, state_order = cosmicCancer_stateOrder, latent = "yes",
 #'   n_shuffles = 100, conf_threshold = 0.001
 #' )
 #'
 #' # plot graph
 #' if(require(igraph)) {
-#'  plot(miic.res)
+#'  plot(miic_res)
 #' }
 #'
 #' # write graph to graphml format. Note that to correctly visualize
 #' # the network we created the miic style for Cytoscape (http://www.cytoscape.org/).
-#' miic.write.network.cytoscape(g = miic.res, file = file.path(tempdir(), "temp"))
+#' writeCytoscapeNetwork(g = miic_res, file = file.path(tempdir(), "temp"))
 #'
 #' # EXAMPLE OHNOLOGS
 #' data(ohno)
 #' data(ohno_stateOrder)
 #' # execute MIIC (reconstruct graph)
-#' miic.res <- miic(
+#' miic_res <- miic(
 #'   input_data = ohno, latent = "yes", state_order = ohno_stateOrder,
 #'   n_shuffles = 100, conf_threshold = 0.001
 #' )
 #'
 #' # plot graph
 #' if(require(igraph)) {
-#'  plot(miic.res)
+#'  plot(miic_res)
 #' }
 #'
 #' # write graph to graphml format. Note that to correctly visualize
 #' # the network we created the miic style for Cytoscape (http://www.cytoscape.org/).
-#' miic.write.network.cytoscape(g = miic.res, file = file.path(tempdir(), "temp"))
+#' writeCytoscapeNetwork(g = miic_res, file = file.path(tempdir(), "temp"))
 #'
 #' # EXAMPLE COVID CASES (time series demo)
 #' data(covidCases)
 #' # execute MIIC (reconstruct graph in temporal mode)
-#' tmiic.res <- miic(input_data = covidCases, mode = "TS", n_layers = 3, delta_t = 1, movavg = 14)
+#' tmiic_res <- miic(input_data = covidCases, mode = "TS", n_layers = 3, delta_t = 1, movavg = 14)
 #'
 #' # to plot the default graph (compact)
 #' if(require(igraph)) {
-#'  plot(tmiic.res)
+#'  plot(tmiic_res)
 #' }
 #'
-#' # to plot the raw temporal network Using igraph
+#' # to plot the raw temporal network
 #' if(require(igraph)) {
-#'   plot(tmiic.res, display="raw")
+#'   plot(tmiic_res, display="raw")
 #' }
 #'
-#' # to plot the full temporal network Using igraph
+#' # to plot the full temporal network
 #' if(require(igraph)) {
-#'   plot(tmiic.res, display="lagged")
+#'   plot(tmiic_res, display="lagged")
 #' }
 #'
 #' }