A Tool for Landscape and Range Expansion Simulation

Biobase, e1071, fgui, grDevices, graphics, googleVis,
maptools, rgeos, rgrass7, raster

Landscape and Range Expansion Simulation
Biobase, e1071, fgui, grDevices, graphics, googleVis,
maptools, rgeos, rgrass7, raster, spatstat, stats, sp,
minpack.lm

e1071, fgui, grDevices, graphics, googleVis, maptools, rgeos,
rgrass7, raster, spatstat, stats, sp, minpack.lm, zipfR

e1071, fgui, grDevices, graphics, googleVis, maptools, rgeos,
rgrass7, raster, spatstat, stats, sp, minpack.lm, zipfR, coda,
knitr
Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita,
Antonio Mira, Pedro Beja.

e1071, fgui, grDevices, graphics, googleVis, maptools, rgeos,
rgrass7, raster, spatstat.geom, spatstat.random, stats, sp,
minpack.lm, zipfR, coda, knitr
Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change). References: Mestre, F., Canovas, F., Pita, R.,
Mira, A., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>; Mestre, F.,
Risk, B., Mira, A., Beja, P., Pita, R. (2017)
<doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R., Mira, A., Beja,
P. (2020) <doi:10.1186/s12898-019-0273-5>.

e1071, fgui, grDevices, graphics, googleVis, maptools, rgeos,
rgrass7, raster, spatstat.geom, spatstat.core, stats, sp,
minpack.lm, zipfR, coda, knitr

Metagenomics Longitudinal Differential Abundant Method
Ahmed Metwally, Patricia Finn, Yang Dai, David Perkins
Identify the time intervals when the microbial features are
differentially abundant between two phenotypic groups using negative binomial
smoothing spline ANOVA (Ahmed Metwally, Patricia Finn, Yang Dai, David Perkins, ACM BCB’17).
ggplot2, gss, plyr, caTools, parallel, doParallel

Metagenomics Longitudinal Differential Abundance Method
Identify time intervals of differentially abundant metagenomic features in longitudinal studies <doi:10.1145/3107411.3107429>.
ggplot2, gss, plyr, caTools, parallel, doParallel,
metagenomeSeq, DESeq2, edgeR