R (>= 3.5.0), ade4, adegraphics, adephylo, ape, phylobase

Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
ade4, adegraphics, adephylo, ape, cluster, methods, phylobase,
phylosignal, phytools, rgl, FactoMineR

ade4, adegraphics, adephylo, ape, cluster, methods, phylobase,
phytools, rgl, FactoMineR

ade4, adegraphics, adephylo, ape, cluster, FactoMineR,
graphics, grDevices, lpSolve, methods, phylobase, phytools,
rgl, stats, utils

ade4, adegraphics, ape, cluster, graphics, grDevices, lpSolve,
methods, phylobase, phytools, rgl, stats, utils

Computes Sensitivity at a Fix Value of Specificity and Vice
Versa
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.

Computing Sensitivity at a Fix Value of Specificity and Vice
Versa

Parameter and Adjusted Probability Estimation for Right-Censored
Data
c(person("Manoj","Khanal",email="themanoj2008@gmail.com",role=c("aut","cre")),
person("Kwang Woo","Ahn",email="kwooahn@mcw.edu",role=c("aut","ths")),
person("Soyoung Kim",email="skim@mcw.edu",role="ctb") )
Manoj Khanal [aut, cre],
Kwang Woo Ahn [aut, ths],
Soyoung Kim [ctb]
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.