diff --git a/DESCRIPTION b/DESCRIPTION index f12b16d..c88278d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,4 +17,5 @@ Imports: graphics, utils License: GPL-2 | file LICENSE +LazyData: true RoxygenNote: 6.0.1 diff --git a/R/biclique.R b/R/biclique.R index efb9809..d8d29bd 100644 --- a/R/biclique.R +++ b/R/biclique.R @@ -16,9 +16,9 @@ #' @param envir biclique environment #' #' @examples -#' bicliques = bi.clique("example1.el") -#' bicliques = bi.clique("example1.el", 3, 2) -#' bicliques = bi.clique("example4.bmat", filetype = 1) +#' bicliques = bi.clique(system.file("extdata", "example1.el", package = "biclique")) +#' bicliques = bi.clique(system.file("extdata", "example1.el", package = "biclique"), 3, 2) +#' bicliques = bi.clique(system.file("extdata", "example4.bmat", package = "biclique"), filetype = 1) #' # check a biclique #' bicliques$biclique1 #' @@ -87,8 +87,8 @@ bi.clique <- function(filename, lleast = 1, rleast = 1, version = 1, filetype = #' @param filetype Input file format . 0-edge list, 1-binary matrix. #' #' @examples -#' degreelist = bi.degree("example1.el") -#' degreelist = bi.degree("example4.bmat", 1) +#' degreelist = bi.degree(system.file("extdata", "example1.el", package = "biclique")) +#' degreelist = bi.degree(system.file("extdata", "example4.bmat", package = "biclique"), 1) #' #get the vertex degree #' degreelist['A'] #' @@ -123,7 +123,7 @@ bi.degree <- function(filename, filetype = 0) #' @param envir biclique environment #' #' @examples -#' bicliques = bi.clique("example1.el") +#' bicliques = bi.clique(system.file("extdata", "example1.el", package = "biclique")) #' bi.print() #' #' @importFrom graphics barplot lines points text @@ -161,8 +161,8 @@ bi.print <- function(envir = .GlobalEnv$.bienv) #' @param filetype Input file format . 0-edge list, 1-binary matrix. #' #' @examples -#' bi.format("example2.el") -#' bi.format("example5.bmat", 1) +#' bi.format(system.file("extdata", "example2.el", package = "biclique")) +#' bi.format(system.file("extdata", "example5.bmat", package = "biclique"), 1) #' #' @importFrom utils read.table write.table #' @export diff --git a/man/bi.clique.Rd b/man/bi.clique.Rd index c59c93d..2979ef9 100644 --- a/man/bi.clique.Rd +++ b/man/bi.clique.Rd @@ -29,9 +29,9 @@ This package supports edgelist and binary matrix file format. Two versions of algorithms are implemented in this function, you can choose either one to get bicliques. } \examples{ -bicliques = bi.clique("example1.el") -bicliques = bi.clique("example1.el", 3, 2) -bicliques = bi.clique("example4.bmat", filetype = 1) +bicliques = bi.clique(system.file("extdata", "example1.el", package = "biclique")) +bicliques = bi.clique(system.file("extdata", "example1.el", package = "biclique"), 3, 2) +bicliques = bi.clique(system.file("extdata", "example4.bmat", package = "biclique"), filetype = 1) # check a biclique bicliques$biclique1 diff --git a/man/bi.degree.Rd b/man/bi.degree.Rd index c2b2496..cef29c7 100644 --- a/man/bi.degree.Rd +++ b/man/bi.degree.Rd @@ -15,8 +15,8 @@ bi.degree(filename, filetype = 0) This function will output the degree of each vertex. } \examples{ -degreelist = bi.degree("example1.el") -degreelist = bi.degree("example4.bmat", 1) +degreelist = bi.degree(system.file("extdata", "example1.el", package = "biclique")) +degreelist = bi.degree(system.file("extdata", "example4.bmat", package = "biclique"), 1) #get the vertex degree degreelist['A'] diff --git a/man/bi.format.Rd b/man/bi.format.Rd index 56d3d35..cba404d 100644 --- a/man/bi.format.Rd +++ b/man/bi.format.Rd @@ -20,7 +20,7 @@ If your input file already have those entries, pleast don't run this command. Ot Please also note that no comment characters are allowed in the input file. } \examples{ -bi.format("example2.el") -bi.format("example5.bmat", 1) +bi.format(system.file("extdata", "example2.el", package = "biclique")) +bi.format(system.file("extdata", "example5.bmat", package = "biclique"), 1) } diff --git a/man/bi.print.Rd b/man/bi.print.Rd index e7f3d0f..09e77ab 100644 --- a/man/bi.print.Rd +++ b/man/bi.print.Rd @@ -13,7 +13,7 @@ bi.print(envir = .GlobalEnv$.bienv) You can pass results from function bi.clique to this function to visualize the bicliques. } \examples{ -bicliques = bi.clique("example1.el") +bicliques = bi.clique(system.file("extdata", "example1.el", package = "biclique")) bi.print() }