popgraph: This is an R package that constructs and manipulates population graphs.

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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.

Author
Rodney J. Dyer
Date of publication
2014-06-03 01:34:35
Maintainer
Rodney J. Dyer <rjdyer@vcu.edu>
License
GPL (>= 2)
Version
1.4

View on CRAN

Man pages

alt
Sonoran desert altitude.
arapat_mv
Araptus attenuatus data
arapat_pop
Arapat popualtion data
as.popgraph
Converts an object of type matrix or igraph into 'popgraph'
baja
Metadata for Baja Populations.
centroid_distance
This function takes a data set and a group set and returns...
centroid_variance
This function takes a data set and a group set and returns...
congruence_topology
Returns congruence topology
decorate_graph
Merge data into popgraph node-wise
geom_edgelabels
Plotting of a population graph edge labels using ggplot...
geom_edgeset
Plotting of a population graph edge set using ggplot neumonic
geom_nodeset
Plotting of a population graph edge set using ggplot neumonic
lopho
Lophocereus population graph
overlay_popgraph
Convience function to plot edges from 'popgraph'
permute_popgraph
Bootstraps indiviudals to see stability of graph topology.
popgraph
Default constructor for a 'PopulationGraph' object
popgraph-operator-minus
Overload '-' operator for pairs of 'popgraph' objects
popgraph-package
Package for the creation of population graph objects
read.popgraph
Reads in a population graph text file
test_congruence
Returns distance congruence between the two graphs
theme_empty
A blank theme for plotting networks
to_data.frame
Converts 'popgraph' to 'data.frame' based upon node...
to_html
Converts population graph to html file for interactive...
to_json
Converts to json representation
to_kml
Converts population graph to KML file
to_matrix
Matrix conversion for Population Graph
to_pgraph
Converts graph to a pgraph file format
to_SpatialLines
Converts edge set to SpatialLines object
to_SpatialPoints
Translate object into a SpatialPoints object
upiga
Upiga population graph
write_popgraph
Convience function for file exports

Files in this package

popgraph
popgraph/inst
popgraph/inst/tests
popgraph/inst/tests/test-popgraph.R
popgraph/inst/tests/test-to_json.R
popgraph/inst/tests/test-to_kml.R
popgraph/inst/tests/test-ops_popgraph.R
popgraph/inst/tests/test-to_matrix.R
popgraph/inst/tests/test-overlay_popgraph.R
popgraph/inst/tests/test-to_html.R
popgraph/inst/tests/test-to_pgraph.R
popgraph/inst/tests/test-as_popgraph.R
popgraph/inst/tests/test-congruence_topology.R
popgraph/inst/tests/test-to_SpatialLines.R
popgraph/inst/tests/test-write_popgraph.R
popgraph/inst/tests/test-read_popgraph.R
popgraph/inst/tests/test-to_SpatialPoints.R
popgraph/inst/tests/test-decorate_popgraph.R
popgraph/inst/tests/test-bootstrap_popgraph.R
popgraph/inst/tests/test-test_congruence.R
popgraph/inst/extdata
popgraph/inst/extdata/d3footer.html
popgraph/inst/extdata/lopho.pgraph
popgraph/inst/extdata/arapat_pops.rda
popgraph/inst/extdata/arapat_mv.rda
popgraph/inst/extdata/d3header.html
popgraph/tests
popgraph/tests/run-testthat-popgraph.R
popgraph/NAMESPACE
popgraph/NEWS
popgraph/data
popgraph/data/upiga.rda
popgraph/data/lopho.rda
popgraph/data/baja.rda
popgraph/data/alt.rda
popgraph/R
popgraph/R/to_data.frame.R
popgraph/R/geom_edgeset.R
popgraph/R/geom_edgelabels.R
popgraph/R/centroid_variance.R
popgraph/R/theme_empty.R
popgraph/R/test_congruence.R
popgraph/R/to_kml.R
popgraph/R/to_SpatialLines.R
popgraph/R/as_popgraph.R
popgraph/R/centroid_distance.R
popgraph/R/to_pgraph.R
popgraph/R/to_html.R
popgraph/R/to_json.R
popgraph/R/write_popgraph.R
popgraph/R/permute_popgraph.R
popgraph/R/geom_nodeset.R
popgraph/R/overlay_popgraph.R
popgraph/R/ops_popgraph.R
popgraph/R/to_SpatialPoints.R
popgraph/R/congruence_topology.R
popgraph/R/to_matrix.R
popgraph/R/popgraph-package.R
popgraph/R/decorate_graph.R
popgraph/R/popgraph.R
popgraph/R/read_popgraph.R
popgraph/vignettes
popgraph/vignettes/Popgraph.tex
popgraph/MD5
popgraph/DESCRIPTION
popgraph/man
popgraph/man/popgraph-operator-minus.Rd
popgraph/man/popgraph-package.Rd
popgraph/man/geom_edgelabels.Rd
popgraph/man/to_data.frame.Rd
popgraph/man/lopho.Rd
popgraph/man/congruence_topology.Rd
popgraph/man/permute_popgraph.Rd
popgraph/man/arapat_mv.Rd
popgraph/man/to_SpatialLines.Rd
popgraph/man/geom_edgeset.Rd
popgraph/man/baja.Rd
popgraph/man/centroid_variance.Rd
popgraph/man/to_pgraph.Rd
popgraph/man/decorate_graph.Rd
popgraph/man/geom_nodeset.Rd
popgraph/man/overlay_popgraph.Rd
popgraph/man/to_html.Rd
popgraph/man/centroid_distance.Rd
popgraph/man/to_json.Rd
popgraph/man/test_congruence.Rd
popgraph/man/to_kml.Rd
popgraph/man/write_popgraph.Rd
popgraph/man/as.popgraph.Rd
popgraph/man/upiga.Rd
popgraph/man/popgraph.Rd
popgraph/man/theme_empty.Rd
popgraph/man/arapat_pop.Rd
popgraph/man/to_SpatialPoints.Rd
popgraph/man/to_matrix.Rd
popgraph/man/read.popgraph.Rd
popgraph/man/alt.Rd