Model-based methods for the detection of disease clusters
using GLMs, GLMMs and zero-inflated models. These methods are described
in 'V. Gómez-Rubio et al.' (2019) <doi:10.18637/jss.v090.i14> and
'V. Gómez-Rubio et al.' (2018) <doi:10.1007/978-3-030-01584-8_1>.

INLA, pscl, RColorBrewer, gridExtra, latticeExtra

DDD 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. 2011, Proc. Roy. Soc. B, doi: 10.1098/rspb.2011.1439

DDD 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. 2011, Proc. Roy. Soc. B, doi: 10.1098/rspb.2011.1439 New
in version 0.3: models with shifts in the parameters at a time
tshift

DDD 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. 2011, Proc. Roy. Soc. B, doi: 10.1098/rspb.2011.1439.

DDD 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.  DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence.  See Etienne & Haegeman
2012, Am. Nat. In press.

DDD 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.  DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence.  See Etienne & Haegeman
2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.

BB, Rcgmin, Rvmmin, minqa, numDeriv, ucminf

DDD 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.  DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence.  See Etienne & Haegeman
2012, Am. Nat. In press, doi: 10.1086/667574.