Last changes for release 0.12.0

- change order of darch() function definitions to provide more
  reasonable parameter ordering
- bump version number and date
- add autoencoder example

.Rbuildignore

@@ -9,4 +9,5 @@
 ^\.gitignore$
 ^\.git$
 ^DARCH_CANCEL_?$
-README\.md
+README\.md
+^tests$

.gitignore

@@ -1,5 +1,6 @@
 .Rproj.user
 .Rhistory
+.Renviron
 .RData
 .gitignore~
 *.Rout
@@ -9,3 +10,6 @@ data/
 helper/
 benchmarks/
 logs/
+local/
+tests/
+

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: darch
 Type: Package
 Title: Package for Deep Architectures and Restricted Boltzmann Machines
-Version: 0.11.9000
-Date: 2016-01-13
+Version: 0.12.0
+Date: 2016-05-22
 Author: Martin Drees [aut, cre, cph],
     Johannes Rueckert [ctb],
     Christoph M. Friedrich [ctb],

R/darch.R

@@ -81,54 +81,6 @@ darch <- function(x, ...)
   UseMethod("darch")
 }
 
-
-#' @param data \code{\link{data.frame}} containing the dataset, if \code{x} is
-#'   a \code{\link{formula}}.
-#' @rdname darch
-#' @export
-darch.formula <- function(x, data, layers, ..., xValid=NULL,
-  dataSet = NULL, dataSetValid = NULL, logLevel = NULL, paramsList = list(),
-  darch = NULL)
-{
-  oldLogLevel <- futile.logger::flog.threshold()
-  on.exit(futile.logger::flog.threshold(oldLogLevel))
-  setLogLevel(logLevel)
-
-  if (is.null(dataSet))
-  {
-    # Use existing DataSet if available
-    # TODO check if formula fit?
-    if (!is.null(darch))
-    {
-      dataSet <- createDataSet(data = data,
-        targets = NULL, dataSet = darch@dataSet)
-    }
-    else
-    {
-      dataSet <- createDataSet(data = data, formula = x, ...)
-    }
-  }
-
-  if (is.null(dataSetValid) && !is.null(xValid))
-  {
-    dataSetValid <- createDataSet(xValid, T, previous.dataSet = dataSet,
-      ...)
-  }
-
-  darch <- darch(dataSet, dataSetValid = dataSetValid, ...,
-    layers = if (missing(layers)) 10 else layers, paramsList = paramsList,
-    darch = darch)
-
-  darch
-}
-
-#' @rdname darch
-#' @export
-darch.DataSet <- function(x, ...)
-{
-  darch.default(x = NULL, y = NULL, ..., dataSet = x)
-}
-
 #' @param x Input data matrix or \code{\link{data.frame}}
 #'   (\code{darch.default}) or \code{\link{formula}} (\code{darch.formula}) or
 #'   \code{\linkS4class{DataSet}} (\code{darch.DataSet}).
@@ -574,3 +526,50 @@ darch.default <- function(
 
   darch
 }
+
+#' @param data \code{\link{data.frame}} containing the dataset, if \code{x} is
+#'   a \code{\link{formula}}.
+#' @rdname darch
+#' @export
+darch.formula <- function(x, data, layers, ..., xValid=NULL,
+                          dataSet = NULL, dataSetValid = NULL, logLevel = NULL, paramsList = list(),
+                          darch = NULL)
+{
+  oldLogLevel <- futile.logger::flog.threshold()
+  on.exit(futile.logger::flog.threshold(oldLogLevel))
+  setLogLevel(logLevel)
+
+  if (is.null(dataSet))
+  {
+    # Use existing DataSet if available
+    # TODO check if formula fit?
+    if (!is.null(darch))
+    {
+      dataSet <- createDataSet(data = data,
+                               targets = NULL, dataSet = darch@dataSet)
+    }
+    else
+    {
+      dataSet <- createDataSet(data = data, formula = x, ...)
+    }
+  }
+
+  if (is.null(dataSetValid) && !is.null(xValid))
+  {
+    dataSetValid <- createDataSet(xValid, T, previous.dataSet = dataSet,
+                                  ...)
+  }
+
+  darch <- darch(dataSet, dataSetValid = dataSetValid, ...,
+                 layers = if (missing(layers)) 10 else layers, paramsList = paramsList,
+                 darch = darch)
+
+  darch
+}
+
+#' @rdname darch
+#' @export
+darch.DataSet <- function(x, ...)
+{
+  darch.default(x = NULL, y = NULL, ..., dataSet = x)
+}

README.md

@@ -28,7 +28,7 @@ install_github("maddin79/[email protected]")
 ```
 
 
-Then, use `?darch` to view its documentation or `example("darch")` to load some examples (these will not directly be executed, but provide `example.*` functions).
+Then, use `?darch` to view its documentation or `example("darch")` to view some simple examples.
 
 ### About
 

examples/example.autoencoder.R

@@ -0,0 +1,11 @@
+example.autoencoder <- function(...)
+{
+  data(iris)
+  darch <- darch(iris[,1:4], iris[,1:4], c(4,100,2,100,4), darch.isClass = F,
+    preProc.params = list(method = c("center", "scale")), preProc.targets = T,
+    darch.numEpochs = 200, darch.batchSize = 3,
+    darch.unitFunction = softplusUnit, bp.learnRate = .1,
+    darch.fineTuneFunction = "backpropagation")
+
+  predict(darch, newdata = iris[,1:4])
+}

examples/examples.R

@@ -18,4 +18,4 @@ plot(model2)
 
 #
 # More examples can be found at
-# https://github.com/maddin79/darch/tree/master/examples/
+# https://github.com/maddin79/darch/tree/v0.12.0/examples