Create different families of functions for @family. #19

andrie · Dec 12, 2014 · 0c4a7b2 · 0c4a7b2
1 parent d2dc2eb
commit 0c4a7b2
Show file tree

Hide file tree

Showing 18 changed files with 62 additions and 73 deletions.
diff --git a/R/addPackages.R b/R/addPackages.R
@@ -88,7 +88,10 @@ readDescriptionGithub <- function(repo, username, branch="master", quiet=TRUE){
 #' @param repo Character vector. Name of repository on github, e.g. \code{"RevolutionAnalytics/checkpoint"}
 #' @param username Optional character vector. Name of repository on github, e.g. \code{"RevolutionAnalytics/checkpoint"}
 #' @param branch name of branch, defaults to \code{"master"}
+
 #' @export
+#' @family github functions
+#' 
 #' @example /inst/examples/example_addPackage.R
 addPackageListingGithub <- function(pdb=pkgAvail(), repo, username=NULL, branch="master"){
   desc <- readDescriptionGithub(repo=repo, username=username, branch=branch)
@@ -102,7 +105,7 @@ addPackageListingGithub <- function(pdb=pkgAvail(), repo, username=NULL, branch=
 
 #' Check for previous versions of packages in a miniCRAN repository.
 #'
-#' Checks for previous versions, and returns the file paths for packages with multiple versions. The admin can subsequently decide which version to keep.
+#' Checks for previous versions, and returns the file paths for packages with multiple versions. You can subsequently decide which version to keep.
 #'
 #' @param pkgs Character vector of packages to be installed. If not provided, checks all files for multiple package versions.
 #'
@@ -115,7 +118,7 @@ addPackageListingGithub <- function(pdb=pkgAvail(), repo, username=NULL, branch=
 #' @return Returns invisibly the filepaths to packages with multiple versions for removal.
 #'
 #' @export
-#' @docType methods
+#' @family update repo functions
 #'
 #' @example /inst/examples/example_checkVersions.R
 #'
@@ -169,7 +172,7 @@ checkVersions <- function(pkgs=NULL, path=NULL, type="source",
 #'
 #' @importFrom tools write_PACKAGES
 #' @export
-#' @docType methods
+#' @family update repo functions
 #'
 #' @example /inst/examples/example_checkVersions.R
 #'
@@ -213,8 +216,8 @@ addPackage <- function(pkgs=NULL, path=NULL, repos=getOption("repos"),
 #'
 #' @importFrom tools write_PACKAGES
 #' @export
-#' @docType methods
-#'
+#' @family update repo functions
+#' 
 #' @example /inst/examples/example_checkVersions.R
 #'
 addOldPackage <- function(pkgs=NULL, path=NULL, vers=NULL,

diff --git a/R/getCranDescription.R b/R/getCranDescription.R
@@ -4,6 +4,7 @@
 #' @inheritParams makeRepo
 #' @import XML
 #' @export
+#' 
 #' @example /inst/examples/example_getCranDescription.R
 getCranDescription <- function(pkg, repos=getOption("repos"), type="source", path, pkgs = pkgDep(pkg, repos=repos, type=type)){
 

diff --git a/R/makeDepGraph.R b/R/makeDepGraph.R
@@ -35,8 +35,10 @@ addDepType <- function(p, type = c("Imports", "Depends", "LinkingTo", "Suggests"
 #'
 #' @import igraph
 #' @export
-#' @family miniCRAN functions
-#' @seealso \code{\link{pkgDep}}, \code{\link{plot.pkgDepGraph}}
+#' @family dependency functions
+#' 
+#' @seealso \code{\link{pkgDep}} to extract package dependencies
+#' 
 #' @example /inst/examples/example_makeDepGraph.R
 makeDepGraph <- function(
   pkg, availPkgs, repos=getOption("repos"), type="source",

diff --git a/R/makeRepo.R b/R/makeRepo.R
@@ -44,7 +44,8 @@
 #' @param writePACKAGES If TRUE, calls \code{\link{write_PACKAGES}} to update the repository PACKAGES file.
 #'
 #' @export
-#' @family miniCRAN functions
+#' @family update repo functions
+#' 
 #' @example /inst/examples/example_makeRepo.R
 makeRepo <- function(pkgs, path, repos=getOption("repos"), type="source",
                      Rversion=R.version, download=TRUE, writePACKAGES=TRUE) {

diff --git a/R/pkgDep.R b/R/pkgDep.R
@@ -3,7 +3,8 @@
 #' Retrieves names of installed packages by calling \code{\link[utils]{installed.packages}} and returning only those packages where \code{Priority} equals "base".
 #'
 #' @export
-#' @family miniCRAN functions
+#' @family dependency functions
+#' 
 #' @seealso \code{\link{pkgDep}}
 basePkgs <- function()names(which(installed.packages()[, "Priority"] == "base"))
 
@@ -25,8 +26,7 @@ basePkgs <- function()names(which(installed.packages()[, "Priority"] == "base"))
 #' @param ... Other arguments passed to \code{\link{available.packages}}
 #'
 #' @export
-#' @seealso \code{\link{makeDepGraph}}
-#' @family miniCRAN functions
+#' @family dependency functions
 #'
 #' @example /inst/examples/example_pkgDep.R
 
@@ -118,7 +118,7 @@ print.pkgDep <- function(x, ...){
 #'
 #' @inheritParams pkgDep
 #' @export
-#' @family miniCRAN functions
+#' @family create repo functions
 #' @seealso \code{\link{pkgDep}}
 pkgAvail <- function(repos=getOption("repos"), type="source", ...){
   if(!grepl("^file", repos[1]) && file.exists(repos[1])) {

diff --git a/R/plot.pkgDepGraph.R b/R/plot.pkgDepGraph.R
@@ -12,8 +12,8 @@
 #'
 #' @import igraph
 #'
-#' @family miniCRAN functions
-#' @seealso \code{\link{makeDepGraph}}
+#' @family dependency functions
+#' 
 #' @example /inst/examples/example_plot.pkgDepGraph.R
 #'
 plot.pkgDepGraph <- function(

diff --git a/R/updatePackages.R b/R/updatePackages.R
@@ -8,7 +8,7 @@
 #'
 #' @param repos character vector, the base URL(s) of the repositories to use, e.g. the URL of a CRAN mirror such as "\code{http://cran.us.r-project.org}".
 #'
-#' @param contriburl  URL(s) of the contrib sections of the repositories. Use this argument if your repository is incomplete. Overrides argument repos.
+#' @param contriburl  URL(s) of the contrib sections of the repositories. Use this argument if your repository is incomplete. Overrides argument \code{repos}.
 #'
 #' @param method  Download method, see \code{\link{download.file}}.
 #'
@@ -26,7 +26,7 @@
 #' @family miniCRAN functions
 #'
 #' @export
-#' @docType methods
+#' @family update repo functions
 #'
 #' @example /inst/examples/example_updatePackages.R
 #'
@@ -95,10 +95,9 @@ oldPackages <- function (path=NULL, repos=getOption("repos"),
 #'
 #' @return \code{NULL} invisibly.
 #'
-#' @seealso \code{\link{oldPackages}}
-#' @family miniCRAN functions
-#' @docType methods
 #' @export
+#' @family update repo functions
+#' 
 #' @example /inst/examples/example_updatePackages.R
 #'
 updatePackages <- function (path=NULL, repos=getOption("repos"),

diff --git a/man/addOldPackage.Rd b/man/addOldPackage.Rd
@@ -1,5 +1,4 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
-\docType{methods}
 \name{addOldPackage}
 \alias{addOldPackage}
 \title{Add old package versions to a miniCRAN repository.}
@@ -91,4 +90,9 @@ pkgList
   unlink(pth, recursive=TRUE)
 }
 }
+\seealso{
+Other update repo functions: \code{\link{addPackage}};
+  \code{\link{checkVersions}}; \code{\link{makeRepo}};
+  \code{\link{oldPackages}}; \code{\link{updatePackages}}
+}
 
diff --git a/man/addPackage.Rd b/man/addPackage.Rd
@@ -1,5 +1,4 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
-\docType{methods}
 \name{addPackage}
 \alias{addPackage}
 \title{Add packages to a miniCRAN repository.}
@@ -87,4 +86,9 @@ pkgList
   unlink(pth, recursive=TRUE)
 }
 }
+\seealso{
+Other update repo functions: \code{\link{addOldPackage}};
+  \code{\link{checkVersions}}; \code{\link{makeRepo}};
+  \code{\link{oldPackages}}; \code{\link{updatePackages}}
+}
 
diff --git a/man/basePkgs.Rd b/man/basePkgs.Rd
@@ -11,10 +11,7 @@ Retrieves names of installed packages by calling \code{\link[utils]{installed.pa
 \seealso{
 \code{\link{pkgDep}}
 
-Other miniCRAN.functions: \code{\link{makeDepGraph}};
-  \code{\link{makeRepo}}; \code{\link{oldPackages}};
-  \code{\link{pkgAvail}}; \code{\link{pkgDep}};
-  \code{\link{plot.pkgDepGraph}};
-  \code{\link{updatePackages}}
+Other dependency functions: \code{\link{makeDepGraph}};
+  \code{\link{pkgDep}}; \code{\link{plot.pkgDepGraph}}
 }
 
diff --git a/man/checkVersions.Rd b/man/checkVersions.Rd
@@ -1,5 +1,4 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
-\docType{methods}
 \name{checkVersions}
 \alias{checkVersions}
 \title{Check for previous versions of packages in a miniCRAN repository.}
@@ -20,7 +19,7 @@ checkVersions(pkgs = NULL, path = NULL, type = "source",
 Returns invisibly the filepaths to packages with multiple versions for removal.
 }
 \description{
-Checks for previous versions, and returns the file paths for packages with multiple versions. The admin can subsequently decide which version to keep.
+Checks for previous versions, and returns the file paths for packages with multiple versions. You can subsequently decide which version to keep.
 }
 \examples{
 ### `checkVersions` and `add.packages.miniCRAN` require an existing miniCRAN repo
@@ -74,4 +73,9 @@ pkgList
   unlink(pth, recursive=TRUE)
 }
 }
+\seealso{
+Other update repo functions: \code{\link{addOldPackage}};
+  \code{\link{addPackage}}; \code{\link{makeRepo}};
+  \code{\link{oldPackages}}; \code{\link{updatePackages}}
+}
 
diff --git a/man/makeDepGraph.Rd b/man/makeDepGraph.Rd
@@ -62,12 +62,9 @@ if(require(igraph)) plot(p)
 }
 }
 \seealso{
-\code{\link{pkgDep}}, \code{\link{plot.pkgDepGraph}}
+\code{\link{pkgDep}} to extract package dependencies
 
-Other miniCRAN.functions: \code{\link{basePkgs}};
-  \code{\link{makeRepo}}; \code{\link{oldPackages}};
-  \code{\link{pkgAvail}}; \code{\link{pkgDep}};
-  \code{\link{plot.pkgDepGraph}};
-  \code{\link{updatePackages}}
+Other dependency functions: \code{\link{basePkgs}};
+  \code{\link{pkgDep}}; \code{\link{plot.pkgDepGraph}}
 }
 
diff --git a/man/makeRepo.Rd b/man/makeRepo.Rd
@@ -100,10 +100,8 @@ unlink(pth, recursive = TRUE)
 }
 }
 \seealso{
-Other miniCRAN.functions: \code{\link{basePkgs}};
-  \code{\link{makeDepGraph}}; \code{\link{oldPackages}};
-  \code{\link{pkgAvail}}; \code{\link{pkgDep}};
-  \code{\link{plot.pkgDepGraph}};
-  \code{\link{updatePackages}}
+Other update repo functions: \code{\link{addOldPackage}};
+  \code{\link{addPackage}}; \code{\link{checkVersions}};
+  \code{\link{oldPackages}}; \code{\link{updatePackages}}
 }
 
diff --git a/man/oldPackages.Rd b/man/oldPackages.Rd
@@ -1,5 +1,4 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
-\docType{methods}
 \name{oldPackages}
 \alias{oldPackages}
 \title{Compare miniCRAN Packages with CRAN-like Repositories}
@@ -14,7 +13,7 @@ oldPackages(path = NULL, repos = getOption("repos"),
 
 \item{repos}{character vector, the base URL(s) of the repositories to use, e.g. the URL of a CRAN mirror such as "\code{http://cran.us.r-project.org}".}
 
-\item{contriburl}{URL(s) of the contrib sections of the repositories. Use this argument if your repository is incomplete. Overrides argument repos.}
+\item{contriburl}{URL(s) of the contrib sections of the repositories. Use this argument if your repository is incomplete. Overrides argument \code{repos}.}
 
 \item{availPkgs}{by default all packages hosted in the miniCRAN repo, \code{\link{pkgAvail}(repos=path, type=type)}. A subset can be specified; currently this must be in the same (character matrix) format as returned by \code{\link{pkgAvail}()}.}
 
@@ -81,10 +80,8 @@ pkgList
 \seealso{
 \code{\link{updatePackages}}, \code{\link{pkgAvail}}.
 
-Other miniCRAN.functions: \code{\link{basePkgs}};
-  \code{\link{makeDepGraph}}; \code{\link{makeRepo}};
-  \code{\link{pkgAvail}}; \code{\link{pkgDep}};
-  \code{\link{plot.pkgDepGraph}};
-  \code{\link{updatePackages}}
+Other update repo functions: \code{\link{addOldPackage}};
+  \code{\link{addPackage}}; \code{\link{checkVersions}};
+  \code{\link{makeRepo}}; \code{\link{updatePackages}}
 }
 
diff --git a/man/pkgAvail.Rd b/man/pkgAvail.Rd
@@ -17,11 +17,5 @@ This is a thin wrapper around \code{\link[utils]{available.packages}}.  If the a
 }
 \seealso{
 \code{\link{pkgDep}}
-
-Other miniCRAN.functions: \code{\link{basePkgs}};
-  \code{\link{makeDepGraph}}; \code{\link{makeRepo}};
-  \code{\link{oldPackages}}; \code{\link{pkgDep}};
-  \code{\link{plot.pkgDepGraph}};
-  \code{\link{updatePackages}}
 }
 
diff --git a/man/pkgDep.Rd b/man/pkgDep.Rd
@@ -46,12 +46,8 @@ pkgDep(pkg=c("ggplot2", "plyr", "reshape2"), pdb)
 
 }
 \seealso{
-\code{\link{makeDepGraph}}
-
-Other miniCRAN.functions: \code{\link{basePkgs}};
-  \code{\link{makeDepGraph}}; \code{\link{makeRepo}};
-  \code{\link{oldPackages}}; \code{\link{pkgAvail}};
-  \code{\link{plot.pkgDepGraph}};
-  \code{\link{updatePackages}}
+Other dependency functions: \code{\link{basePkgs}};
+  \code{\link{makeDepGraph}};
+  \code{\link{plot.pkgDepGraph}}
 }
 
diff --git a/man/plot.pkgDepGraph.Rd b/man/plot.pkgDepGraph.Rd
@@ -60,11 +60,7 @@ plot(dg, legendPosition=c(1, 1), vertex.size=20,  cex=0.5)
 
 }
 \seealso{
-\code{\link{makeDepGraph}}
-
-Other miniCRAN.functions: \code{\link{basePkgs}};
-  \code{\link{makeDepGraph}}; \code{\link{makeRepo}};
-  \code{\link{oldPackages}}; \code{\link{pkgAvail}};
-  \code{\link{pkgDep}}; \code{\link{updatePackages}}
+Other dependency functions: \code{\link{basePkgs}};
+  \code{\link{makeDepGraph}}; \code{\link{pkgDep}}
 }
 
diff --git a/man/updatePackages.Rd b/man/updatePackages.Rd
@@ -1,5 +1,4 @@
 % Generated by roxygen2 (4.0.2): do not edit by hand
-\docType{methods}
 \name{updatePackages}
 \alias{updatePackages}
 \title{Compare miniCRAN Packages with CRAN-like Repositories}
@@ -14,7 +13,7 @@ updatePackages(path = NULL, repos = getOption("repos"),
 
 \item{repos}{character vector, the base URL(s) of the repositories to use, e.g. the URL of a CRAN mirror such as "\code{http://cran.us.r-project.org}".}
 
-\item{contriburl}{URL(s) of the contrib sections of the repositories. Use this argument if your repository is incomplete. Overrides argument repos.}
+\item{contriburl}{URL(s) of the contrib sections of the repositories. Use this argument if your repository is incomplete. Overrides argument \code{repos}.}
 
 \item{method}{Download method, see \code{\link{download.file}}.}
 
@@ -81,11 +80,8 @@ pkgList
 }
 }
 \seealso{
-\code{\link{oldPackages}}
-
-Other miniCRAN.functions: \code{\link{basePkgs}};
-  \code{\link{makeDepGraph}}; \code{\link{makeRepo}};
-  \code{\link{oldPackages}}; \code{\link{pkgAvail}};
-  \code{\link{pkgDep}}; \code{\link{plot.pkgDepGraph}}
+Other update repo functions: \code{\link{addOldPackage}};
+  \code{\link{addPackage}}; \code{\link{checkVersions}};
+  \code{\link{makeRepo}}; \code{\link{oldPackages}}
 }