Updating documentation and preparing for release

USCCANA · May 20, 2021 · a15928b · a15928b
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -36,3  36,4 @@ makefile
 ^_pkgdown\.yml$
 ^netdiffuseR\.tar\.gz$
 ^\.github
 netdiffuseR\.Rcheck
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -52,7  52,7 @@ LinkingTo: Rcpp, RcppArmadillo
 RoxygenNote: 7.1.1
 Encoding: UTF-8
 URL: https://github.com/USCCANA/netdiffuseR,
- https://USCCANA.github.io/netdiffuseR
  https://USCCANA.github.io/netdiffuseR/
 BugReports: https://github.com/USCCANA/netdiffuseR/issues
 Classification/MSC: 90C35, 90B18, 91D30
 Collate: 

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -209,7  209,7 @@ rgraph_er_cpp <- function(n = 10L, p = 0.3, undirected = TRUE, weighted = FALSE,
 #' @return A sparse matrix of class \code{\link[Matrix:dgCMatrix-class]{dgCMatrix}} of size
 #' \eqn{n\times n}{n * n}.
 #' @references Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of
-#' “small-world” networks. Nature, 393(6684), 440–2. \url{http://doi.org/10.1038/30918}
 #' “small-world” networks. Nature, 393(6684), 440–2. \doi{10.1038/30918}
 #' @export
 #' @family simulation functions
 ring_lattice <- function(n, k, undirected = FALSE) {

diff --git a/R/random_graph.R b/R/random_graph.R
@@ -23,7  23,7 @@
 #' networks are uncorrelated.
 #' @references
 #' Barabasi, Albert-Laszlo. "Network science book" Retrieved November 1 (2015)
-#' \url{http://barabasi.com/book/network-science}.
 #' \url{https://barabasi.com/book/network-science}.
 #' @return A graph represented by an adjacency matrix (if \code{t=1}), or an array of
 #' adjacency matrices (if \code{t>1}).
 #' @export

diff --git a/R/rewire.r b/R/rewire.r
@@ -134,7  134,7 @@
 #' Milo, R., Kashtan, N., Itzkovitz, S., Newman, M. E. J., & Alon, U.
 #' (2004). On the uniform generation of random graphs with prescribed degree sequences.
 #' Arxiv Preprint condmat0312028, cond-mat/0, 1–4. Retrieved from
-#' \url{http://arxiv.org/abs/cond-mat/0312028}
 #' \url{https://arxiv.org/abs/cond-mat/0312028}
 #'
 #' Ray, J., Pinar, A., and Seshadhri, C. (2012).
 #' Are we there yet? When to stop a Markov chain while generating random graphs.
@@ -358,7  358,7 @@ rewire_graph.array <-function(graph, p, algorithm, both.ends, self, multiple, un
 #'
 #' Mantel, N. (1967). The detection of disease clustering and a generalized
 #' regression approach. Cancer Research, 27(2), 209–20.
-#' \url{http://cancerres.aacrjournals.org/content/27/2_Part_1/209}
 #' \url{https://cancerres.aacrjournals.org/content/27/2_Part_1/209}
 #'
 #' @seealso This function can be used as null distribution in \code{struct_test}
 #' @family simulation functions

diff --git a/man/permute_graph.Rd b/man/permute_graph.Rd
diff --git a/man/rewire_graph.Rd b/man/rewire_graph.Rd
diff --git a/man/rgraph_er.Rd b/man/rgraph_er.Rd
diff --git a/man/ring_lattice.Rd b/man/ring_lattice.Rd
diff --git a/src/rgraph.cpp b/src/rgraph.cpp
@@ -83,7  83,7 @@ arma::sp_mat rgraph_er_cpp(
 //' @return A sparse matrix of class \code{\link[Matrix:dgCMatrix-class]{dgCMatrix}} of size
 //' \eqn{n\times n}{n * n}.
 //' @references Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of
-//' “small-world” networks. Nature, 393(6684), 440–2. \url{http://doi.org/10.1038/30918}
 //' “small-world” networks. Nature, 393(6684), 440–2. \doi{10.1038/30918}
 //' @export
 //' @family simulation functions
 // [[Rcpp::export]]