cleans check and imports

DESCRIPTION

@@ -2,7 +2,18 @@ Package: gslope
 Type: Package
 Title: Graphical SLOPE
 Version: 0.1.0
-Authors: Krystyna Grzesiak, Zofia Dziedzic, Tomasz Kulik, Michał Makowski, Mateusz Staniak
+Authors@R: 
+  c(person("Mateusz", "Staniak",
+           role = c("aut")),
+    person("Krystyna", "Grzesiak",
+           role = c("aut", "cre"), 
+            email = "krysiagrzesiak11@wp.pl"),
+    person("Zofia", "Dziedzic",
+           role = c("aut")),
+    person("Tomasz", "Kulik",
+           role = c("aut")),
+    person("Michal", "Makowski",
+           role = c("com", "ths")))
 Description: Computation of precision matrix based on graphical SLOPE.
 License: GPL-3
 Encoding: UTF-8

NAMESPACE

@@ -13,20 +13,23 @@ export(plot)
 export(prepare_lambda)
 export(summary)
 importFrom(Rcpp,sourceCpp)
-importFrom(ggplot2,"aes")
-importFrom(ggplot2,"coord_fixed")
-importFrom(ggplot2,"element_text")
-importFrom(ggplot2,"geom_tile")
-importFrom(ggplot2,"ggplot")
-importFrom(ggplot2,"ggtitle")
-importFrom(ggplot2,"labs")
-importFrom(ggplot2,"scale_fill_gradient")
-importFrom(ggplot2,"scale_fill_gradient2")
-importFrom(ggplot2,"theme")
-importFrom(ggplot2,"xlab")
-importFrom(ggplot2,"ylab")
-importFrom(igraph,"clusters")
-importFrom(igraph,"graph_from_adjacency_matrix")
-importFrom(igraph,"layout.circle")
-importFrom(igraph,"plot.igraph")
+importFrom(ggplot2,aes)
+importFrom(ggplot2,coord_fixed)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_fill_gradient)
+importFrom(ggplot2,scale_fill_gradient2)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,xlab)
+importFrom(ggplot2,ylab)
+importFrom(igraph,clusters)
+importFrom(igraph,graph_from_adjacency_matrix)
+importFrom(igraph,layout.circle)
+importFrom(igraph,plot.igraph)
+importFrom(stats,cov)
+importFrom(stats,cov2cor)
+importFrom(stats,qt)
 useDynLib(gslope, .registration = TRUE)

R/graph_plot.R

@@ -1,6 +1,3 @@
-#' @importFrom igraph "graph_from_adjacency_matrix"
-#' @importFrom igraph "plot.igraph"
-#' @importFrom igraph "layout.circle"
 
 #' @title Plot graph for gslope.
 #'

R/gslope-package.R

@@ -1,7 +1,27 @@
-## usethis namespace: start
+#' gslope
+#'
+#' @docType package
+#' @description R package that estimates a sparse precision matrix based on regularization by the SLOPE.
+#' @name gslope-package
 #' @useDynLib gslope, .registration = TRUE
-## usethis namespace: end
-## usethis namespace: start
 #' @importFrom Rcpp sourceCpp
-## usethis namespace: end
+#' @importFrom igraph graph_from_adjacency_matrix
+#' @importFrom igraph clusters
+#' @importFrom ggplot2 ggplot
+#' @importFrom ggplot2 geom_tile
+#' @importFrom ggplot2 scale_fill_gradient
+#' @importFrom ggplot2 scale_fill_gradient2
+#' @importFrom ggplot2 coord_fixed
+#' @importFrom ggplot2 aes
+#' @importFrom ggplot2 ggtitle
+#' @importFrom ggplot2 xlab
+#' @importFrom ggplot2 ylab
+#' @importFrom ggplot2 theme
+#' @importFrom ggplot2 labs
+#' @importFrom ggplot2 element_text
+#' @importFrom igraph graph_from_adjacency_matrix
+#' @importFrom igraph plot.igraph
+#' @importFrom igraph layout.circle
+#' @importFrom stats cov cov2cor qt
+#'
 NULL

R/gslope.R

@@ -1,5 +1,3 @@
-#' @importFrom igraph "graph_from_adjacency_matrix"
-#' @importFrom igraph "clusters"
 
 #' @title Preparation of lambda
 #' @description  Prepares penalty parameters \eqn{\lambda} for further computations in graphical SLOPE.
@@ -37,7 +35,6 @@ prepare_lambda = function(lambda, low_tri_size) {
 #'
 #' @param data a matrix containing observations of variables of interest.
 #' @param lambda vector of regularizers for SLOPE. By default computed based on Benjamini-Hochberg's method.
-#' @param sample_cov variance-covariance matrix.
 #' @param scaled {logical. The data need to be scaled so that it has mean = 0 and variance = 1. If TRUE, build-in data scaling will be omitted.}
 #' @param mu correction for lambda scaling in ADMM algorithm.
 #' @param max_iter maximum number of iterations allowed in ADMM algorithm. Default 10 000.
@@ -80,15 +77,19 @@ gslope = function(data,
                   epsilon = 1e-4,
                   threshold = 1e-4,
                   alpha = 0.05) {
+  sample_cov = NULL
 
   call = match.call()
   if(is.null(colnames(data)))
     names = 1:ncol(data) else
       names = colnames(data)
-  sample_cov = if(!scaled) cov(scale(data)) else cov(data)
-   if(is.null(lambda)) {
+
+  if(!scaled)
+    sample_cov = cov(scale(data)) else
+      sample_cov = cov(data)
+
+   if(is.null(lambda))
     lambda = gslope::create_lambda(sample_cov, nrow(data), alpha)
-  }
 
   p = ncol(data)
   lambda = prepare_lambda(lambda, p*(p-1)/2)
@@ -103,7 +104,7 @@ gslope = function(data,
   scaled_precision_matrix = -cov2cor(precision_matrix)
   scaled_precision_matrix[abs(scaled_precision_matrix) < threshold] = 0
 
-  graph = graph_from_adjacency_matrix(scaled_precision_matrix,
+  graph = igraph::graph_from_adjacency_matrix(scaled_precision_matrix,
                                       mode = c("undirected"),
                                       weighted = TRUE,
                                       diag = FALSE,
@@ -116,7 +117,7 @@ gslope = function(data,
                 lambda = lambda,
                 iterations = ADMM_results[[2]],
                 graph = graph,
-                clusters = clusters(graph),
+                clusters = igraph::clusters(graph),
                 call = call)
   class(result) <- "gslope"
   result

R/plot.R

@@ -1,22 +1,10 @@
-#' @importFrom ggplot2 "ggplot"
-#' @importFrom ggplot2 "geom_tile"
-#' @importFrom ggplot2 "scale_fill_gradient"
-#' @importFrom ggplot2 "scale_fill_gradient2"
-#' @importFrom ggplot2 "coord_fixed"
-#' @importFrom ggplot2 "aes"
-#' @importFrom ggplot2 "ggtitle"
-#' @importFrom ggplot2 "xlab"
-#' @importFrom ggplot2 "ylab"
-#' @importFrom ggplot2 "theme"
-#' @importFrom ggplot2 "labs"
-#' @importFrom ggplot2 "element_text"
 
 #' @title Plot precision matrix
 #'
 #' @param x an object of class `'gslope'`
 #' @param col a character, color name. Default "black"
 #' @param plt a plot type. Accepts either \code{'precision'}, \code{'covariance'}, \code{'corr'} or \code{'scaled_precision'}. Default \code{'precision'}.
-#'
+#' @param ... Other parameters
 #' @return Prints output on the screen
 #'
 #' @examples
@@ -27,14 +15,16 @@
 
 #' @export
 
-plot <- function(x, plt, col){
+plot <- function(x, plt, col, ...){
   UseMethod('plot')
 }
 
 #' @rdname plot
+#' @param ... Other parameters
 #' @export
 #'
-plot.gslope = function(x, plt = "scaled_precision", col = "black"){
+plot.gslope = function(x, plt = "scaled_precision", col = "black", ...){
+  Y = value = NULL
 
   if(!(plt %in% c("precision", "corr", "scaled_precision", "covariance"))) stop("Plt must be either precision, covariance, corr or scaled_precision")