Merge pull request #13 from computational-metabolomics/sequence-development

Sequence development

Author: grlloyd

.travis.yml

@@ -1,5 +1,5 @@
 language: r
-r: bioc-devel
+r: bioc-release
 sudo: false
 cache: packages
 warnings_are_errors: false

DESCRIPTION

@@ -9,29 +9,27 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Collate:
- 'generics.R'
- 'struct_class.R'
- 'parameter_class.R'
- 'chart_class.R'
- 'stato_class.R'
- 'dataset_class.R'
- 'entity_class.R'
- 'entity_stato_class.R'
- 'enum_class.R'
- 'enum_stato_class.R'
- 'output_class.R'
- 'method_class.R'
- 'model_class.R'
- 'example_objects.R'
- 'model_list_class.R'
- 'metric_class.R'
- 'iterator_class.R'
- 'method_seq_class.R'
- 'optimiser_class.R'
- 'preprocess_class.R'
- 'resampler_class.R'
- 'struct.R'
- 'struct_templates.R'
+    'generics.R'
+    'struct_class.R'
+    'parameter_class.R'
+    'chart_class.R'
+    'stato_class.R'
+    'dataset_class.R'
+    'entity_class.R'
+    'entity_stato_class.R'
+    'enum_class.R'
+    'enum_stato_class.R'
+    'output_class.R'
+    'model_class.R'
+    'example_objects.R'
+    'model_list_class.R'
+    'metric_class.R'
+    'iterator_class.R'
+    'optimiser_class.R'
+    'preprocess_class.R'
+    'resampler_class.R'
+    'struct.R'
+    'struct_templates.R'
 RoxygenNote: 6.1.1
 Suggests: 
  testthat,

NAMESPACE

@@ -5,7 +5,6 @@ export("dataset.sample_meta<-")
 export("dataset.variable_meta<-")
 export("description<-")
 export("max_length<-")
-export("method.steps<-")
 export("models<-")
 export("name<-")
 export("output.list<-")
@@ -34,19 +33,15 @@ export(enum.stato)
 export(evaluate)
 export(example_chart)
 export(example_iterator)
-export(example_method)
 export(example_model)
 export(iris_dataset)
 export(is.output)
 export(is.param)
 export(iterator)
 export(max_length)
-export(method)
-export(method.apply)
-export(method.seq)
-export(method.steps)
 export(metric)
 export(model)
+export(model.apply)
 export(model.predict)
 export(model.reverse)
 export(model.seq)
@@ -94,7 +89,6 @@ exportMethods("dataset.sample_meta<-")
 exportMethods("dataset.variable_meta<-")
 exportMethods("description<-")
 exportMethods("max_length<-")
-exportMethods("method.steps<-")
 exportMethods("models<-")
 exportMethods("name<-")
 exportMethods("output.obj<-")
@@ -118,8 +112,7 @@ exportMethods(is.output)
 exportMethods(is.param)
 exportMethods(length)
 exportMethods(max_length)
-exportMethods(method.apply)
-exportMethods(method.steps)
+exportMethods(model.apply)
 exportMethods(model.predict)
 exportMethods(model.reverse)
 exportMethods(model.train)

R/example_objects.R

@@ -133,66 +133,6 @@ setMethod(f="chart.plot",
     }
 )
 
-#' Example method
-#'
-#' An example model for testing
-#' @export example_method
-#' @return test method object
-#' @param M example_method object
-#' @param D dataset object
-#' @rdname example_method
-#' @include method_class.R
-#' @examples
-#' M = example_method()
-#' M = example_method(value_1 = 10, value_2 = 20)
-#'
-example_method=setClass('example_method',
-    contains = c('method','stato'),
-    slots=c(
-        'params.value_0'='entity',
-        'params.value_1'='entity.stato',
-        'params.value_2'='numeric',
-        'outputs.result_1'='entity',
-        'outputs.result_2'='dataset'
-    ),
-    prototype = list(
-        name='A test model',
-        description='An example method object. Adds value_1 counts to
-        a dataset.',
-        type='test',
-        stato.id='OBI:0000011',
-        predicted='result_1',
-        params.value_0=entity(name='Value 0',value=0,type='numeric'),
-        params.value_1=entity.stato(value=10,name='Value 1',type='numeric',
-            description='An example entity.stato object',
-            stato.id='STATO:0000047'),
-        params.value_2=20,
-        outputs.result_1=entity(name='Result 1',type='dataset',
-            description='An example entity object',value=dataset()),
-        outputs.result_2=dataset()
-    )
-)
-
-#' method.apply example
-#'
-#' applies the example method, which adds value_1 to the raw data of a dataset
-#' @export
-#' @return dataset object
-#' @rdname example_method
-#' @examples
-#' D = iris_dataset()
-#' M = example_method(value_1 = 10, value_2 = 20)
-#' M = method.apply(M,D)
-#'
-setMethod(f='method.apply',
-    signature=c('example_method','dataset'),
-    definition = function(M,D) {
-        D$data = D$data + M$value_1
-        M$result_1=D
-        return(M)
-    }
-)
-
 
 
 

R/generics.R

@@ -356,26 +356,23 @@ setGeneric("description",function(obj)standardGeneric("description"))
 setGeneric("description<-",function(obj,value)standardGeneric("description<-"))
 
 #################################
-###### method class generics ####
+###### model class generics #####
 #################################
 
-#' Apply a method
+#' Apply a model
 #'
 #' Applies a method to the input dataset
 #' @param M a method object
 #' @param D another object used by the first
 #' @return Returns a modified method object
-#' @rdname method.apply
+#' @rdname model.apply
 #' @export
 #' @examples
-#' M = example_method()
-#' M = method.apply(M,iris_dataset())
+#' M = example_model()
+#' M = model.apply(M,iris_dataset())
 #'
-setGeneric("method.apply",function(M,D)standardGeneric("method.apply"))
+setGeneric("model.apply",function(M,D)standardGeneric("model.apply"))
 
-#################################
-###### model class generics #####
-#################################
 
 #' Train a model
 #'
@@ -746,29 +743,3 @@ setGeneric("stato.definition",function(obj)standardGeneric("stato.definition"))
 #' @export
 setGeneric("stato.summary",function(obj)standardGeneric("stato.summary"))
 
-######################################
-###### method.seq class generics #####
-######################################
-
-#' Get/set methods of a method.seq
-#'
-#' Returns the list of method in a method.seq object
-#' @param ML a method.seq object
-#' @param value a list containing only method objects
-#' @rdname methods
-#' @return
-#' \describe{
-#' \item{\code{method.steps(ML)}}{returns a list of methods}
-#' \item{\code{method.steps(ML)<-}}{sets the list of methods for a sequence}
-#' }
-#' @export
-#' @examples
-#' ML = example_method() + example_method()
-#' method.steps(ML)
-#' method.steps(ML) = list(example_method(),example_method())
-#'
-setGeneric("method.steps",function(ML)standardGeneric("method.steps"))
-
-#' @export
-#' @rdname methods
-setGeneric("method.steps<-",function(ML,value)standardGeneric("method.steps<-"))