nloptr - R Interface to NLopt

Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.

Last updated 5 months ago

16.80 score 105 stars 1.7k packages 960 scripts 437k downloads

roahd - Robust Analysis of High Dimensional Data

A collection of methods for the robust analysis of univariate and multivariate functional data, possibly in high-dimensional cases, and hence with attention to computational efficiency and simplicity of use. See the R Journal publication of Ieva et al. (2019) <doi:10.32614/RJ-2019-032> for an in-depth presentation of the 'roahd' package. See Aleman-Gomez et al. (2021) <arXiv:2103.08874> for details about the concept of depthgram.

Last updated 3 years ago

6.28 score 2 stars 2 packages 159 scripts 283 downloads

fdacluster - Joint Clustering and Alignment of Functional Data

Implementations of the k-means, hierarchical agglomerative and DBSCAN clustering methods for functional data which allows for jointly aligning and clustering curves. It supports functional data defined on one-dimensional domains but possibly evaluating in multivariate codomains. It supports functional data defined in arrays but also via the 'fd' and 'funData' classes for functional data defined in the 'fda' and 'funData' packages respectively. It currently supports shift, dilation and affine warping functions for functional data defined on the real line and uses the SRSF framework to handle boundary-preserving warping for functional data defined on a specific interval. Main reference for the k-means algorithm: Sangalli L.M., Secchi P., Vantini S., Vitelli V. (2010) "k-mean alignment for curve clustering" <doi:10.1016/j.csda.2009.12.008>. Main reference for the SRSF framework: Tucker, J. D., Wu, W., & Srivastava, A. (2013) "Generative models for functional data using phase and amplitude separation" <doi:10.1016/j.csda.2012.12.001>.

Last updated 9 months ago

6.03 score 5 stars 1 packages 24 scripts 377 downloads

flipr - Flexible Inference via Permutations in R

A flexible permutation framework for making inference such as point estimation, confidence intervals or hypothesis testing, on any kind of data, be it univariate, multivariate, or more complex such as network-valued data, topological data, functional data or density-valued data.

Last updated 1 years ago

5.76 score 6 stars 1 packages 16 scripts 240 downloads

nevada - Network-Valued Data Analysis

A flexible statistical framework for network-valued data analysis. It leverages the complexity of the space of distributions on graphs by using the permutation framework for inference as implemented in the 'flipr' package. Currently, only the two-sample testing problem is covered and generalization to k samples and regression will be added in the future as well. It is a 4-step procedure where the user chooses a suitable representation of the networks, a suitable metric to embed the representation into a metric space, one or more test statistics to target specific aspects of the distributions to be compared and a formula to compute the permutation p-value. Two types of inference are provided: a global test answering whether there is a difference between the distributions that generated the two samples and a local test for localizing differences on the network structure. The latter is assumed to be shared by all networks of both samples. References: Lovato, I., Pini, A., Stamm, A., Vantini, S. (2020) "Model-free two-sample test for network-valued data" <doi:10.1016/j.csda.2019.106896>; Lovato, I., Pini, A., Stamm, A., Taquet, M., Vantini, S. (2021) "Multiscale null hypothesis testing for network-valued data: Analysis of brain networks of patients with autism" <doi:10.1111/rssc.12463>.

Last updated 1 years ago

4.40 score 5 stars 3 scripts 150 downloads

rgeomstats - Interface to 'Geomstats'

Provides an interface to the Python package 'Geomstats' authored by Miolane et al. (2020) <arXiv:2004.04667>.

Last updated 2 years ago

3.78 score 4 stars 1 packages 5 scripts 178 downloads

midi - Microstructure Information from Diffusion Imaging

An implementation of a taxonomy of models of restricted diffusion in biological tissues parametrized by the tissue geometry (axis, diameter, density, etc.). This is primarily used in the context of diffusion magnetic resonance (MR) imaging to model the MR signal attenuation in the presence of diffusion gradients. The goal is to provide tools to simulate the MR signal attenuation predicted by these models under different experimental conditions. The package feeds a companion 'shiny' app available at <https://midi-pastrami.apps.math.cnrs.fr> that serves as a graphical interface to the models and tools provided by the package. Models currently available are the ones in Neuman (1974) <doi:10.1063/1.1680931>, Van Gelderen et al. (1994) <doi:10.1006/jmrb.1994.1038>, Stanisz et al. (1997) <doi:10.1002/mrm.1910370115>, Soderman & Jonsson (1995) <doi:10.1006/jmra.1995.0014> and Callaghan (1995) <doi:10.1006/jmra.1995.1055>.

Last updated 6 months ago

3.75 score 1 stars 14 scripts 126 downloads

distops - Usual Operations for Distance Matrices in R

It provides the subset operator for dist objects and a function to compute medoid(s) that are fully parallelized leveraging the 'RcppParallel' package. It also provides functions for package developers to easily implement their own parallelized dist() function using a custom 'C++'-based distance function.

Last updated 10 months ago

3.48 score 2 stars 3 scripts 159 downloads

squat - Statistics for Quaternion Temporal Data

An implementation of statistical tools for the analysis of rotation-valued time series and functional data. It relies on pre-existing quaternion data structure provided by the 'Eigen' 'C++' library.

Last updated 11 months ago

3.00 score 2 stars 5 scripts 152 downloads