test_that on fc_reorder

DESCRIPTION

@@ -5,15 +5,17 @@ Version: 0.1
 Date: 2015-06-13
 Author: Jim Porzak
 Maintainer: Jim Porzak <[email protected]>
-Description: A set of tools for doing customer segmentatio with R. Initially focused on using flexclust package.
+Description: A set of tools for doing customer segmentatio with R. Initially focused on
+    using flexclust package.
 License: GPL-2
 LazyData: TRUE
-Imports: 
+Imports:
   dplyr,
   flexclust,
   grid,
   ggplot2,
   MASS,
   tidyr
-Suggests: knitr
+Suggests: knitr,
+    testthat
 VignetteBuilder: knitr

R/fc_rclust.R

@@ -1,7 +1,8 @@
 #' Generate a List of Random kcca Objects.
 #'
 #' For a given number of clusters, \code{k}, \code{nrep} kcca objects are generated.
-#' Each is re-ordered so clusters are in decending size order. Cluster summary information is
+#'
+#' Each is kcca object is re-ordered so clusters are in decending size order. Cluster summary information is
 #' pulled out of each object from the \code{clusinfo} slot. This includes the sizes of the clusters.
 #'
 #' To look for stable cluster solutions, each random run is characterized by the sizes of the first
@@ -15,10 +16,11 @@
 #' @param k Integer. Number of clusters for this run.
 #' @param fc_contol The flexclust control object for this run.
 #' @param nrep Integer. Number of repititions to run.
-#' @param verbose Logical. Override for fc_control@verbose.
+#' @param verbose Logical. Override for fc_control slot verbose.
 #' @param FUN flexclust function.
 #' @param seed Integer. Starting set.seed value for this run.
 #' @param plotme Logical. Should plot be produced as side-effect?
+#' @return A list(best, sizes, peak_at, tries)
 fc_rclust <- function(x, k, fc_cont, nrep=100, verbose=FALSE, FUN = kcca, seed=1234, plotme=TRUE){
   fc_seed = seed
   fc_tries <- NULL
@@ -27,7 +29,7 @@ fc_rclust <- function(x, k, fc_cont, nrep=100, verbose=FALSE, FUN = kcca, seed=1
     set.seed(fc_seed)
     cli <- flexclust::kcca(x, k, save.data = TRUE,
                            control = fc_cont, family = kccaFamily(fc_family))
-    cli.re <- fc_reorder(cli, orderby = "decending size")
+    cli.re <- CustSegs::fc_reorder(cli, orderby = "decending size")
     cli_info <- cli.re@clusinfo %>%
       dplyr::mutate(clust_num = row_number(),
                     clust_rank = min_rank(desc(size))) %>%

man/fc_rclust.Rd

@@ -0,0 +1,51 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/fc_rclust.R, R/fc_stable.R
+\name{fc_rclust}
+\alias{fc_rclust}
+\title{Generate a List of Random kcca Objects.}
+\usage{
+fc_rclust(x, k, fc_cont, nrep = 100, verbose = FALSE, FUN = kcca,
+  seed = 1234, plotme = TRUE)
+
+fc_rclust(x, k, fc_cont, nrep = 100, verbose = FALSE, FUN = kcca,
+  seed = 1234, plotme = TRUE)
+}
+\arguments{
+\item{x}{Integer. matrix. Input to kcca.}
+
+\item{k}{Integer. Number of clusters for this run.}
+
+\item{nrep}{Integer. Number of repititions to run.}
+
+\item{verbose}{Logical. Override for fc_control slot verbose.}
+
+\item{FUN}{flexclust function.}
+
+\item{seed}{Integer. Starting set.seed value for this run.}
+
+\item{plotme}{Logical. Should plot be produced as side-effect?}
+
+\item{fc_contol}{The flexclust control object for this run.}
+}
+\value{
+A list(best, sizes, peak_at, tries)
+
+tbl_df of k * nrep rows with cluster summary for k, seed, cluster #
+}
+\description{
+For a given number of clusters, \code{k}, \code{nrep} kcca objects are generated.
+
+Repeat flexclust runs
+}
+\details{
+Each is kcca object is re-ordered so clusters are in decending size order. Cluster summary information is
+pulled out of each object from the \code{clusinfo} slot. This includes the sizes of the clusters.
+
+To look for stable cluster solutions, each random run is characterized by the sizes of the first
+two clusters; which will be the largest after reording. \code{kde2d()} from the MASS package is
+used to find density contours. The highest peak is determined and the distance of each solution
+to the peak is retained for each cluster.
+
+Optionally, the scatter plot of the sizes and corresponding coutour in plotted.
+}
+

man/fc_reorder.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/fc_reorder.R
+\name{fc_reorder}
+\alias{fc_reorder}
+\title{Reorder clusters in a kcca object.}
+\usage{
+fc_reorder(x, orderby = "decending size")
+}
+\arguments{
+\item{x}{A kcca object.}
+
+\item{orderby}{A string. Specifying the method to order by. Currently only "decending size".}
+}
+\value{
+The kcca object with clusters reordered.
+}
+\description{
+Since running kcca with different seeds will result, at least, in equivalent
+clusters having different cluster sequence numbers which makes interpretation
+of repeated runs difficult.
+}
+\details{
+\code{fc_reorder} simply rearranges the clusters within the kcca object according
+to the requested method.
+}
+\examples{
+\dontrun{
+fc_reorder(kcca(x, k, save.data = TRUE, control = fc_cont, family = kccaFamily(fc_family)))
+}
+}
+

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(CustSegs)
+
+test_check("CustSegs")

tests/testthat/test-reorder.r

@@ -0,0 +1,53 @@
+library(CustSegs)
+library(flexclust)
+context("flexclust kcca object re-order")
+
+data("volunteers")
+vol_ch <- volunteers[-(1:2)]
+vol.mat <- as.matrix(vol_ch)
+fc_cont <- new("flexclustControl")  ## flexclustControl object holds "hyperparameters"
+fc_cont@tolerance <- 0.1   ## kcca only uses if classify == "weighted"
+fc_cont@iter.max <- 30
+fc_cont@verbose <- 0
+fc_family <- "ejaccard"             ## distance metric
+
+#####
+# check reorder on object already in order does nothing at al
+##
+num_clusters <- 3
+fc_seed <- 577 ## magic seed to get result in order
+set.seed(fc_seed)
+vol.cl.A <- kcca(vol.mat, k = num_clusters, save.data = TRUE,
+                 control = fc_cont, family = kccaFamily(fc_family))
+summary(vol.cl.A)
+sizes.A <- vol.cl.A@clusinfo[[1]]
+vol.cl.A.re <- fc_reorder(vol.cl.A)
+test_that("fc_reorder does not clobber already ordered kcca object", {
+  expect_is(vol.cl.A.re, "kcca")
+  expect_equal(sizes.A, c(1078, 258, 79))
+  expect_identical(vol.cl.A, vol.cl.A.re)
+})
+
+#####
+# check reorder on object that needs reordering
+##
+fc_seed <- 243 ## magic seed to get result needing reordering
+set.seed(fc_seed)
+vol.cl.B <- kcca(vol.mat, k = num_clusters, save.data = TRUE,
+                 control = fc_cont, family = kccaFamily(fc_family))
+summary(vol.cl.B)
+sizes.B <- vol.cl.B@clusinfo[[1]]
+vol.cl.B.re <- fc_reorder(vol.cl.B)
+sizes.B.re <- vol.cl.B.re@clusinfo[[1]]
+test_that("fc_reorder does in-fact reorder clusters within kcca object", {
+  expect_is((vol.cl.B.re), "kcca")
+  expect_equal(sizes.B, c(260, 1080, 75))
+  expect_equal(sizes.B.re, c(1080, 260, 75))
+  expect_equal_to_reference(vol.cl.B.re, file = "VolClBre.rds")
+})
+
+
+
+
+
+