Simulating Multistate Movements in River/Heterogeneous
Landscapes
Provides functions to generate and analyze spatially-explicit individual-based multistate movements in rivers,
heterogeneous and homogeneous spaces. This is done by incorporating landscape bias on local behaviour, based on
resistance rasters. Although originally conceived and designed to simulate trajectories of species constrained to
linear habitats/dendritic ecological networks (e.g. river networks), the simulation algorithm is built to be
highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism, independently on the
landscape in which it moves. Thus, the user will be able to use the package to simulate movements either in
homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using
the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input
parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as
mechanistic null models (Potts & Lewis 2014, <DOI:10.1098/rspb.2014.0231>) to test a variety of 'Movement Ecology'
hypotheses (Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), including landscape effects (e.g. resources,
infrastructures) on animal movement and species site fidelity, or for predictive purposes (e.g. road mortality risk,
dispersal/connectivity). The package should be relevant to explore a broad spectrum of ecological phenomena, such as
those at the interface of animal behaviour, management, landscape and movement ecology, disease and invasive species
spread, and population dynamics.

A Phylogenetic Simulator for Reticulate Evolution
c(person("Joshua", "Justison", email = "justisnojo@gmail.com", role = c("aut", "cre","cph")),
person(c("Claudia","Solis-Lemus"), role=c("aut","cph")),
person(c("Tracy","A."), "Heath", role=c("aut","cph")),
person("Klaus", "Schliep", role = c("cph"), comment = c("modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder")),
person("Emmanuel", "Paradis", role = c("cph"), comment = c("modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder")),
person("Daniel", "Lawson", role = c("cph"), comment = c("modified code from ape in 'write.net.R' and 'read.net.R'. Crediting original copyright holder"))
)
A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.
Joshua Justison [aut, cre, cph],
Claudia Solis-Lemus [aut, cph],
Tracy A. Heath [aut, cph],
Klaus Schliep [cph] (modified code from ape in 'write.net.R' and
'read.net.R'. Crediting original copyright holder),
Emmanuel Paradis [cph] (modified code from ape in 'write.net.R' and
'read.net.R'. Crediting original copyright holder),
Daniel Lawson [cph] (modified code from ape in 'write.net.R' and
'read.net.R'. Crediting original copyright holder)