Merge 1ce16d3 into 2132ed1

syberia · Jan 1, 2016 · e0c8fb6 · e0c8fb6
2 parents 2132ed1 + 1ce16d3
commit e0c8fb6
Show file tree

Hide file tree

Showing 20 changed files with 51 additions and 37 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -7,7 +7,7 @@ install:
 - ./travis-tool.sh install_deps
 - ./travis-tool.sh install_r testthat
 - ./travis-tool.sh install_github syberia/stagerunner robertzk/Ramd
-- ./travis-tool.sh install_github robertzk/statsUtils robertzk/mungebits
+- ./travis-tool.sh install_github robertzk/statsUtils robertzk/mungebits2 robertzk/mungebits
 - ./travis-tool.sh install_github robertzk/syberiaMungebits robertzk/testthatsomemore
 - "./travis-tool.sh install_github jimhester/covr"
 script: ./travis-tool.sh run_tests

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,17 @@
+# Version 0.2.3.9000
+
+ * Start development version and use mungebits2 package throughout.
+
+# Version 0.2.3
+
+ * The `munge_procedure` passed to a `tundraContainer` can now be a stageRunner,
+   in preparation for hierarchical munging in the mungebits2 package.
+
+# Version 0.2.2
+
+ * tundraContainer objects can now add pre-munge and post-munge hooks - functions
+   that will be executed before and after munging when the `train` or
+   `predict` methods are called. You can add a hook using
+   `container$add_hook('train_pre_munge', function() { ... })`. Note these functions
+   can modify the tundraContainer's internals, like `input` or `output`.
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Description: Tundra provides a standardized container format for classifiers
     developed in R. This allows easier deployment by keeping both the data
     preparation procedure and the statistics in one place with an easy
     interface.
-Version: 0.3.0
+Version: 0.3.0.9000
 Author: Robert Krzyzanowski <technoguyrob@gmail.com>
 Maintainer: Robert Krzyzanowski <technoguyrob@gmail.com>
 Authors@R: c(person("Robert", "Krzyzanowski",
@@ -13,12 +13,13 @@ Depends:
     R (>= 3.0.1)
 Imports:
     crayon,
-    mungebits,
     R6,
     stagerunner
 License: MIT + file LICENSE
 LazyData: true
 Suggests:
+    mungebits2,
     testthat,
     testthatsomemore
 Roxygen: list(wrap = FALSE)
+RoxygenNote: 5.0.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(print,tundraContainer)
 S3method(summary,tundraContainer)

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
 # Version 0.2.3
 
  * The `munge_procedure` passed to a `tundraContainer` can now be a stageRunner,
-   in preparation for hierarchical munging in the mungebits package.
+   in preparation for hierarchical munging in the mungebits2 package.
 
 # Version 0.2.2
 

diff --git a/R/package.tundra.R b/R/package.tundra.R
@@ -25,7 +25,7 @@
 #'     a \code{train} method.}
 #' }
 #'
-#' The former is provided by the \href{https://github.com/robertzk/mungebits22}{mungebits2}
+#' The former is provided by the \href{https://github.com/syberia/mungebits2}{mungebits2}
 #' package, while the latter is fully customizable to any R function. This
 #' approach allows arbitrary data preparation and statistical methods, unlike
 #' attempts such as PMML (Predictive Modeling Markup Language) which constrain

diff --git a/R/tundraContainer-initialize.R b/R/tundraContainer-initialize.R
@@ -12,7 +12,7 @@
 #'    output (such as whether to return a probabilistic or absolute
 #'    value).
 #' @param munge_procedure list. A list of trained
-#'    \code{\link[mungebits]{mungepiece}}s to apply to data sets
+#'    \code{\link[mungebits2]{mungepiece}}s to apply to data sets
 #'    during prediction. 
 #' @param default_args list. A list of default arguments to provide to
 #'    the second argument of the \code{train_function}. The additional

diff --git a/R/tundraContainer-train.R b/R/tundraContainer-train.R
@@ -55,7 +55,7 @@ munge <- function(dataframe, munge_procedure, verbose) {
   if (isTRUE(verbose)) {
     capture.output(Recall(dataframe, munge_procedure, FALSE))
   } else {
-    mungebits::munge(dataframe, munge_procedure)
+    mungebits2::munge(dataframe, munge_procedure)
   }
 }
 
diff --git a/R/tundraContainer.R b/R/tundraContainer.R
@@ -22,7 +22,7 @@ tundraContainer <- R6::R6Class("tundraContainer",
     add_hook   = add_hook,
 
     munge      = function(dataframe, steps = TRUE) {
-      mungebits::munge(dataframe, munge_procedure[steps])
+      mungebits2::munge(dataframe, munge_procedure[steps])
     },
     show       = function() {
       cat("A tundraContainer of type ", sQuote(self$.keyword), "\n")

diff --git a/R/tundra_container.r b/R/tundra_container.r
@@ -49,12 +49,12 @@ tundra_container <- setRefClass('tundraContainer',  #define reference classes to
       .run_hooks('train_pre_munge')
 
       if (length(munge_procedure) > 0 && identical(munge, TRUE)) {
-        require(mungebits)
+        require(mungebits2)
         triggers <- unlist(lapply(munge_procedure,
                               function(x) inherits(x, 'trigger')))
 
         (if (!verbose) capture.output else function(...) eval.parent(...))(
-          dataframe <- mungebits::munge(dataframe, munge_procedure)) # Apply munge_procedure to dataframe
+          dataframe <- mungebits2::munge(dataframe, munge_procedure)) # Apply munge_procedure to dataframe
 
         # Store trained munge_procedure
         munge_procedure <<- attr(dataframe, 'mungepieces')[!triggers]
@@ -90,10 +90,10 @@ tundra_container <- setRefClass('tundraContainer',  #define reference classes to
       .run_hooks('predict_pre_munge')
 
       if (length(munge_procedure) > 0 && identical(munge, TRUE)) {
-        require(mungebits)
+        require(mungebits2)
         initial_nrow <- nrow(dataframe)
         (if (!verbose) capture.output else function(...) eval.parent(...))(
-          dataframe <- mungebits::munge(dataframe, munge_procedure)) # Apply munge_procedure to dataframe
+          dataframe <- mungebits2::munge(dataframe, munge_procedure)) # Apply munge_procedure to dataframe
         if (nrow(dataframe) != initial_nrow)
           warning(paste("Some rows were removed during data preparation.",
                         "Predictions will not match input dataframe."))
@@ -119,7 +119,7 @@ tundra_container <- setRefClass('tundraContainer',  #define reference classes to
     },
 
     munge = function(dataframe, steps = TRUE) {
-      mungebits::munge(dataframe, munge_procedure[steps]) 
+      mungebits2::munge(dataframe, munge_procedure[steps]) 
     },
 
     show = function() {

diff --git a/man/call_with.Rd b/man/call_with.Rd
diff --git a/man/hooks.Rd b/man/hooks.Rd
diff --git a/man/initialize.Rd b/man/initialize.Rd
diff --git a/man/list_merge.Rd b/man/list_merge.Rd
diff --git a/man/predict.Rd b/man/predict.Rd
diff --git a/man/train.Rd b/man/train.Rd
diff --git a/man/tundra.Rd b/man/tundra.Rd
diff --git a/man/tundraContainer.Rd b/man/tundraContainer.Rd
diff --git a/man/tundra_container.Rd b/man/tundra_container.Rd
diff --git a/tests/testthat/test-hooks.R b/tests/testthat/test-hooks.R
@@ -3,10 +3,11 @@ context("hooks")
 let(container, tundraContainer$new("foo"))
 let(container_with_munge_side_effect, function(env) {
   force(env)
-  mb <- mungebits:::mungebit(function(data) { 
+  mb <- mungebits2::mungebit$new(function(data) { 
     env$effect <- c(env$effect, "mungebit")
+    data
   })
-  mp <- mungebits:::mungepiece(mb)
+  mp <- mungebits2::mungepiece$new(mb)
   tundraContainer$new("foo", munge_procedure = list(mp))
 })