version 1.1

DESCRIPTION

@@ -1,14 +1,21 @@
 Package: ChangepointTesting
 Type: Package
 Title: Change Point Estimation for Clustered Signals
-Version: 1.0
-Date: 2016-02-01
+Version: 1.1
+Date: 2022-06-05
 Author: Hongyuan Cao, Wei Biao Wu, and Shannon T.  Holloway
-Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
-Description: A multiple testing procedure for clustered alternative hypotheses. It is assumed that the p-values under the null hypotheses follow U(0,1) and that the distributions of p-values from the alternative hypotheses are stochastically smaller than U(0,1). By aggregating information, this method is more sensitive to detecting signals of low magnitude than standard methods. Additionally, sporadic small p-values appearing within a null hypotheses sequence are avoided by averaging on the neighboring p-values.
+Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
+Description: A multiple testing procedure for clustered alternative hypotheses. 
+    It is assumed that the p-values under the null hypotheses follow U(0,1) and 
+    that the distributions of p-values from the alternative hypotheses are 
+    stochastically smaller than U(0,1). By aggregating information, this 
+    method is more sensitive to detecting signals of low magnitude than 
+    standard methods. Additionally, sporadic small p-values appearing 
+    within a null hypotheses sequence are avoided by averaging on the 
+    neighboring p-values.
 License: GPL-2
 Depends: graphics, methods, stats
 NeedsCompilation: no
-Packaged: 2016-05-23 22:36:17 UTC; sthollow
+Packaged: 2022-06-05 18:52:12 UTC; 19194
 Repository: CRAN
-Date/Publication: 2016-05-24 05:38:52
+Date/Publication: 2022-06-06 23:10:38 UTC

MD5

@@ -1,10 +1,10 @@
-4254834451e9eb9fee6e042f118b4437 *DESCRIPTION
+ab2bca882c8f17fd9a63940e4b8b0900 *DESCRIPTION
 f5ef67fb18bf6344b7e85801409c01bd *NAMESPACE
 aabf760616ad70f3b5847a19459a3998 *R/All-Classes.R
 57041279050527370f64c07fad6a6e5a *R/BHmethod.R
 688ff009f27ca950041418edf4b4532c *R/changePoint.R
 81baab79c3225c0f7718b2e5cad4525e *R/methods-retrieve.R
 31db7110b9931f5dede1b554252b1649 *R/zhang.R
-6d665c26c1cdfe96dc6f9de7115f7f58 *man/ChangepointTesting-package.Rd
-ee126828a6d79c107afce4f4227538f2 *man/changePoint-class.Rd
-0d8fd49234fe9091e719da97c55cbfeb *man/changePoint.Rd
+db55212b3cdde6c1c00100d2f1ac8b3f *man/ChangepointTesting-package.Rd
+dcec1563c69ca577bb374c0874363241 *man/changePoint-class.Rd
+a849242a24810a82a49b49bd8b3527b3 *man/changePoint.Rd

man/ChangepointTesting-package.Rd

@@ -1,36 +1,36 @@
-\name{ChangepointTesting-package}
-\alias{ChangepointTesting-package}
-\alias{ChangepointTesting}
-\docType{package}
-\title{ Change Point Estimation for Clustered Signals }
-\description{ A multiple testing procedure for clustered alternative 
-              hypotheses. It is assumed that the p-values under the 
-              null hypotheses follow U(0,1) and that the distributions
-              of p-values from the alternative hypotheses are
-              stochastically smaller than U(0,1).
-              By aggregating information, this method is more
-              sensitive to detecting signals of low magnitude than
-              standard methods. Additionally,
-              sporadic small p-values appearing within a
-              null hypotheses sequence are avoided 
-              by averaging on the neighboring p-values. }
-\details{
-\tabular{ll}{
-Package: \tab ChangepointTesting\cr
-Type: \tab Package\cr
-Version: \tab 1.0\cr
-Date: \tab 2016-02-02\cr
-License: GPL-2\cr
-}
-}
-\author{
-Hongyuan Cao, Wei Biao Wu, and Shannon T.  Holloway
-Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
-}
-\references{
-Cao, H. and Wu, W. B. (2015)
-Changepoint estimation: Another look at multiple testing problems.
-Biometrika, 102, 974--980.
-}
-\keyword{ package }
-
+\name{ChangepointTesting-package}
+\alias{ChangepointTesting-package}
+\alias{ChangepointTesting}
+\docType{package}
+\title{ Change Point Estimation for Clustered Signals }
+\description{ A multiple testing procedure for clustered alternative 
+              hypotheses. It is assumed that the p-values under the 
+              null hypotheses follow U(0,1) and that the distributions
+              of p-values from the alternative hypotheses are
+              stochastically smaller than U(0,1).
+              By aggregating information, this method is more
+              sensitive to detecting signals of low magnitude than
+              standard methods. Additionally,
+              sporadic small p-values appearing within a
+              null hypotheses sequence are avoided 
+              by averaging on the neighboring p-values. }
+\details{
+\tabular{ll}{
+Package: \tab ChangepointTesting\cr
+Type: \tab Package\cr
+Version: \tab 1.1\cr
+Date: \tab 2022-06-05\cr
+License: GPL-2\cr
+}
+}
+\author{
+Hongyuan Cao, Wei Biao Wu, and Shannon T.  Holloway
+Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
+}
+\references{
+Cao, H. and Wu, W. B. (2015)
+Changepoint estimation: Another look at multiple testing problems.
+Biometrika, 102, 974--980.
+}
+\keyword{ package }
+

man/changePoint-class.Rd

@@ -1,134 +1,134 @@
-\name{changePoint-class}
-\Rdversion{1.0}
-\docType{class}
-\alias{changePoint-class}
-\alias{BH,changePoint-method}
-\alias{blocks,changePoint-method}
-\alias{CW,changePoint-method}
-\alias{changePts,changePoint-method}
-\alias{critical,changePoint-method}
-\alias{numAlt,changePoint-method}
-\alias{piAlt,changePoint-method}
-\alias{FDRL,changePoint-method}
-\alias{sigmaSq,changePoint-method}
-\alias{print,changePoint-method}
-\alias{plot,changePoint,missing-method}
-\alias{show,changePoint-method}
-
-\title{Class \code{"changePoint"}}
-
-\description{Value object returned by call to \code{changePoint()}. 
-}
-\section{Objects from the Class}{This object should not be created by users.}
-
-\section{Slots}{
-  \describe{
-    \item{\code{CW}:        }{Object of class \code{numeric} or NULL. 
-                              A vector of 1/0 values; 1 indicates  
-                              that hypothesis was rejected by the  
-                              Cao-Wu method.}
-    \item{\code{chgPts}:    }{Object of class \code{numeric} or NULL.  
-                              The vector of change points identified  
-                              by the Cao-Wu method. If no change  
-                              points are identified, NULL.}
-    \item{\code{pi_alt}:    }{Object of class \code{numeric}. 
-                              The estimated proportion of alternative  
-                              hypotheses calculated using the Cao-Wu  
-                              method.}
-    \item{\code{num_alt}:   }{Object of class \code{numeric}. 
-                              The estimated number of alternative hypotheses
-                              calculated using the Cao-Wu method.}
-    \item{\code{FDRL}:      }{Object of class \code{numeric} or NULL.  
-                              A vector of 1/0 values; 1 indicates that  
-                              hypothesis was rejected by the FDR_L  
-                              method.}
-    \item{\code{BH}:        }{Object of class \code{numeric} or NULL.  
-                              A vector of 1/0 values; 1 indicates that  
-                              hypothesis was rejected by the FDR_L  
-                              method.}
-    \item{\code{gammaStar}: }{Object of class \code{numeric}.  The  
-                              estimated critical value for testing  
-                              used by the Cao-Wu method.}
-    \item{\code{sigmaSq}:   }{Object of class \code{numeric}.  The  
-                              estimated variance used to determine  
-                              the critical value of the Cao-Wu method.}
-    \item{\code{pVals}:     }{Object of class \code{numeric}.  The  
-                              original p-values provided as input.}
-  }
-}
-\section{Methods}{
-  \describe{
-    \item{BH}{\code{signature(x = "changePoint")}: 
-              Retrieves a vector of integer values. 
-              An elements is 1 if the null hypothesis is rejected
-              by the Benjamini-Hochberg (1995) method.}
-
-    \item{blocks}{\code{signature(x = "changePoint")}: 
-              Retrieves a list, each element of which is 
-              a vector of integer values. 
-              Each vector contains the indices of 
-              an alternative hypothesis block.}
-
-    \item{CW}{\code{signature(x = "changePoint")}: 
-              Retrieves a vector of integer values. 
-              An element is 1 if the null hypothesis is rejected 
-              by the Cao-Wu change point (2015) method.}
-
-    \item{changePts}{\code{signature(x = "changePoint")}:
-              Retrieves a vector of integer values.
-              The vector of change points identified by the
-              Cao-Wu (2015) method. If no change points are
-              identified, NULL is returned.}
-
-    \item{FDRL}{\code{signature(x = "changePoint")}:  
-              Retrieves a vector of integer values. 
-              Elements are 1 if the null hypothesis is rejected 
-              by the FDR_L (Zhang et al. 2011) method. }
-
-    \item{critical}{\code{signature(x = "changePoint")}: Retrieves the
-        estimated critical value for testing used by
-        the Cao-Wu (2015) method.}
-
-    \item{numAlt}{\code{signature(x = "changePoint")}: Retrieves the
-        estimated number of alternative hypotheses
-        obtained by the Cao-Wu (2015) method. }
-
-    \item{piAlt}{\code{signature(x = "changePoint")}: Retrieves the
-        estimated proportion of alternative hypotheses
-        obtained by the Cao-Wu (2015) method. }
-
-    \item{plot}{\code{signature(x = "changePoint", y = "missing", 
-                                logp = FALSE, ...)}: 
-        Generates x-y plots
-        of -log(p) vs position or p-value vs position for
-        each alternative hypothesis block obtained
-        by the Cao-Wu (2015) method. logp is TRUE/FALSE
-        indicating if -log(p)/p-values are plotted on the y-axis.}
-
-    \item{sigmaSq}{\code{signature(x = "changePoint")}: Retrieves the
-        estimated variance used to determine the critical value of
-        the Cao-Wu (2015) method.}
-
-}}
-\references{
-Benjamini, Y. and Hochberg, Y. (1995).
-Controlling the false discovery rate: A practical and powerful approach to 
-multiple testing.
-{Journal of the Royal Statistical Society: Series B}, 57, 289--300.
-
-Cao, H. and Wu, W. B. (2015)
-Changepoint estimation: Another look at multiple testing problems.
-Biometrika, 102, 974--980.
-
-Zhang, C., Fan, J., and Yu, T. (2011).
-Multiple testing via FDRL for large-scale imaging data.
-Anals of Statistics, 39, 613--642.
-}
-\author{
-Hongyuan Cao, Wei Biao Wu, and Shannon T.  Holloway
-Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
-}
-\examples{
-showClass("changePoint")
-}
-\keyword{classes}
+\name{changePoint-class}
+\Rdversion{1.0}
+\docType{class}
+\alias{changePoint-class}
+\alias{BH,changePoint-method}
+\alias{blocks,changePoint-method}
+\alias{CW,changePoint-method}
+\alias{changePts,changePoint-method}
+\alias{critical,changePoint-method}
+\alias{numAlt,changePoint-method}
+\alias{piAlt,changePoint-method}
+\alias{FDRL,changePoint-method}
+\alias{sigmaSq,changePoint-method}
+\alias{print,changePoint-method}
+\alias{plot,changePoint,missing-method}
+\alias{show,changePoint-method}
+
+\title{Class \code{"changePoint"}}
+
+\description{Value object returned by call to \code{changePoint()}. 
+}
+\section{Objects from the Class}{This object should not be created by users.}
+
+\section{Slots}{
+  \describe{
+    \item{\code{CW}:        }{Object of class \code{numeric} or NULL. 
+                              A vector of 1/0 values; 1 indicates  
+                              that hypothesis was rejected by the  
+                              Cao-Wu method.}
+    \item{\code{chgPts}:    }{Object of class \code{numeric} or NULL.  
+                              The vector of change points identified  
+                              by the Cao-Wu method. If no change  
+                              points are identified, NULL.}
+    \item{\code{pi_alt}:    }{Object of class \code{numeric}. 
+                              The estimated proportion of alternative  
+                              hypotheses calculated using the Cao-Wu  
+                              method.}
+    \item{\code{num_alt}:   }{Object of class \code{numeric}. 
+                              The estimated number of alternative hypotheses
+                              calculated using the Cao-Wu method.}
+    \item{\code{FDRL}:      }{Object of class \code{numeric} or NULL.  
+                              A vector of 1/0 values; 1 indicates that  
+                              hypothesis was rejected by the FDR_L  
+                              method.}
+    \item{\code{BH}:        }{Object of class \code{numeric} or NULL.  
+                              A vector of 1/0 values; 1 indicates that  
+                              hypothesis was rejected by the FDR_L  
+                              method.}
+    \item{\code{gammaStar}: }{Object of class \code{numeric}.  The  
+                              estimated critical value for testing  
+                              used by the Cao-Wu method.}
+    \item{\code{sigmaSq}:   }{Object of class \code{numeric}.  The  
+                              estimated variance used to determine  
+                              the critical value of the Cao-Wu method.}
+    \item{\code{pVals}:     }{Object of class \code{numeric}.  The  
+                              original p-values provided as input.}
+  }
+}
+\section{Methods}{
+  \describe{
+    \item{BH}{\code{signature(x = "changePoint")}: 
+              Retrieves a vector of integer values. 
+              An elements is 1 if the null hypothesis is rejected
+              by the Benjamini-Hochberg (1995) method.}
+
+    \item{blocks}{\code{signature(x = "changePoint")}: 
+              Retrieves a list, each element of which is 
+              a vector of integer values. 
+              Each vector contains the indices of 
+              an alternative hypothesis block.}
+
+    \item{CW}{\code{signature(x = "changePoint")}: 
+              Retrieves a vector of integer values. 
+              An element is 1 if the null hypothesis is rejected 
+              by the Cao-Wu change point (2015) method.}
+
+    \item{changePts}{\code{signature(x = "changePoint")}:
+              Retrieves a vector of integer values.
+              The vector of change points identified by the
+              Cao-Wu (2015) method. If no change points are
+              identified, NULL is returned.}
+
+    \item{FDRL}{\code{signature(x = "changePoint")}:  
+              Retrieves a vector of integer values. 
+              Elements are 1 if the null hypothesis is rejected 
+              by the FDR_L (Zhang et al. 2011) method. }
+
+    \item{critical}{\code{signature(x = "changePoint")}: Retrieves the
+        estimated critical value for testing used by
+        the Cao-Wu (2015) method.}
+
+    \item{numAlt}{\code{signature(x = "changePoint")}: Retrieves the
+        estimated number of alternative hypotheses
+        obtained by the Cao-Wu (2015) method. }
+
+    \item{piAlt}{\code{signature(x = "changePoint")}: Retrieves the
+        estimated proportion of alternative hypotheses
+        obtained by the Cao-Wu (2015) method. }
+
+    \item{plot}{\code{signature(x = "changePoint", y = "missing", 
+                                logp = FALSE, ...)}: 
+        Generates x-y plots
+        of -log(p) vs position or p-value vs position for
+        each alternative hypothesis block obtained
+        by the Cao-Wu (2015) method. logp is TRUE/FALSE
+        indicating if -log(p)/p-values are plotted on the y-axis.}
+
+    \item{sigmaSq}{\code{signature(x = "changePoint")}: Retrieves the
+        estimated variance used to determine the critical value of
+        the Cao-Wu (2015) method.}
+
+}}
+\references{
+Benjamini, Y. and Hochberg, Y. (1995).
+Controlling the false discovery rate: A practical and powerful approach to 
+multiple testing.
+{Journal of the Royal Statistical Society: Series B}, 57, 289--300.
+
+Cao, H. and Wu, W. B. (2015)
+Changepoint estimation: Another look at multiple testing problems.
+Biometrika, 102, 974--980.
+
+Zhang, C., Fan, J., and Yu, T. (2011).
+Multiple testing via FDRL for large-scale imaging data.
+Anals of Statistics, 39, 613--642.
+}
+\author{
+Hongyuan Cao, Wei Biao Wu, and Shannon T.  Holloway
+Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
+}
+\examples{
+showClass("changePoint")
+}
+\keyword{classes}