This is an R package that constructs and manipulates population
graphs.
This is a generic package that produces "Population
Graphs" a graph-theoretic topology based upon conditional
genetic covariance.  This functionality used to be within the
gstudio package, but has been taken out to focus on spatial
integration of graph topologies with existing packages like sp,
raster, and ggplot2.
'congruence_topology.R' 'decorate_popgraph.R'
'population_graph.R' 'test_congruence.R' 'centroid_distance.R'
'to_html.R' 'to_kml.R' 'popgraph-package.R' 'to_json.R'
'to_matrix.R' 'to_SpatialLines.R' 'to_SpatialPoints.R'
'as_population_graph.R' 'centroid_variance.R'
'read_population_graph.R' 'to_pgraph.R'
'write_population_graph.R' 'overlay_population_graph.R'

This is a generic package that produces "Population Graphs"
a graph-theoretic topology based upon conditional genetic covariance.  This
functionality used to be within the gstudio package, but has been taken out
to focus on spatial integration of graph topologies with existing packages
like sp, raster, and ggplot2.
'as_popgraph.R' 'centroid_distance.R' 'centroid_variance.R'
'congruence_topology.R' 'decorate_graph.R' 'geom_edgeset.R'
'geom_nodeset.R' 'ops_popgraph.R' 'overlay_popgraph.R'
'popgraph-package.R' 'popgraph.R' 'read_popgraph.R'
'test_congruence.R' 'theme_empty.R' 'to_SpatialLines.R'
'to_SpatialPoints.R' 'to_data.frame.R' 'to_html.R' 'to_json.R'
'to_kml.R' 'to_matrix.R' 'to_pgraph.R' 'write_popgraph.R'

Estimate Kinship and FST under Arbitrary Population Structure
Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index).  Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
Rcpp (>= 0.12.10), RColorBrewer, graphics
BEDMatrix, testthat, knitr, rmarkdown, lfa

Rcpp (>= 0.12.10), RColorBrewer, graphics, grDevices

Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index).  Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.
Rcpp (>= 0.12.10), RColorBrewer, graphics, grDevices, ape
BEDMatrix, testthat, knitr, rmarkdown, lfa, bnpsd