For some reason which I cannot understand the package cannot be installed. The usual error I get is:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'htmltools' 0.3.6 is already loaded, but >= 0.4.0 is required
Calls: ... asNamespace -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'nonlinearTseries'

Hi there,
I would very much like to check this R package out, but I'm running into trouble with loading it into R on my Mac. I'm able to install the package into my R library (I've checked that it is there in the '.libPaths()' directory), but when I try to load it into my workspace, it never loads. I've tried in Rgui and and I don't get an error, just the unresponsive wheel banner. In Rstudio, all I get is the following warning, but it remains "running" and basically unresponsive.

library(nonlinearTseries)
Registered S3 method overwritten by 'htmlwidgets':
method from
print.htmlwidget tools:rstudio

What are the other packages 'nonlinearTseries' depends on? Perhaps I need to install those first?

Thank you.
Any insight you can give would be helpful,
Alison

Hi, there,

Thanks for the incredibly helpful package! I noticed that estimateEmbeddingDim returns a 0 when there is no suitable embedding dimension below the chosen maximum. Would it be possible to shift this so that it gives something else (e.g., NA) instead? I'd happily submit a PR to address it, if you'd like.

Cheers,
Alex

Hello,

interesting project you work on, I might have a silly question about your build_takens implementation why do you need to maintain an extra local set of indexes when you could just compute them on the fly?

NumericMatrix build_takens(
	  const NumericVector & timeSeries
	, size_t embeddingDimension
	, size_t timeLag
) {
	size_t maxJump        = (embeddingDimension - 1) * timeLag;
	size_t nTakensVectors = timeSeries.size() - maxJump;
	NumericMatrix takensSpace(
		  nTakensVectors
		, embeddingDimension
	);
	for (size_t i = 0; i < nTakensVectors; i++) {
		for (size_t j = 0; j < embeddingDimension; j++){
			takensSpace(i, j) = timeSeries[i + (j * timeLag)];
		}
	}
	return takensSpace;
}

I am trying to run a simple rqa using nonlinearTseries in R using version 0.2.12 of the library

a <- c(1,2,1,2,1,2)
a.rqa <- rqa(time.series = a, embedding.dim = 1, time.lag = 1, radius = .1)

While I never had any issue with this in the past, I noticed that since I upgraded the library to 0.2.12 I have an error:

Error in validObject(r) :
invalid class “nsTMatrix” object: uplo="U" but there are entries below the diagonal

I know other colleagues are having the same issue

I also tried removing the library and downgrading it to 0.2.5 (the one that worked), but the C++ compiler (‘Apple clang version 14.0.0 (clang-1400.0.29.102)’) returns the following error:

require(remotes)
install_version("nonlinearTseries", dependencies = TRUE, version = "0.2.5", repos = "https://cran.ma.imperial.ac.uk/")

....

clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -IANN -DRANN -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c neighbour_search_wrapper.cpp -o neighbour_search_wrapper.o
neighbour_search_wrapper.cpp:8:25: error: no member named 'bind2nd' in namespace 'std'
std::bind2nd(std::plus(), 1));
~~~~~^
1 error generated.
make: *** [neighbour_search_wrapper.o] Error 1
ERROR: compilation failed for package ‘nonlinearTseries’

• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/nonlinearTseries’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/0z/nw3d1p6x2c78rd6pg3rlh5dr0000gn/T//RtmpoLcdh3/remotes4a603cc634c1/nonlinearTseries’ had non-zero exit status

Any idea how to either fix the error in the current version or help me reinstall the old one?

Thanks!

Dear Constantino,

I am wondering if you are aware of publications that used nonlinearTseries.
Can you share those references? It would be helpful to add a section in the
README.md called "portfolio of publications used nonlinearTseries.
Additionally, it would be useful that you provide information about
the citation of nonlinearTseries package. Something like this:

  @Manual{,
    title = {nonlinearTseries: Nonlinear Time Series Analysis},
    author = {Constantino A. Garcia and Gunther Sawitzki},
    year = {2016},
    note = {R package version 0.2.4 --- For new features, see the 'Changelog' file (in the package source)},
 }

NB. I can pull a request for the README if you update the previous information.

Kind regards,
Miguel