Preparing CRAN release

.Rbuildignore

@@ -1,3 +1,4 @@
+^Meta$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^data-raw$

.gitignore

@@ -1,28 +1,24 @@
+Meta
+doc
 .Rproj.user
 .Rhistory
 .RData
 inst/doc
 
-
 # Binary files
 *.so
 *.o
 *.xls*
 *.doc*
 *.ppt*
-
 *.ods
-
 *.zip
 *.gz
 *.tar
-
 # Tempfiles
 *.dta
-*.ods
 *.log
 *.out
 *.tex
-
 playground/
 doc/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: netdiffuseR
 Title: Analysis of Diffusion and Contagion Processes on Networks
-Version: 1.20.0
-Date: 2018-06-06
+Version: 1.20.1
+Date: 2019-03-22
 Authors@R: c(
   person("George", "Vega Yon", email="g.vegayon@gmail.com", role=c("aut", "cre"),
     comment=c(ORCID = "0000-0002-3171-0844", what="Rewrite functions with Rcpp, plus new features")
@@ -39,7 +39,7 @@ Imports:
     utils,
     boot,
     igraph,
-    viridis
+    viridisLite
 Suggests:
     covr,
     testthat,
@@ -49,7 +49,7 @@ Suggests:
     survival
 VignetteBuilder: knitr
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 6.0.1.9000
+RoxygenNote: 6.1.1
 Encoding: UTF-8
 URL: https://github.com/USCCANA/netdiffuseR,
  https://USCCANA.github.io/netdiffuseR

NAMESPACE

@@ -250,6 +250,8 @@ importFrom(stats,var)
 importFrom(utils,getFromNamespace)
 importFrom(utils,head)
 importFrom(utils,str)
-importFrom(viridis,viridis_pal)
+importFrom(viridisLite,inferno)
+importFrom(viridisLite,magma)
+importFrom(viridisLite,viridis)
 importMethodsFrom(Matrix,t)
 useDynLib(netdiffuseR, .registration = TRUE)

NEWS.md

@@ -1,3 +1,17 @@
+# Changes in netdiffuseR version 1.20.1 (2019-03-22)
+
+* This version has no user level visible changes.
+
+## Other changes
+
+* Changing `PI` macros in C++ code as requested by RcppCore.
+
+* Setting 3.5 seed version for tests so that test won't break following message
+  from CRAN.
+
+
+
+
 # Changes in netdiffuseR version 1.20.0 (2018-06-06)
 
 ## New functions and features

R/diffnet-methods.r

@@ -957,7 +957,7 @@ plot_infectsuscep <- function(
   xlab          = "Infectiousness of ego",
   ylab          = "Susceptibility of ego",
   sub           = ifelse(logscale, "(in log-scale)", NA),
-  color.palette = viridis::viridis_pal(),
+  color.palette = function(n) viridisLite::viridis(n),
   include.grid  = TRUE,
   exclude.zeros = FALSE,
   valued        = getOption("diffnet.valued",FALSE),

R/imports.r

@@ -8,7 +8,7 @@ NULL
 #' @importFrom network as.edgelist is.multiplex is.directed has.loops as.network
 #'  get.network.attribute list.vertex.attributes
 #' @importFrom networkDynamic networkDynamic network.extract network.collapse
-#' @importFrom viridis viridis_pal
+#' @importFrom viridisLite viridis inferno magma
 NULL
 
 #' @useDynLib netdiffuseR, .registration = TRUE

R/misc.r

@@ -132,7 +132,7 @@ drawColorKey <- function(
   key.pos       = c(.925,.975,.05,.95),
   pos           = 2,
   nlevels       = length(tick.marks),
-  color.palette = viridis::viridis(nlevels),
+  color.palette = viridisLite::viridis(nlevels),
   tick.width    = c(.01,.0075),
   add.box       = TRUE,
   na.col        = NULL,

R/plot_diffnet2.r

@@ -95,7 +95,7 @@ plot_diffnet2.default <- function(
   graph,
   toa,
   pers          = min(toa, na.rm = TRUE):max(toa, na.rm = TRUE),
-  color.ramp    = grDevices::colorRamp(viridis::magma(20)),
+  color.ramp    = grDevices::colorRamp(viridisLite::magma(20)),
   layout        = NULL,
   key.width     = 0.1,
   key.args      = list(),

README.Rmd

@@ -163,7 +163,7 @@ data("medInnovationsDiffNet")
 set.seed(131)
 plot_threshold(
   medInnovationsDiffNet,
-  vertex.color     = viridis::inferno(4)[medInnovationsDiffNet[["city"]]],
+  vertex.color     = viridisLite::inferno(4)[medInnovationsDiffNet[["city"]]],
   vertex.sides     = medInnovationsDiffNet[["city"]] + 2,
   sub = "Note: Vertices' sizes and shapes given by degree and city respectively",
   jitter.factor = c(1,1), jitter.amount = c(.25,.025)
@@ -215,7 +215,7 @@ diffnet.toa(x) <- sample(x$toa, size = nnodes(x))
 dm1 <- diffusionMap(x, layout = dm0$coords, kde2d.args=list(n=150, h=.5))
 
 oldpar <- par(no.readonly = TRUE)
-col <- viridis::plasma(100)
+col <- viridisLite::plasma(100)
 par(mfrow=c(1,2), oma=c(1,0,0,0), cex=.8)
 image(dm0, col=col, main="Non-random Times of Adoption\nAdoption from the core.")
 image(dm1, col=col, main="Random Times of Adoption")
@@ -234,11 +234,11 @@ ftable(out)
 # Plotting 
 oldpar <- par(no.readonly = TRUE)
 par(xpd=TRUE)
-plot(out, color=viridis::inferno(5), las = 2, xlab="Time of Adoption",
+plot(out, color=viridisLite::inferno(5), las = 2, xlab="Time of Adoption",
      ylab="Threshold", main="")
 
 # Adding key
-legend("bottom", legend = levels(out$thr), fill=viridis::inferno(5), horiz = TRUE,
+legend("bottom", legend = levels(out$thr), fill=viridisLite::inferno(5), horiz = TRUE,
        cex=.6, bty="n", inset=c(0,-.1))
 par(oldpar)
 ```