Prepare CRAN submission:

- update version number
- Add S3 exports
- Remove C++11 from makevars

.Rbuildignore

@@ -8,3 +8,4 @@ README.md
 ^cran-comments.md
 ^doc$
 ^Meta$
+.github

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: nonlinearTseries
 Type: Package
 Title: Nonlinear Time Series Analysis
-Version: 0.2.13
-Date: 2022-3-28
+Version: 0.3.0
+Date: 2024-4-1
 Maintainer: Constantino A. Garcia <constantino.garciama@ceu.es>
 Authors@R: c(person("Constantino A.", "Garcia",
                     email = "constantino.garciama@ceu.es",
@@ -40,5 +40,5 @@ Suggests:
     rmarkdown,
     testthat
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Encoding: UTF-8

NAMESPACE

@@ -8,6 +8,7 @@ S3method(corrMatrix,corrDim)
 S3method(divTime,maxLyapunov)
 S3method(divergence,maxLyapunov)
 S3method(embeddingDims,corrDim)
+S3method(embeddingDims,default)
 S3method(embeddingDims,infDim)
 S3method(embeddingDims,maxLyapunov)
 S3method(embeddingDims,sampleEntropy)
@@ -18,7 +19,10 @@ S3method(estimate,maxLyapunov)
 S3method(estimate,sampleEntropy)
 S3method(fixedMass,infDim)
 S3method(fluctuationFunction,dfa)
+S3method(freq,spectrogram)
+S3method(getAlpha,spectralIndex)
 S3method(getContourLines,spaceTimePlot)
+S3method(getHurst,spectralIndex)
 S3method(logRadius,infDim)
 S3method(nlOrder,corrDim)
 S3method(nlOrder,sampleEntropy)
@@ -30,13 +34,20 @@ S3method(plot,mutualInf)
 S3method(plot,rqa)
 S3method(plot,sampleEntropy)
 S3method(plot,spaceTimePlot)
+S3method(plot,spectralIndex)
+S3method(plot,spectrogram)
 S3method(plot,surrogateTest)
 S3method(plotLocalScalingExp,corrDim)
 S3method(plotLocalScalingExp,infDim)
 S3method(print,corrDim)
 S3method(radius,corrDim)
+S3method(radius,default)
 S3method(radius,sampleEntropy)
 S3method(sampleEntropyFunction,sampleEntropy)
+S3method(spectrogram,default)
+S3method(spectrogram,ts)
+S3method(spectrogram,zoo)
+S3method(time,spectrogram)
 S3method(windowSizes,dfa)
 export(FFTsurrogate)
 export(buildTakens)

R/generics.R

@@ -32,6 +32,7 @@ embeddingDims = function(x){
   UseMethod("embeddingDims")
 }
 
+#' @export
 embeddingDims.default = function(x){
   x$embedding.dims
 }
@@ -50,6 +51,7 @@ radius = function(x){
   UseMethod("radius")
 }
 
+#' @export
 radius.default = function(x){
   x$radius
 }

R/spectralIndex.R

@@ -45,7 +45,7 @@ spectralIndexObject = function(fit, spec) {
   spectral_index_fit
 }
 
-# @export
+#' @export
 plot.spectralIndex = function(x, type = "l", log = "xy", 
                               ylab = "spectrum", xlab = "normalized frequency",
                               ...) {
@@ -59,13 +59,12 @@ plot.spectralIndex = function(x, type = "l", log = "xy",
 }
 
 
-# @export
 getHurst = function(x) {
   UseMethod("getHurst")
 }
 
 
-# @export
+#' @export
 getHurst.spectralIndex = function(x) {
   beta = x$spectral_index_fit[[1]]
   Hs = c(H_fgn = NA, H_fbm = NA)
@@ -78,12 +77,11 @@ getHurst.spectralIndex = function(x) {
   Hs
 }
 
-# @export
 getAlpha = function(x) {
   UseMethod("getAlpha")  
 }
 
-# @export 
+#' @export 
 getAlpha.spectralIndex = function(x) {
   (x$spectral_index_fit[[1]] + 1) / 2
 }

R/spectral_functions.R

@@ -1,14 +1,11 @@
-# @export
 hamming = function(n, alpha = 0.54, beta = 0.46){
   alpha - beta * cospi (2 * (0:(n - 1)) / (n - 1))
 }
 
-# @export
 hanning = function(n) {
   0.5 * (1 - cospi( 2* (0:(n - 1)) / (n - 1)))
 }
 
-# @export
 blackman = function(n, alpha = 0.16) {
   a0 = (1 - alpha) / 2
   a1 = 1 / 2
@@ -19,12 +16,11 @@ blackman = function(n, alpha = 0.16) {
 
 
 #' @import zoo
-# @export
-spectrogram = function(x, ...){
+spectrogram = function(x, width, by, pad = 0){
   UseMethod("spectrogram")
 }
 
-# @export
+#' @export
 spectrogram.default = function(x, width, by, pad = 0) {
   if (width < 2) {
     stop("width must be >= 2")
@@ -47,21 +43,21 @@ spectrogram.default = function(x, width, by, pad = 0) {
   spec
 }
 
-# @export
+#' @export
 spectrogram.ts = function(x, width, by, pad = 0) {
   spec = spectrogram(as.numeric(x), width = width, by = by, pad = pad)
   attr(spec,"freq") = attr(spec,"freq") * frequency(x)
   attr(spec, "time") = attr(spec, "time") / frequency(x) 
   spec
 }
 
-# @export
+#' @export
 spectrogram.zoo = function(x, width, by, pad = 0) {
   spectrogram.ts(as.ts(x), width = width, by = by, pad = pad)
 }
 
 
-# @export
+#' @export
 plot.spectrogram = function(x, color.palette = terrain.colors, 
                             xlab = "Time", ylab = "Frequency(Hz)",
                             main = "Spectrogram", 
@@ -77,17 +73,16 @@ plot.spectrogram = function(x, color.palette = terrain.colors,
                  zlim = zlim, ...)
 }
 
-# @export
-time.spectrogram = function(x) {
+#' @export
+time.spectrogram = function(x, ...) {
   attr(x, "time")  
 }
 
-# @export
 freq = function(x){
   UseMethod("freq")
 }
 
-# @export
+#' @export
 freq.spectrogram = function(x){
   attr(x, "freq")  
 }

src/Makevars

@@ -1,3 +1,2 @@
-CXX_STD=CXX11
 PKG_CPPFLAGS=-I. -IANN -DRANN
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,3 +1,2 @@
-CXX_STD=CXX11
 PKG_LIBS=-lws2_32 $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 PKG_CPPFLAGS=-I. -IANN -O3 -DWIN32 -DDLL_EXPORTS -DANN_NO_RANDOM -DRANN