Removed redundant R code

Author: dirmeier

DESCRIPTION

@@ -1,11 +1,13 @@
 Package: diffusr
 Type: Package
 Title: Network Diffusion Algorithms
-Version: 0.1.1
-Authors@R: person("Simon", "Dirmeier", email = "simon.dirmeier@gmx.de", role = c("aut", "cre"))
+Version: 0.1.2
+Authors@R: person("Simon", "Dirmeier", 
+                  email = "simon.dirmeier@gmx.de",
+                  role = c("aut", "cre"))
 Maintainer: Simon Dirmeier <simon.dirmeier@gmx.de>
-Description: Implementation of network diffusion algorithms such as insulated
-  heat propagation or Markov random walks. Network diffusion algorithms generally
+Description: Implementation of network diffusion algorithms such as
+  heat diffusrion or Markov random walks. Network diffusion algorithms generally
   spread information in the form of node weights along the edges of a graph to other nodes.
   These weights can for example be interpreted as temperature, an initial amount
   of water, the activation of neurons in the brain, or the location of a random

R/RcppExports.R

@@ -1,31 +1,27 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-insulated_heat_diffusion_ <- function(v0, W, b) {
-    .Call('diffusr_insulated_heat_diffusion_', PACKAGE = 'diffusr', v0, W, b)
-}
-
-laplacian_diffusion_ <- function(v0, W, t) {
-    .Call('diffusr_laplacian_diffusion_', PACKAGE = 'diffusr', v0, W, t)
+heat_diffusion_ <- function(v0, W, t) {
+    .Call('_diffusr_heat_diffusion_', PACKAGE = 'diffusr', v0, W, t)
 }
 
 stoch_col_norm_ <- function(W) {
-    .Call('diffusr_stoch_col_norm_', PACKAGE = 'diffusr', W)
+    .Call('_diffusr_stoch_col_norm_', PACKAGE = 'diffusr', W)
 }
 
 laplacian_ <- function(W) {
-    .Call('diffusr_laplacian_', PACKAGE = 'diffusr', W)
+    .Call('_diffusr_laplacian_', PACKAGE = 'diffusr', W)
 }
 
-mrwr_ <- function(p0, W, r) {
-    .Call('diffusr_mrwr_', PACKAGE = 'diffusr', p0, W, r)
+mrwr_ <- function(p0, W, r, thresh, niter, do_analytical) {
+    .Call('_diffusr_mrwr_', PACKAGE = 'diffusr', p0, W, r, thresh, niter, do_analytical)
 }
 
 neighbors_ <- function(node_idxs, W, k) {
-    .Call('diffusr_neighbors_', PACKAGE = 'diffusr', node_idxs, W, k)
+    .Call('_diffusr_neighbors_', PACKAGE = 'diffusr', node_idxs, W, k)
 }
 
 # Register entry points for exported C++ functions
 methods::setLoadAction(function(ns) {
-    .Call('diffusr_RcppExport_registerCCallable', PACKAGE = 'diffusr')
+    .Call('_diffusr_RcppExport_registerCCallable', PACKAGE = 'diffusr')
 })

R/diffusr-package.R

@@ -17,6 +17,7 @@
 # You should have received a copy of the GNU General Public License
 # along with diffusr. If not, see <http://www.gnu.org/licenses/>.
 
+
 #' diffusr
 #'
 #' Network diffusion algorithms in R.

R/laplacian_heat_diffusion.R R/heat_diffusion.RR/laplacian_heat_diffusion.R renamed to R/heat_diffusion.R

@@ -17,17 +17,21 @@
 # You should have received a copy of the GNU General Public License
 # along with diffusr. If not, see <http://www.gnu.org/licenses/>.
 
+
 #' Graph diffusion using a heat diffusion process on a Laplacian matrix.
 #'
-#' @description An amount of starting heat gets distribution using the Laplacian matrix of a graph.
-#' Every iteration (or time interval) \code{t} heat streams from the starting nodes into surrounding nodes.
+#' @description An amount of starting heat gets distribution using the
+#' Laplacian matrix of a graph. Every iteration (or time interval) \code{t}
+#'heat streams from the starting nodes into surrounding nodes.
 #'
 #' @export
 #' @docType methods
-#' @rdname laplacian-diffusion-methods
+#' @rdname heat-diffusion-methods
 #'
-#' @param h0   an \code{n}-dimensional numeric non-negative vector of starting temperatures
-#' @param graph  an (\code{n x n})-dimensional numeric non-negative adjacence matrix representing the graph
+#' @param h0   an \code{n x p}-dimensional numeric non-negative vector/matrix
+#'  of starting temperatures
+#' @param graph  an (\code{n x n})-dimensional numeric non-negative adjacence
+#'  matrix representing the graph
 #' @param t  time point when heat is measured
 #' @param ...  additional parameters
 #' @return  returns the heat on every node as numeric vector
@@ -44,34 +48,46 @@
 #' # adjacency matrix (either normalized or not)
 #' graph <- matrix(abs(rnorm(n*n)), n, n)
 #' # computation of stationary distribution
-#' ht <- laplacian.heat.diffusion(h0, graph)
+#' ht <- heat.diffusion(h0, graph)
 setGeneric(
-  "laplacian.heat.diffusion",
+  "heat.diffusion",
   function(h0, graph, t=.5, ...)
   {
     standardGeneric("laplacian.heat.diffusion")
   },
   package="diffusr"
 )
 
-#' @rdname laplacian-diffusion-methods
-#' @aliases laplacian.heat.diffusion,numeric,matrix-method
+#' @rdname heat-diffusion-methods
+#' @aliases heat.diffusion,numeric,matrix-method
 setMethod(
-  "laplacian.heat.diffusion",
+  "heat.diffusion",
   signature = signature(h0="numeric", graph="matrix"),
   function(h0, graph, t=.5, ...)
+  {
+    h0 <- as.matrix(h0, ncol=1)
+    heat.diffusion(h0, graph, t, ...)
+  }
+)
+
+#' @rdname heat-diffusion-methods
+#' @aliases heat.diffusion,matrix,matrix-method
+setMethod(
+  "heat.diffusion",
+  signature = signature(h0="matrix", graph="matrix"),
+  function(h0, graph, t=.5, ...)
   {
     stopifnot(length(t) == 1)
     if (t < 0) stop("pls provide positive t")
-    .check.vector(h0)
+    .check.starting.matrix(h0)
     .check.graph(graph, h0)
     if (any(diag(graph) != 0))
     {
       message("setting diag of graph to zero")
       diag(graph) <- 0
     }
-    invisible(laplacian_diffusion_(h0,
-                                   normalize.laplacian(graph),
-                                   t))
+    invisible(heat_diffusion_(h0,
+                              normalize.laplacian(graph),
+                              t))
   }
 )

R/insulated_heat_process.R

@@ -17,6 +17,7 @@
 # You should have received a copy of the GNU General Public License
 # along with diffusr. If not, see <http://www.gnu.org/licenses/>.
 
+
 #' Create a stochastically normalized matrix/vector
 #'
 #' @export
@@ -40,8 +41,6 @@ normalize.stochastic.numeric <- function(obj, ...)
     stop('please provide an object with only non-negative values!')
   if (is.matrix(obj))
   {
-    if (nrow(obj) != ncol(obj))
-      stop('please provide a square matrix!')
     if (!all(.equals.double(colSums(obj), 1, .001)))
     {
       message("normalizing column vectors!")

R/mat_util.R

@@ -17,18 +17,25 @@
 # You should have received a copy of the GNU General Public License
 # along with diffusr. If not, see <http://www.gnu.org/licenses/>.
 
+
 #' Graph diffusion using a Markov random walk
 #'
-#' @description A Markov Random Walk takes an inital distribution \code{p0} and calculates the stationary distribution of that.
-#' The diffusion process is regulated by a restart probability \code{r} which controls how often the MRW jumps back to the initial values.
+#' @description A Markov Random Walk takes an inital distribution \code{p0}
+#' and calculates the stationary distribution of that.
+#' The diffusion process is regulated by a restart probability \code{r} which
+#' controls how often the MRW jumps back to the initial values.
 #'
 #' @export
 #' @docType methods
 #' @rdname random-walk-methods
 #'
-#' @param p0  an \code{n}-dimensional numeric non-negative vector representing the starting distribution of the Markov chain (does not need to sum to one)
-#' @param graph  an (\code{n x n})-dimensional numeric non-negative adjacence matrix representing the graph
-#' @param r  a scalar between (0, 1). restart probability if a Markov random walk with restart is desired
+#' @param p0  an \code{n x p}-dimensional numeric non-negative vector/matrix
+#'  representing the starting distribution of the Markov chain
+#'  (does not need to sum to one).
+#' @param graph  an (\code{n x n})-dimensional numeric non-negative adjacence
+#' matrix representing the graph
+#' @param r  a scalar between (0, 1). restart probability if a Markov random
+#' walk with restart is desired
 #' @param ...  additional parameters
 #' @return  returns the stationary distribution as numeric vector
 #'
@@ -57,17 +64,28 @@ setGeneric(
   package="diffusr"
 )
 
-
 #' @rdname random-walk-methods
 #' @aliases random.walk,numeric,matrix-method
 setMethod(
   "random.walk",
   signature = signature(p0="numeric", graph="matrix"),
   function(p0, graph, r=.5, ...)
+  {
+    p0 <- as.matrix(p0, ncol=1)
+    random.walk(p0, graph, r, ...)
+  }
+)
+
+#' @rdname random-walk-methods
+#' @aliases random.walk,matrix,matrix-method
+setMethod(
+  "random.walk",
+  signature = signature(p0="matrix", graph="matrix"),
+  function(p0, graph, r=.5, ...)
   {
     stopifnot(length(r) == 1)
     .check.restart(r)
-    .check.vector(p0)
+    .check.starting.matrix(p0)
     .check.graph(graph, p0)
     if (any(diag(graph) != 0))
     {
@@ -79,6 +97,7 @@ setMethod(
       stop("the provided graph has more than one component. It is likely not ergodic.")
     invisible(mrwr_(normalize.stochastic(p0),
                     stoch.graph,
-                    r))
+                    r)
+              )
   }
 )

R/mrw.R

@@ -55,11 +55,11 @@
 }
 
 #' @noRd
-.check.vector <- function(v)
+.check.starting.matrix <- function(v)
 {
   name <- deparse(substitute(v))
   if (any(v < 0))
     stop(paste(name, "can only contain non-negative values!"))
-  if (!is.vector(v))
-    stop(paste("vectorial", name, "required"))
+  if (!is.matrix(v))
+    stop(paste("matrix-shaped", name, "required"))
 }

R/util.R

@@ -32,4 +32,4 @@ Basically that is all you have to know.
 
 ## Author
 
-* Simon Dirmeier <a href="mailto:mail@simon-dirmeier.net">mail@simon-dirmeier.net</a>
+* Simon Dirmeier <a href="simon.dirmeier@gmx.de">simon.dirmeier@gmx.de</a>