Applying CRAN changes

.Rbuildignore

@@ -34,3 +34,4 @@ makefile
 ^docs$
 ^LICENSE\.md$
 ^_pkgdown\.yml$
+^netdiffuseR\.tar\.gz$

.travis.yml

@@ -2,15 +2,19 @@ dist: trusty
 language: r
 sudo: false
 
-r:
-  - release
-  - oldrel
-
-os:
-  - linux
-  - osx
-
-osx_image: xcode7.3
+matrix:
+include:
+  - os: linux
+    r: oldrel
+  - os: linux
+    r: release
+    env:
+      - R_CODECOV=true
+      - BUILD_WWW_HERE=true
+  - os: linux
+    r: devel
+  - os: osx
+    osx_image: xcode10.2
 
 env:
  global:
@@ -36,3 +40,13 @@ notifications:
   email:
     on_success: change
     on_failure: change
+
+# For automatic deploy of the website
+before_deploy: Rscript -e 'remotes::install_cran("pkgdown")'
+deploy:
+  provider: script
+  script: Rscript -e 'pkgdown::deploy_site_github()'
+  skip_cleanup: true
+  on:
+    branch: master
+    condition: $BUILD_WWW_HERE = true

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.20.2
-Date: 2019-03-25
+Version: 1.20.999
+Date: 2020-02-03
 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")
@@ -49,7 +49,7 @@ Suggests:
     survival
 VignetteBuilder: knitr
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Encoding: UTF-8
 URL: https://github.com/USCCANA/netdiffuseR,
  https://USCCANA.github.io/netdiffuseR

R/adjmat.r

@@ -465,12 +465,16 @@ toa_mat <- function(obj, labels=NULL, t0=NULL, t1=NULL) {
     if (!length(t1)) t1 <- max(obj, na.rm = TRUE)
   }
 
-  ans <- switch(class(obj),
-    numeric = toa_mat.numeric(obj, labels, t0, t1),
-    integer = toa_mat.integer(obj, labels, t0, t1),
-    diffnet = with(obj, list(adopt=adopt,cumadopt=cumadopt)),
-    stopifnot_graph(obj)
-  )
+  cls <- class(obj)
+  ans <- if ("numeric" %in% cls) {
+    toa_mat.numeric(obj, labels, t0, t1)
+    } else if ("integer" %in% cls) {
+    toa_mat.integer(obj, labels, t0, t1)
+    } else if  ("diffnet" %in% cls) {
+    with(obj, list(adopt=adopt,cumadopt=cumadopt))
+    } else
+      stopifnot_graph(obj)
+
 
   if (inherits(obj, "diffnet")) {
     dimnames(ans$adopt) <- with(obj$meta, list(ids,pers))

R/diffnet-methods.r

@@ -1525,16 +1525,22 @@ as.array.diffnet <- function(x, ...) {
 #' nedges(graph_mat)
 #' nedges(graph_dgCMatrix)
 nvertices <- function(graph) {
-  switch(class(graph),
-         array     = nrow(graph),
-         matrix    = nrow(graph),
-         dgCMatrix = nrow(graph),
-         list      = nrow(graph[[1]]),
-         diffnet   = graph$meta$n,
-         igraph    = igraph::vcount(graph),
-         network   = network::network.size(graph),
-         stopifnot_graph(graph)
-         )
+
+  cls <- class(graph)
+
+  if (any(c("array", "matrix", "dgCMatrix") %in% cls)) {
+    nrow(graph)
+  } else if ("list" %in% cls) {
+    nrow(graph[[1]])
+  } else if ("diffnet" %in% cls) {
+    graph$meta$n
+  } else if ("igraph" %in% cls) {
+    igraph::vcount(graph)
+  } else if ("network" %in% cls) {
+    network::network.size(graph)
+  } else
+    stopifnot_graph(graph)
+
 }
 
 #' @rdname nvertices
@@ -1544,32 +1550,41 @@ nnodes <- nvertices
 #' @export
 #' @rdname nvertices
 nedges <- function(graph) {
-  switch (class(graph),
-    array     = {
-      # Computing and coercing into a list
-      x <- as.list(apply(graph, 3, function(x) sum(x!=0)))
-
-      # Naming
-      tnames <- names(x)
-      if (!length(tnames)) names(x) <- 1:length(x)
-      x
-      },
-    matrix    = sum(graph != 0),
-    dgCMatrix = length(graph@i),
-    list      = {
-      # Computing
-      x <- lapply(graph, function(x) length(x@i))
-
-      # Naming
-      tnames <- names(x)
-      if (!length(tnames)) names(x) <- 1:length(x)
-      x
-      },
-    diffnet   = lapply(graph$graph, function(x) sum(x@x != 0)),
-    igraph    = igraph::ecount(graph),
-    network   = network::network.edgecount(graph),
+
+  cls <- class(graph)
+
+  if ("matrix" %in% cls) {
+    sum(graph != 0)
+  } else if ("array" %in% cls) {
+    # Computing and coercing into a list
+    x <- as.list(apply(graph, 3, function(x) sum(x!=0)))
+
+    # Naming
+    tnames <- names(x)
+    if (!length(tnames)) names(x) <- 1:length(x)
+    x
+
+  } else if ("dgCMatrix" %in% cls) {
+    length(graph@i)
+  } else if ("list" %in% cls) {
+
+    # Computing
+    x <- lapply(graph, function(x) length(x@i))
+
+    # Naming
+    tnames <- names(x)
+    if (!length(tnames)) names(x) <- 1:length(x)
+    x
+
+  } else if ("diffnet" %in% cls) {
+    lapply(graph$graph, function(x) sum(x@x != 0))
+  } else if ("igraph" %in% cls) {
+    igraph::ecount(graph)
+  } else if ("network" %in% cls) {
+    network::network.edgecount(graph)
+  } else
     stopifnot_graph(graph)
-  )
+
 }
 
 #' @export
@@ -1579,14 +1594,22 @@ nlinks <- nedges
 #' @export
 #' @rdname nvertices
 nslices <- function(graph) {
-  switch (class(graph),
-    array     = dim(graph)[3],
-    matrix    = 1L,
-    dgCMatrix = 1L,
-    diffnet   = graph$meta$nper,
-    list      = length(graph),
+
+  cls <- class(graph)
+
+  if ("matrix" %in% cls) {
+    1L
+  } else if ("array" %in% cls)  {
+    dim(graph)[3]
+  } else if ("dgCMatrix" %in% cls)  {
+    1L
+  } else if ("diffnet" %in% cls)  {
+    graph$meta$nper
+  } else if ("list" %in% cls) {
+    length(graph)
+  } else
     stopifnot_graph(graph)
-  )
+
 }
 
 #' @export

R/egonets.R

@@ -167,9 +167,10 @@ egonet_attrs <- function(
            1, " and ", nnodes(graph), ".")
   }
 
-  switch(
-    class(graph),
-    diffnet  = egonet_attrs.list(
+  cls <- class(graph)
+
+  if ("diffnet" %in% cls) {
+    egonet_attrs.list(
       graph  = graph$graph,
       attrs  = attrs,
       V      = V,
@@ -179,8 +180,9 @@ egonet_attrs <- function(
       self   = self,
       valued = valued,
       ...
-      ),
-    list     = egonet_attrs.list(
+    )
+  } else if ("list" %in% cls) {
+    egonet_attrs.list(
       graph  = graph,
       attrs  = attrs,
       V      = V,
@@ -190,8 +192,9 @@ egonet_attrs <- function(
       self   = self,
       valued = valued,
       ...
-      ),
-    matrix    = egonet_attrs.matrix(
+    )
+  } else if ("matrix" %in% cls) {
+    egonet_attrs.matrix(
       graph  = as_spmat(graph),
       attrs  = attrs,
       V      = V,
@@ -201,8 +204,9 @@ egonet_attrs <- function(
       self   = self,
       valued = valued,
       ...
-      ),
-    dgCMatrix = egonet_attrs.matrix(
+    )
+  } else if ("dgCMatrix" %in% cls) {
+    egonet_attrs.matrix(
       graph  = graph,
       attrs  = attrs,
       V      = V,
@@ -212,8 +216,9 @@ egonet_attrs <- function(
       self   = self,
       valued = valued,
       ...
-      ),
-    array     = egonet_attrs.array(
+    )
+  } else if ("array" %in% cls) {
+    egonet_attrs.array(
       graph  = graph,
       attrs  = attrs,
       V      = V,
@@ -223,9 +228,10 @@ egonet_attrs <- function(
       self   = self,
       valued = valued,
       ...
-      ),
+    )
+  } else
     stopifnot_graph(graph)
-  )
+
 }
 
 egonet_attrs.matrix <- function(graph, attrs, V, outer, fun, as.df, self, valued, ...) {

_pkgdown.yml

@@ -0,0 +1,4 @@
+template:
+  params:
+    ganalytics: UA-40608305-5
+

makefile

@@ -1,11 +1,15 @@
-news:
+netdiffuseR.tar.gz: */*.R
+	rm netdiffuseR.tar.gz ; \
+	R CMD build . && \
+		mv netdiffuseR*.tar.gz netdiffuseR.tar.gz
+
+inst/NEWS: NEWS.md
 	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
 	head -n 80 inst/NEWS
-check:
-	cd ..&&R CMD build netdiffuseR/ && \
-		R CMD check --as-cran netdiffuseR*.tar.gz
+check: netdiffuseR.tar.gz
+	R CMD check --as-cran netdiffuseR.tar.gz
 
-checkv:
+checkv: netdiffuseR.tar.gz
 	cd ..&&R CMD build netdiffuseR/ && \
 		R CMD check --as-cran --use-valgrind netdiffuseR*.tar.gz