Imports: ade4, adegraphics, adephylo, ape, cluster, FactoMineR,
graphics, grDevices, lpSolve, methods, phylobase, phytools,
Packaged: 2021-09-27 13:19:55 UTC; SandrineP

Packaged: 2022-05-20 08:15:39 UTC; SandrineP

Packaged: 2021-08-21 13:31:19 UTC; SandrineP

Imports: ade4, adegraphics, ape, cluster, graphics, grDevices, lpSolve,
methods, phylobase, phytools, rgl, stats, utils
Packaged: 2022-10-06 11:06:06 UTC; SandrineP

Title: Computes Sensitivity at a Fix Value of Specificity and Vice
Maintainer: E. F. Haghish <haghish@uio.no>
Description: For a binary classification the adjusted sensitivity and specificity are measured for a given fixed threshold. If the threshold for either sensitivity or specificity is not given, the crossing point between the sensitivity and specificity curves are returned.
Packaged: 2022-03-21 11:53:45 UTC; U-Shaped-Valley

Title: Computing Sensitivity at a Fix Value of Specificity and Vice
Packaged: 2022-03-23 09:54:22 UTC; U-Shaped-Valley

Title: Parameter and Adjusted Probability Estimation for Right-Censored
Description: Functions in this package fit a stratified Cox proportional hazards and a proportional subdistribution hazards model by extending Zhang et al., (2007) <doi: 10.1016/j.cmpb.2007.07.010>
and Zhang et al., (2011) <doi: 10.1016/j.cmpb.2010.07.005> respectively to clustered right-censored data. The functions also provide the estimates of the cumulative baseline hazard along with their standard errors. Furthermore, the adjusted survival and cumulative incidence probabilities are also provided along with their standard errors. Finally, the estimate of cumulative incidence and survival probabilities given a vector of covariates along with their standard errors are also provided.
Packaged: 2021-12-14 15:09:48 UTC; manojkhanal

Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Description: 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
Imports: Matrix, matrixStats, snpStats, methods, utils, HiTC,
Suggests: BiocStyle, knitr, testthat, rmarkdown, rioja