Correcting warning and errors

USCCANA · Nov 30, 2022 · df68caa · df68caa
1 parent 666ad47
commit df68caa
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6  1,6 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.22.4
 Version: 1.22.5
 Authors@R: c(
   person("George", "Vega Yon", email="[email protected]", role=c("aut", "cre"),
     comment=c(ORCID = "0000-0002-3171-0844", what="Rewrite functions with Rcpp, plus new features")
@@ -50,7  50,7 @@ Suggests:
     survival
 VignetteBuilder: knitr
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 7.2.1
 RoxygenNote: 7.2.2
 Encoding: UTF-8
 URL: https://github.com/USCCANA/netdiffuseR,
  https://USCCANA.github.io/netdiffuseR/

diff --git a/NAMESPACE b/NAMESPACE
@@ -43,6  43,14 @@ S3method(ftable,diffnet_adopters)
 S3method(hist,diffnet_bootnet)
 S3method(hist,diffnet_struct_test)
 S3method(image,diffnet_diffmap)
 S3method(is_multiple,default)
 S3method(is_multiple,diffnet)
 S3method(is_self,default)
 S3method(is_self,diffnet)
 S3method(is_undirected,default)
 S3method(is_undirected,diffnet)
 S3method(is_valued,default)
 S3method(is_valued,diffnet)
 S3method(plot,diffnet)
 S3method(plot,diffnet_adopters)
 S3method(plot,diffnet_bass)
@@ -118,6  126,10 @@ export(hazard_rate)
 export(igraph_to_diffnet)
 export(igraph_vertex_rescale)
 export(infection)
 export(is_multiple)
 export(is_self)
 export(is_undirected)
 export(is_valued)
 export(isolated)
 export(leader_matching)
 export(matrix_compare)

diff --git a/NEWS.md b/NEWS.md
@@ -1,8  1,19 @@
 # Changes in netdiffuseR version 1.22.5 (2022-11-30)
 
 * Solved warning and errors reported by CRAN before the package was archived.
 
 * New S3 generic functions `is_self`, `is_multiple`, `is_valued`, and
   `is_undirected` allow querying graph information for some methods.
 
 * Fixed bug in `diag_expand`. Graphs with self ties were not transformed correctly
   (diagonals were excluded.)
 
 
 # Changes in netdiffuseR version 1.22.4 (2022-09-16)
 
 * Replaced `getMethod("t"...)` by `t` responding to changes in the
   `Matrix` package.
-
   
 
 # Changes in netdiffuseR version 1.22.1 (2021-05-27)
 

diff --git a/R/bass.r b/R/bass.r
@@ -61,7  61,8 @@
 #'
 #' @references
 #' Bass's Basement Institute Institute. The Bass Model. (2010).
-#' Available at: \url{http://www.bassbasement.org/BassModel/Default.aspx}. (Accessed: 29th March 2017)
 #' Available at: \url{https://web.archive.org/web/20220331222618/http://www.bassbasement.org/BassModel/}.
 #' (accessed live for the last time on March 29th, 2017.)
 #' @name bass
 #' @author George G. Vega Yon
 #' @family statistics

diff --git a/R/diffnet-methods.r b/R/diffnet-methods.r
@@ -1699,3  1699,78 @@ dim.diffnet <- function(x) {
   as.integer(with(x$meta, c(n, k, nper)))
 }
 
 #' @rdname diffnet-class
 #' @details The function `is_undirected` returns TRUE if the network is marked
 #' as undirected. In the case of `diffnet` objects, this information is stored
 #' in the `meta` element as `undirected`. The default method is to try to find
 #' an attribute called `undirected`, i.e., `attr(x, "undirected")`, if no
 #' attribute is found, then the function returns `FALSE`.
 #'
 #' The functions `is_self`, `is_valued`, and `is_multiple` work exactly the same
 #' as `is_undirected`. `diffnet` networks are not valued.
 #' @export
 is_undirected <- function(x) UseMethod("is_undirected")
 
 #' @export
 #' @rdname diffnet-class
 is_undirected.diffnet <- function(x) x$meta$undirected
 
 #' @export
 #' @rdname diffnet-class
 is_undirected.default <- function(x) {
   und <- attr(x, "undirected", exact = TRUE)
   if (!length(und))
     return(FALSE)
   und
 }
 
 #' @export
 #' @rdname diffnet-class
 is_self <- function(x) UseMethod("is_self")
 
 #' @export
 #' @rdname diffnet-class
 is_self.diffnet <- function(x) x$meta$self
 
 #' @export
 #' @rdname diffnet-class
 is_self.default <- function(x) {
   und <- attr(x, "self", exact = TRUE)
   if (!length(und))
     return(FALSE)
   und
 }
 
 #' @export
 #' @rdname diffnet-class
 is_multiple <- function(x) UseMethod("is_multiple")
 
 #' @export
 #' @rdname diffnet-class
 is_multiple.diffnet <- function(x) x$meta$multiple
 
 #' @export
 #' @rdname diffnet-class
 is_multiple.default <- function(x) {
   und <- attr(x, "multiple", exact = TRUE)
   if (!length(und))
     return(FALSE)
   und
 }
 
 #' @export
 #' @rdname diffnet-class
 is_valued <- function(x) UseMethod("is_valued")
 
 #' @export
 #' @rdname diffnet-class
 is_valued.diffnet <- function(x) return(FALSE)
 
 #' @export
 #' @rdname diffnet-class
 is_valued.default <- function(x) {
   und <- attr(x, "valued", exact = TRUE)
   if (!length(und))
     return(FALSE)
   und
 }
diff --git a/R/random_graph.R b/R/random_graph.R
@@ -176,7  176,14 @@ NULL
 
 #' @export
 #' @rdname rgraph_ba
-rgraph_ba <- function(m0=1L, m=1L, t=10L, graph=NULL, self=TRUE, eta=NULL) {
 rgraph_ba <- function(
     m0    = 1L,
     m     = 1L,
     t     = 10L,
     graph = NULL,
     self  = TRUE,
     eta   = NULL
     ) {
 
   # Eta should be numeric vector
   if (length(eta)) {

diff --git a/R/rdiffnet.r b/R/rdiffnet.r
@@ -153,6  153,7 @@ rdiffnet_make_threshold <- function(x, n) {
 }
 
 rdiffnet_check_seed_graph <- function(seed.graph, rgraph.args, t, n) {
 
   test <- class(seed.graph)
 
   if ("function" %in% test) {
@@ -337,7  338,6 @@ rdiffnet <- function(
   # Checking the class of the seed.graph
   sgraph <- rdiffnet_check_seed_graph(seed.graph, rgraph.args, t, n)
 
-
   # Checking baseline graph --------------------------------------------------
   meta <- classify_graph(sgraph)
 

diff --git a/R/spatial.R b/R/spatial.R
@@ -20,9  20,12 @@
 #' @export
 diag_expand <- function(...) UseMethod("diag_expand")
 
-.diag_expand <- function(graph, nper,
-                                self=getOption("diffnet.self"),
-                                valued=getOption("diffnet.valued")) {
 .diag_expand <- function(
   graph,
   nper,
   self   = getOption("diffnet.self"),
   valued = getOption("diffnet.valued")
   ) {
 
   # Checking class
   meta <- classify_graph(graph)
@@ -66,32  69,48 @@ diag_expand <- function(...) UseMethod("diag_expand")
 
 #' @export
 #' @rdname diag_expand
-diag_expand.list <- function(graph, self=getOption("diffnet.self"),
-                                valued=getOption("diffnet.valued"), ...) {
 diag_expand.list <- function(
     graph,
     self   = is_self(graph),
     valued = is_valued(graph),
     ...
     ) {
   .diag_expand(graph, length(graph), self, valued)
 }
 
 
 #' @export
 #' @rdname diag_expand
-diag_expand.diffnet <- function(graph, self=getOption("diffnet.self"),
-                                valued=getOption("diffnet.valued"), ...) {
 diag_expand.diffnet <- function(
     graph,
     self   = is_self(graph),
     valued = is_valued(graph),
     ...
     ) {
   .diag_expand(graph$graph, graph$meta$nper, self, valued)
 }
 
 #' @export
 #' @rdname diag_expand
-diag_expand.matrix <- function(graph, nper, self=getOption("diffnet.self"),
-                            valued=getOption("diffnet.valued"), ...) {
 diag_expand.matrix <- function(
     graph,
     nper,
     self   = is_self(graph),
     valued = is_valued(graph),
     ...) {
 
   .diag_expand(list(methods::as(graph, "dgCMatrix")), nper, self, valued)
 }
 
 
 #' @export
 #' @rdname diag_expand
-diag_expand.array <- function(graph, self=getOption("diffnet.self"),
-                              valued=getOption("diffnet.valued"), ...) {
 diag_expand.array <- function(
     graph,
     self   = is_self(graph),
     valued = is_valued(graph),
     ...
     ) {
 
   graph <- apply(graph, 3, function(x) methods::as(x, "dgCMatrix"))
   diag_expand(graph, nslices(graph), self, valued)
@@ -100,8  119,12 @@ diag_expand.array <- function(graph, self=getOption("diffnet.self"),
 
 #' @export
 #' @rdname diag_expand
-diag_expand.dgCMatrix <- function(graph, nper, self=getOption("diffnet.self"),
-                               valued=getOption("diffnet.valued"), ...) {
 diag_expand.dgCMatrix <- function(
     graph,
     nper,
     self   = is_self(graph),
     valued = is_valued(graph),
     ...) {
 
   .diag_expand(list(graph), nper, self, valued)
 }
diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3  1,14 @@
 Changes in netdiffuseR version 1.22.5 (2022-11-30)
 
 -   Solved warning and errors reported by CRAN before the package was
     archived.
 
 -   New S3 generic functions is_self, is_multiple, is_valued, and
     is_undirected allow querying graph information for some methods.
 
 -   Fixed bug in diag_expand. Graphs with self ties were not transformed
     correctly (diagonals were excluded.)
 
 Changes in netdiffuseR version 1.22.4 (2022-09-16)
 
 -   Replaced getMethod("t"...) by t responding to changes in the Matrix

diff --git a/man/bass.Rd b/man/bass.Rd
diff --git a/man/diag_expand.Rd b/man/diag_expand.Rd