phytools, subplex, Matrix, expoRkit, SparseM

Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>.
Finally, DDD contains a function to simulate the diversity-dependent process.

Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>.
Also contains functions to simulate the diversity-dependent process.

phytools, subplex, Matrix, expoRkit, SparseM, pracma

phytools, subplex, Matrix, expm, SparseM, pracma, testthat

deSolve, ape, phytools, subplex, Matrix, expm, SparseM,
testthat
Implements maximum likelihood and bootstrap methods based on
the diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent, under various
models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
<DOI:10.1098/rspb.2011.1439>,
Etienne & Haegeman 2012, Am. Nat. 180: E75-E89,
<DOI:10.1086/667574> and
Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099,
<DOI:10.1111/2041-210X.12565>.
Also contains functions to simulate the diversity-dependent
process.

deSolve, ape, phytools, subplex, Matrix, expm, SparseM

deSolve, ape, phytools, subplex, Matrix, expm, SparseM, Rcpp
(>= 1.0.5)

Variance Stabilization by Data-Driven Haar-Fisz (for Microarrays)
Efthimios S. Motakis, Guy P. Nason, Piotr Fryzlewicz
The package contains the normalizing and variance stabilizing
Data-Driven Haar-Fisz algorithm. Also contains related algorithms
for simulating from certain microarray gene intensity models and
evaluation of certain transformations.