Changes for revision round.

DESCRIPTION

@@ -1,29 +1,31 @@
-Package: BTR
-Type: Package
-Title: Tools For Training and Analysing Asynchronous Boolean Models
-Version: 1.1.3
-Date: 2015-10-22
-Author: Chee Yee Lim
-Maintainer: Chee Yee Lim <cyl49@cam.ac.uk>
-Description: This package contains tools for inferring asynchronous Boolean
-    models from single-cell expression data.
-Depends:
-    R (>= 3.0.3),
-    methods
-Imports:
-    parallel,
-    Rcpp (>= 0.11.4),
-    foreach (>= 1.4.1),
-    doParallel (>= 1.0.8),
-    poweRlaw (>= 0.30.0),
-    diptest (>= 0.75-7),
-    igraph (>= 1.0.1)
-LinkingTo: Rcpp
-License: GPL-3
-LazyData: true
-Suggests:
-    bnlearn (>= 3.8.1),
-    knitr,
-    rmarkdown
-VignetteBuilder: knitr
-RoxygenNote: 5.0.1
+Package: BTR
+Type: Package
+Title: Tools For Training and Analysing Asynchronous Boolean Models
+Version: 1.2.2
+Date: 2015-10-22
+Author: Chee Yee Lim
+Maintainer: Chee Yee Lim <cyl49@cam.ac.uk>
+Description: This package contains tools for inferring asynchronous Boolean
+    models from single-cell expression data.
+Depends:
+    R (>= 3.0.3),
+    methods
+Imports:
+    parallel,
+    Rcpp (>= 0.11.4),
+    foreach (>= 1.4.1),
+    doParallel (>= 1.0.8),
+    poweRlaw (>= 0.30.0),
+    diptest (>= 0.75-7),
+    igraph (>= 1.0.1),
+    infotheo (>= 1.2.0),
+    entropy (>= 1.2.1)
+LinkingTo: Rcpp
+License: GPL-3
+LazyData: true
+Suggests:
+    bnlearn (>= 3.8.1),
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(BoolModel)
 export(amat_to_bm)

R/boolmodel_class.R

@@ -1,17 +1,17 @@
-#' @title An S4 class to represent a Boolean Model
-#' 
-#' @description
-#' This class represents Boolean Model in a S4 BoolModel object.
-#' 
-#' @field target character vector. It should contain gene symbols.
-#' @field targer_var character vector. It should contain the internal representation of gene variables, in the form of "v[0-9]+s"
-#' @field rule_act list of character vectors. Each element in the list should contain the activating gene variables for a particular target gene.
-#' @field rule_inh list of character vectors. Each element in the list should contain the inhibiting gene variables for a particular target gene.
-#' 
-#' @export BoolModel
-#' @exportClass BoolModel
-BoolModel = setClass('BoolModel',
-                       slots=c(target='character', target_var='character', 
-                               rule_act='list', rule_inh='list')
-                     )
-
+#' @title An S4 class to represent a Boolean Model
+#' 
+#' @description
+#' This class represents Boolean Model in a S4 BoolModel object.
+#' 
+#' @field target character vector. It should contain gene symbols.
+#' @field targer_var character vector. It should contain the internal representation of gene variables, in the form of "v[0-9]+s"
+#' @field rule_act list of character vectors. Each element in the list should contain the activating gene variables for a particular target gene.
+#' @field rule_inh list of character vectors. Each element in the list should contain the inhibiting gene variables for a particular target gene.
+#' 
+#' @export BoolModel
+#' @exportClass BoolModel
+BoolModel = setClass('BoolModel',
+                       slots=c(target='character', target_var='character', 
+                               rule_act='list', rule_inh='list')
+                     )
+

R/btr.R

@@ -1,19 +1,19 @@
-#' @title BTR: A package for studying asynchronous Boolean models
-#' 
-#' @description
-#' This package contains tools for Boolean model manipulation, as well as the search for the best Boolean model.
-#' 
-#' @docType package
-#' @name BTR
-NULL
-
-## All the Roxygen codes below are for generating the correct NAMESPACE file.
-#' @import methods
-#' @import parallel
-#' @import foreach
-#' @import doParallel
-NULL
-
-#' @useDynLib BTR
-#' @importFrom Rcpp sourceCpp evalCpp
+#' @title BTR: A package for studying asynchronous Boolean models
+#' 
+#' @description
+#' This package contains tools for Boolean model manipulation, as well as the search for the best Boolean model.
+#' 
+#' @docType package
+#' @name BTR
+NULL
+
+## All the Roxygen codes below are for generating the correct NAMESPACE file.
+#' @import methods
+#' @import parallel
+#' @import foreach
+#' @import doParallel
+NULL
+
+#' @useDynLib BTR
+#' @importFrom Rcpp sourceCpp evalCpp
 NULL