Title: Tools to Read, Analyze and Visualize Metadynamics HILLS Files
Authors@R: person("Vojtech", "Spiwok", email = "spiwokv@vscht.cz",
Description: Metadynamics is a state of the art biomolecular simulation technique.
'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes
it possible to perform metadynamics using various simulation codes. The results of
metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package
'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package.
It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037>
to calculate a free energy surface from hills. Minima can be located and plotted on
the free energy surface. Transition states can be analyzed by Nudged Elastic Band
method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy
surfaces, minima and transition paths can be plotted to produce publication quality
Author: Vojtech Spiwok [aut, cre] (<https://orcid.org/0000-0001-8108-2033>)

Title: Tools to Read, Analyze and Visualize Metadynamics 3D HILLS Files
Depends: R (>= 3.3.0), metadynminer, rgl
As an addendum, 'metadynaminer3d' is used to visualize 3D hills. It uses
a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037>
the free energy surface. Free energy surfaces and minima can be plotted to produce

Title: Metapopulation simulations for conserving salmon through
Authors@R: c(person(c("Sean", "C."), "Anderson", email =
"sean@seananderson.ca", role = c("aut", "cre")),
person(c("Jonathan", "W."), "Moore", role = "ctb"),
person(c("Michelle", "M."), "McClure", role = "ctb"),
person(c("Nicholas", "K."), "Dulvy", role = "ctb"),
person(c("Andrew", "B."), "Cooper", role = "ctb"))
Description: The metafolio R package is a tool to simulate salmon
metapopulations and apply financial portfolio optimization concepts. The
package accompanies the paper 'Portfolio conservation of metapopulations
under climate change'. See citation("metafolio").
Imports: Rcpp (>= 0.11.2), plyr, colorspace, MASS
Suggests: knitr, devtools, TeachingDemos, RColorBrewer, reshape2
Packaged: 2014-07-10 05:35:22 UTC; seananderson