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SOM Bound to Realize Euclidean and Relational Outputs

The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)

Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation

Infer log-linear Poisson Graphical Model with an auxiliary data
set. Hot-deck multiple imputation method is used to improve the reliability
of the inference with an auxiliary dataset. Standard log-linear Poisson
graphical model can also be used for the inference and the Stability
Approach for Regularization Selection (StARS) is implemented to drive the
selection of the regularization parameter. The method is fully described in

Select Intervals Suited for Functional Regression

Interval fusion and selection procedures for regression with
functional inputs. Methods include a semiparametric approach based
on Sliced Inverse Regression (SIR), as described in

Monazite Dating for the NiLeDAM Team

Th-U-Pb electron microprobe age dating of monazite, as originally
described in

Omics Data Integration Using Kernel Methods

Kernel-based methods are powerful methods for integrating
heterogeneous types of data. mixKernel aims at providing methods to combine
kernel for unsupervised exploratory analysis. Different solutions are
provided to compute a meta-kernel, in a consensus way or in a way that
best preserves the original topology of the data. mixKernel also integrates
kernel PCA to visualize similarities between samples in a non linear space
and from the multiple source point of view

Testing Differences Between Families of Trees

Perform test to detect differences in structure between families of trees. The method is based on cophenetic distances and aggregated Student's tests.

Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix

Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and only
adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Ambroise et al (2019)

Inverse Probability of Censoring Weights to Deal with Treatment Switch in Randomized Clinical Trials

Contains functions for formatting clinical trials data and implementing inverse probability of censoring weights to handle treatment switches when estimating causal treatment effect in randomized clinical trials.

Weighted Cox-Regression for Nested Case-Control Data

Fit Cox proportional hazard models with a weighted
partial likelihood. It handles one or multiple endpoints, additional matching
and makes it possible to reuse controls for other endpoints
Stoer NC and Samuelsen SO (2016)

Excess Hazard Modelling Considering Inappropriate Mortality Rates

Fits relative survival regression models with or without proportional excess hazards and with the additional possibility to correct for background mortality by one or more parameter(s). These models are relevant when the observed mortality in the studied group is not comparable to that of the general population or in population-based studies where the available life tables used for net survival estimation are insufficiently stratified. In the latter case, the proposed model by Touraine et al. (2020)