From 6bf27ce88e41236d0d24dc30aae674dc05c0e66b Mon Sep 17 00:00:00 2001 From: itsrainingdata Date: Fri, 2 Dec 2016 08:58:47 -0500 Subject: [PATCH 1/5] Starting work on v0.0.3 --- DESCRIPTION | 8 ++++++-- NEWS.md | 8 ++++++++ 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4e65de2..6512986 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: sparsebn Title: Learning Sparse Bayesian Networks from High-Dimensional Data -Version: 0.0.2 -Date: 2016-11-28 +Version: 0.0.3 +Date: 2016-12-01 Authors@R: person("Bryon", "Aragam", email = "sparsebn@gmail.com", role = c("aut", "cre")) Maintainer: Bryon Aragam Description: Fast methods for learning sparse Bayesian networks from high-dimensional data using sparse regularization. Designed to incorporate mixed experimental and observational data with thousands of variables with either continuous or discrete observations. @@ -17,6 +17,10 @@ Suggests: igraph, graph, testthat +Remotes: + itsrainingdata/sparsebnUtils@dev, + itsrainingdata/ccdrAlgorithm@dev, + itsrainingdata/discretecdAlgorithm URL: https://github.com/itsrainingdata/sparsebn BugReports: https://github.com/itsrainingdata/sparsebn/issues License: GPL (>= 2) diff --git a/NEWS.md b/NEWS.md index 1986590..05a63cc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +# sparsebn 0.0.3 + +## Features + +## Notes + +## Bug fixes + # sparsebn 0.0.2 ## Features From df18e8182540cb34c2df763fdcfcfe3e89b248d8 Mon Sep 17 00:00:00 2001 From: itsrainingdata Date: Sat, 28 Jan 2017 20:01:32 -0500 Subject: [PATCH 2/5] Bugfix: Missing ... in generic for plotDAG --- R/sparsebn-plotting.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/sparsebn-plotting.R b/R/sparsebn-plotting.R index 3155c1b..d38104f 100644 --- a/R/sparsebn-plotting.R +++ b/R/sparsebn-plotting.R @@ -30,7 +30,7 @@ #' @param ... Additional arguments to \code{\link{plot}}. #' #' @export -plotDAG <- function(x){ +plotDAG <- function(x, ...){ ### Must use igraph for the default method current_plot_pkg <- getPlotPackage() if(current_plot_pkg != "igraph"){ From 0a2a31441facc7839ab7c0cff447aa615b0e4c45 Mon Sep 17 00:00:00 2001 From: itsrainingdata Date: Thu, 9 Mar 2017 11:40:34 -0500 Subject: [PATCH 3/5] Roxygen updates --- DESCRIPTION | 2 +- man/cytometryContinuous.Rd | 1 - man/cytometryDiscrete.Rd | 1 - man/estimate.covariance.Rd | 2 +- man/estimate.dag.Rd | 1 - man/pathfinder.Rd | 1 - man/plotDAG.Rd | 3 +-- man/sparsebn.Rd | 1 - 8 files changed, 3 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6512986..5fa55b6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,6 +24,6 @@ Remotes: URL: https://github.com/itsrainingdata/sparsebn BugReports: https://github.com/itsrainingdata/sparsebn/issues License: GPL (>= 2) -RoxygenNote: 5.0.1 +RoxygenNote: 6.0.1 VignetteBuilder: knitr LazyData: true diff --git a/man/cytometryContinuous.Rd b/man/cytometryContinuous.Rd index 8efc2ee..424497b 100644 --- a/man/cytometryContinuous.Rd +++ b/man/cytometryContinuous.Rd @@ -27,4 +27,3 @@ dat <- sparsebnData(cytometryContinuous$data, type = "c", ivn = cytometryContinu } \keyword{datasets} - diff --git a/man/cytometryDiscrete.Rd b/man/cytometryDiscrete.Rd index 911b20c..09cc2ca 100644 --- a/man/cytometryDiscrete.Rd +++ b/man/cytometryDiscrete.Rd @@ -27,4 +27,3 @@ dat <- sparsebnData(cytometryDiscrete$data, type = "d", ivn = cytometryDiscrete$ } \keyword{datasets} - diff --git a/man/estimate.covariance.Rd b/man/estimate.covariance.Rd index 6e3baa4..fe71f07 100644 --- a/man/estimate.covariance.Rd +++ b/man/estimate.covariance.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/sparsebn-main.R \name{estimate.covariance} \alias{estimate.covariance} +\alias{estimate.covariance} \alias{estimate.precision} \title{Covariance estimation} \usage{ @@ -38,4 +39,3 @@ estimate.precision(dat) # estimate precision } } - diff --git a/man/estimate.dag.Rd b/man/estimate.dag.Rd index f232abb..0280d6b 100644 --- a/man/estimate.dag.Rd +++ b/man/estimate.dag.Rd @@ -62,4 +62,3 @@ estimate.dag(dat) } } - diff --git a/man/pathfinder.Rd b/man/pathfinder.Rd index da6be49..dcede12 100644 --- a/man/pathfinder.Rd +++ b/man/pathfinder.Rd @@ -42,4 +42,3 @@ pathfinder.data <- rmvnorm(n = 1000, sigma = as.matrix(covMat)) } \keyword{datasets} - diff --git a/man/plotDAG.Rd b/man/plotDAG.Rd index aef1cc1..f3d076f 100644 --- a/man/plotDAG.Rd +++ b/man/plotDAG.Rd @@ -4,7 +4,7 @@ \alias{plotDAG} \title{Plot a DAG} \usage{ -plotDAG(x) +plotDAG(x, ...) } \arguments{ \item{x}{An \code{\link{edgeList}}, \code{\link{sparsebnFit}}, or \code{\link{sparsebnPath}} object.} @@ -21,4 +21,3 @@ This method is not intended for customization. For more control over the output, \code{\link{setGraphPackage}} for even more control. These methods grants the user the full feature set of the selected package. } - diff --git a/man/sparsebn.Rd b/man/sparsebn.Rd index 8ef774e..c3060d4 100644 --- a/man/sparsebn.Rd +++ b/man/sparsebn.Rd @@ -23,4 +23,3 @@ The workhorse behind \code{\link{sparsebn}} is the \code{\link[sparsebnUtils]{sp package, which provides various S3 classes and methods for representing and manipulating graphs. For more details on this package and the functionality it provides, see \code{?sparsebnUtils}. } - From 0507aad24516f5e043207bedd20b4ab8360be070 Mon Sep 17 00:00:00 2001 From: itsrainingdata Date: Fri, 10 Mar 2017 08:12:22 -0500 Subject: [PATCH 4/5] Update examples --- R/sparsebn-main.R | 4 ---- man/estimate.covariance.Rd | 2 -- man/estimate.dag.Rd | 2 -- 3 files changed, 8 deletions(-) diff --git a/R/sparsebn-main.R b/R/sparsebn-main.R index 9dafbbe..e3ba8d7 100644 --- a/R/sparsebn-main.R +++ b/R/sparsebn-main.R @@ -47,12 +47,10 @@ #' #' @examples #' -#' \dontrun{ #' # Estimate a DAG from the cytometry data #' data(cytometryContinuous) #' dat <- sparsebnData(cytometryContinuous$data, type = "c", ivn = cytometryContinuous$ivn) #' estimate.dag(dat) -#' } #' #' @export estimate.dag <- function(data, @@ -133,12 +131,10 @@ estimate.dag <- function(data, #' #' @examples #' -#' \dontrun{ #' data(cytometryContinuous) #' dat <- sparsebnData(cytometryContinuous$data, type = "c", ivn = cytometryContinuous$ivn) #' estimate.covariance(dat) # estimate covariance #' estimate.precision(dat) # estimate precision -#' } #' #' @name estimate.covariance #' @rdname estimate.covariance diff --git a/man/estimate.covariance.Rd b/man/estimate.covariance.Rd index fe71f07..5fd0707 100644 --- a/man/estimate.covariance.Rd +++ b/man/estimate.covariance.Rd @@ -31,11 +31,9 @@ see Sections 2.1 and 2.2 (equation (6)) of Aragam and Zhou (2015) for more detai } \examples{ -\dontrun{ data(cytometryContinuous) dat <- sparsebnData(cytometryContinuous$data, type = "c", ivn = cytometryContinuous$ivn) estimate.covariance(dat) # estimate covariance estimate.precision(dat) # estimate precision -} } diff --git a/man/estimate.dag.Rd b/man/estimate.dag.Rd index 0280d6b..9bc5d46 100644 --- a/man/estimate.dag.Rd +++ b/man/estimate.dag.Rd @@ -54,11 +54,9 @@ and \code{\link[discretecdAlgorithm]{cd.run}}. } \examples{ -\dontrun{ # Estimate a DAG from the cytometry data data(cytometryContinuous) dat <- sparsebnData(cytometryContinuous$data, type = "c", ivn = cytometryContinuous$ivn) estimate.dag(dat) -} } From 064827913d04cfe51d7ffcd97751f30533baa0bb Mon Sep 17 00:00:00 2001 From: itsrainingdata Date: Sat, 11 Mar 2017 14:20:42 -0500 Subject: [PATCH 5/5] CRAN updates --- DESCRIPTION | 12 ++++-------- NEWS.md | 6 ++---- cran-comments.md | 11 ++++------- 3 files changed, 10 insertions(+), 19 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5fa55b6..4bfbc4c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,15 @@ Package: sparsebn Title: Learning Sparse Bayesian Networks from High-Dimensional Data Version: 0.0.3 -Date: 2016-12-01 +Date: 2017-03-10 Authors@R: person("Bryon", "Aragam", email = "sparsebn@gmail.com", role = c("aut", "cre")) Maintainer: Bryon Aragam Description: Fast methods for learning sparse Bayesian networks from high-dimensional data using sparse regularization. Designed to incorporate mixed experimental and observational data with thousands of variables with either continuous or discrete observations. Depends: R (>= 3.2.3), - sparsebnUtils (>= 0.0.3), - ccdrAlgorithm (>= 0.0.2), - discretecdAlgorithm (>= 0.0.2) + sparsebnUtils (>= 0.0.4), + ccdrAlgorithm (>= 0.0.3), + discretecdAlgorithm (>= 0.0.3) Suggests: knitr, rmarkdown, @@ -17,10 +17,6 @@ Suggests: igraph, graph, testthat -Remotes: - itsrainingdata/sparsebnUtils@dev, - itsrainingdata/ccdrAlgorithm@dev, - itsrainingdata/discretecdAlgorithm URL: https://github.com/itsrainingdata/sparsebn BugReports: https://github.com/itsrainingdata/sparsebn/issues License: GPL (>= 2) diff --git a/NEWS.md b/NEWS.md index 05a63cc..f71d919 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,11 +1,9 @@ # sparsebn 0.0.3 -## Features - -## Notes - ## Bug fixes +* Minor bug fixes + # sparsebn 0.0.2 ## Features diff --git a/cran-comments.md b/cran-comments.md index 97b6088..7fd8719 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,19 +1,16 @@ ## Test environments -* local OS X install, R 3.3.2 -* ubuntu 12.04.5 (travis-ci), R 3.3.2 (oldrel, devel, and release) +* local OS X install, R 3.3.3 +* ubuntu 12.04.5 (travis-ci), R 3.3.3 (oldrel, devel, and release) * win-builder (devel and release) +* r-hub (oldrel, devel, and release) ## R CMD check results There were no ERRORs, WARNINGs, or NOTEs. -## CRAN notes - -The current warnings listed for v0.0.1 at https://cran.rstudio.com/web/checks/check_results_sparsebn.html are a result of recent updates to the dependencies for this submission. The current submission remedies all of these issues. - ## Dependencies CHECK has been run on all dependencies and passed. ## Reverse dependencies -There are no reverse dependencies. \ No newline at end of file +There are no reverse dependencies.