Still working on cran release

ChangeLog

@@ -1,3 +1,10 @@
+2016-07-07  George G. Vega Yon <[email protected]>
+  * R/diffnet-indexing.R: Adding method for [[.diffnet <- NULL
+  * tests/testthat/*: Adding more tests + small changes to reduce time.
+
+2016-07-06  George G. Vega Yon <[email protected]>
+  * R/struc_test.R: Changing defaults in n_rewires.
+
 2016-06-26  George G. Vega Yon <[email protected]>
   * R/egonets.R: Fixing small bug on the matrix methods
   * R/diffnet-methods.R: No actual significant changes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: netdiffuseR
 Title: Network Analysis for Diffusion of Innovations
-Version: 1.16.6
-Date: 2016-06-21
+Version: 1.16.7
+Date: 2016-07-07
 Authors@R: c(
   person("George", "Vega Yon", email="[email protected]", role=c("aut", "cre"), comment="Rewrite functions with Rcpp, plus new features"),
   person("Stephanie", "Dyal", email="[email protected]", role=c("aut"), comment="Package's first version"),

NEWS.md

@@ -1,4 +1,4 @@
-# Changes in netdiffuseR version 1.16.6 (2016-06-21)
+# Changes in netdiffuseR version 1.16.7 (2016-07-07)
 
 ## Bug fixes
 

R/diffnet-indexing.R

@@ -317,7 +317,34 @@ diffnet_check_attr_class <- function(value, meta) {
   # Checking and preparing the data
   meta <- x$meta
   if (length(j) < meta$n) meta$n <- length(j)
-  value <- diffnet_check_attr_class(value, meta)
+  if (length(value)) value <- diffnet_check_attr_class(value, meta)
+  else {
+
+    if (i %in% colnames(x$vertex.static.attrs)) {
+
+      # Static case
+      tokeep <- colnames(x$vertex.static.attrs)
+      tokeep <- tokeep[which(tokeep != i)]
+      x$vertex.static.attrs <- subset(x$vertex.static.attrs, select=tokeep)
+      return(x)
+
+    } else if (i %in% colnames(x$vertex.dyn.attrs[[1]])) {
+
+      # Dynamic case
+      tokeep <- colnames(x$vertex.dyn.attrs[[1]])
+      tokeep <- tokeep[which(tokeep != i)]
+      x$vertex.dyn.attrs <-
+        lapply(x$vertex.dyn.attrs, subset, select=tokeep)
+      return(x)
+    } else {
+
+      # Nothing case
+      warning('There is no attribute called -',i,'-. Returning the diffnet intact.')
+      return(x)
+    }
+
+
+  }
 
   # Adding the attribute
   if (!inherits(value, "list")) {

R/struct_test.R

@@ -63,10 +63,10 @@
 #' @examples
 #' # Creating a random graph
 #' set.seed(881)
-#' diffnet <- rdiffnet(300, 5, seed.graph="small-world")
+#' diffnet <- rdiffnet(100, 5, seed.graph="small-world")
 #'
 #' # Testing structure-dependency of threshold
-#' res <- struct_test(diffnet, function(g) mean(threshold(g), na.rm=TRUE), R=50)
+#' res <- struct_test(diffnet, function(g) mean(threshold(g), na.rm=TRUE), R=100)
 #' res
 #' hist(res)
 #'

cran-comments.md

@@ -1,19 +1,18 @@
 ## Test environments
-* Local Ubuntu 14.04, R version 3.3.0 (2016-05-03)
-* Ubuntu 12.04.5 LTS (on travis-ci), R version 3.3.0 (2016-05-03).
-* Windows Server 2012 R2 x64 (on AppVeyor), R Under development (3.2.5 Patched (2016-04-18 r70556).
-* OS X 10.9.5 (Mavericks) (on travis-ci), R version 3.2.4 (2016-03-10).
+
+* Local Ubuntu 14.04, R version 3.3.1 (2016-06-21).
+* Ubuntu 12.04.5 LTS (on travis-ci), version 3.3.1 (2016-06-21).
+* Windows Server 2012 R2 x64 (on AppVeyor), R version 3.3.1 Patched (2016-06-28 r70858).
+* OS X 10.9.5 (Mavericks) (on travis-ci), R version 3.3.1 (2016-06-21).
 
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
 
+* Possible invalid URLs in man/rgraph_ws.Rd is false positive.
 * Install size > 1Mb in libs. Using Rcpp increases the size. Still, working on
   reducing it.
 * Also, possible mis-spelled words in DESCRIPTION have the correct spelling.
-* CRAN repository db overrides: X-CRAN-Comment: Archived on 2016-05-02 as ...
-  fixed (see below).
-* Possible invalid URLs in man/rgraph_ws.Rd is false positive.
 
 ## Reverse dependencies
 
@@ -23,13 +22,5 @@ There are no reverse dependencies.
 
 This is a resubmission. In this version I have:
 
-* Included rgb (grDevices), polygon (graphics) and setNames (stats) as importFrom
-  in the package's NAMESPACE.
-* Fixed the problem with "Vignette sources missing".
-* About "Memtest notes: clang-UBSAN valgrind", the issue was actually a bug in
-  RcppArmadillo. This has been solved in RcppArmadillo v 0.6.700.6.0 (which is
-  already on CRAN). R CMD check --use-valgrind no longer reports memory leaks
-  or 'Conditional jump...' issues.
-* Updated tests in testthat/*.R following the testthat package update (all passing).
-  (Fixed errors that caused CRAN archiving the previous version).
+* Reduced the times on examples, tests and vignettes as requested by CRAN.
 

inst/NEWS

@@ -1,6 +1,6 @@
 
 
-CHANGES IN NETDIFFUSER VERSION 1.16.6 (2016-06-21)
+CHANGES IN NETDIFFUSER VERSION 1.16.7 (2016-07-07)
 
 
 Bug fixes

tests/testthat/test-diffnet-methods.R

@@ -1,8 +1,6 @@
 context("Plotting functions 1 (plot_diffnet, threshold, and exposure)")
 
-################################################################################
-# plot_diffnet
-################################################################################
+# plot_diffnet -----------------------------------------------------------------
 
 test_that("Should return coords of dim n x 2 (plot_diffnet)", {
   # Creating the graph
@@ -28,9 +26,7 @@ test_that("Should return coords of dim n x 2 (plot_diffnet)", {
   expect_equal(dim(coords), c(11,2), info = "applying to diffnet")
 })
 
-################################################################################
-# plot_threshold, threshold and exposure
-################################################################################
+# plot_threshold, threshold and exposure ---------------------------------------
 
 test_that("Returning threshold equal to the threshold fun (plot_threshold and )", {
   # Generating a random graph
@@ -66,9 +62,8 @@ test_that("Returning threshold equal to the threshold fun (plot_threshold and )"
   expect_equivalent(th, thdn)
 })
 
-################################################################################
-# plot_infectsuscept, infection, susceptibility
-################################################################################
+# plot_infectsuscept, infection, susceptibility --------------------------------
+
 
 test_that("Returning threshold equal to the infect/suscept funs", {
   # Generating a random graph
@@ -129,3 +124,25 @@ test_that("summary.diffnet with slices", {
   }
 })
 
+# Concatenating diffnet --------------------------------------------------------
+test_that('concatenating diffnet', {
+
+  # Spliting and putting together
+  index <- medInnovationsDiffNet[['city']]<2
+  mi1 <- medInnovationsDiffNet[which(index)]
+  mi2 <- medInnovationsDiffNet[which(!index)]
+
+  mi <- c(mi1, mi2)
+  test <- all(mapply(identical, mi$graph, medInnovationsDiffNet$graph))
+
+  expect_true(test)
+
+  # Errors
+  expect_error(c(mi1, 1), 'Some objects are not of class')
+  expect_error(c(mi1, mi1), 'No pair of diffnets')
+  expect_error(c(mi1[,,1:4], mi2), 'same time range')
+  # mi1less <- mi1[['city']] <- NULL
+  # colnames(mi1less)
+  # expect_error(c())
+
+})

tests/testthat/test-stats.R

@@ -27,45 +27,45 @@ test_that("exposure calculations", {
   # expect_equivalent(exp_1_diffnet, exp_1_manual)
 })
 
-# test_that("Times of Adoption", {
-#   # Creating the data
-#   set.seed(13131)
-#   toa <- sample(c(NA, 1:10), 100, TRUE)
-#
-#   toa_mat2 <- function(
-#     times, labels=NULL,
-#     t0=min(times, na.rm=TRUE), t1=max(times, na.rm=TRUE)) {
-#
-#     # Counting number of rows
-#     n <- length(times)
-#
-#     # Checking names
-#     if (length(labels)) rn <- labels
-#     else {
-#       rn <- names(times)
-#       if (!length(rn)) rn <- 1:n
-#     }
-#
-#     cn <- t0:t1
-#
-#     # Computing
-#     m <- matrix(0, nrow=n, ncol= t1-t0 + 1, dimnames = list(rn, cn))
-#     m[cbind(cn, times - t0 + 1)] <- 1
-#     m <- list(adopt=m, cumadopt=t(apply(m, 1, cumsum)))
-#
-#     # Assigning names
-#     dimnames(m[[2]]) <- dimnames(m[[1]])
-#
-#     m
-#   }
-#
-#   expect_equal(toa_mat(toa), toa_mat2(toa))
-# #   library(microbenchmark)
-# #   tm1 <- toa_mat(toa)
-# #   tm2 <- toa_mat2(toa)
-# #
-# #   microbenchmark(
-# #     toa_mat(toa),
-# #     toa_mat2(toa), times = 1
-# #   )
-# })
+test_that("Times of Adoption", {
+  # Creating the data
+  set.seed(13131)
+  toa <- sample(c(NA, 1:10), 100, TRUE)
+
+  toa_mat2 <- function(
+    times, labels=NULL,
+    t0=min(times, na.rm=TRUE), t1=max(times, na.rm=TRUE)) {
+
+    # Counting number of rows
+    n <- length(times)
+
+    # Checking names
+    if (length(labels)) rn <- labels
+    else {
+      rn <- names(times)
+      if (!length(rn)) rn <- 1:n
+    }
+
+    cn <- t0:t1
+
+    # Computing
+    m <- matrix(0, nrow=n, ncol= t1-t0 + 1, dimnames = list(rn, cn))
+    m[cbind(rn, times - t0 + 1)] <- 1
+    m <- list(adopt=m, cumadopt=t(apply(m, 1, cumsum)))
+
+    # Assigning names
+    dimnames(m[[2]]) <- dimnames(m[[1]])
+
+    m
+  }
+
+  expect_equal(toa_mat(toa), toa_mat2(toa))
+  # library(microbenchmark)
+  # tm1 <- toa_mat(toa)
+  # tm2 <- toa_mat2(toa)
+  #
+  # microbenchmark(
+  #   toa_mat(toa),
+  #   toa_mat2(toa), times = 1000
+  # )
+})

tests/testthat/test-struct_test.R

@@ -19,6 +19,9 @@ test_that("struct_test should be reproducible (serial version)", {
 
 test_that("struct_test should be reproducible (parallel version)", {
 
+  # I don't want to run this test
+  skip_on_cran()
+
   # Generating data
   set.seed(1231)
   graph <- rdiffnet(150, 5, seed.graph = "small-world")
@@ -27,11 +30,11 @@ test_that("struct_test should be reproducible (parallel version)", {
   # RNG algorithm to be L'Ecuyer so the sequences can be reproduced
 
   N <- 100
-  set.seed(123, "L'Ecuyer-CMRG")
+  set.seed(123, "L'Ecuyer")
   b1 <- struct_test(graph, function(x) mean(threshold(x), na.rm = TRUE), R=N, ncpus=2,
                  parallel="multicore")
 
-  set.seed(123, "L'Ecuyer-CMRG")
+  set.seed(123, "L'Ecuyer")
   b2 <- struct_test(graph, function(x) mean(threshold(x), na.rm = TRUE), R=N, ncpus=2,
                  parallel="multicore")