popgraph: This is an R package that constructs and manipulates population graphs.
Version 1.4

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.

AuthorRodney J. Dyer
Date of publication2014-06-03 01:34:35
MaintainerRodney J. Dyer <rjdyer@vcu.edu>
LicenseGPL (>= 2)
Version1.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("popgraph")

Getting started

Package overview

Popular man pages

alt: Sonoran desert altitude.
centroid_variance: This function takes a data set and a group set and returns...
decorate_graph: Merge data into popgraph node-wise
lopho: Lophocereus population graph
overlay_popgraph: Convience function to plot edges from 'popgraph'
popgraph-operator-minus: Overload '-' operator for pairs of 'popgraph' objects
popgraph-package: Package for the creation of population graph objects
See all...

All man pages Function index File listing

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

Functions

-.popgraph Man page
alt Man page
arapat_mv Man page
arapat_pop Man page
as.popgraph Man page
baja Man page
centroid_distance Man page
centroid_variance Man page
congruence_topology Man page
decorate_graph Man page
geom_edgelabels Man page
geom_edgeset Man page
geom_nodeset Man page
lopho Man page
overlay_popgraph Man page
permute_popgraph Man page
popgraph Man page
popgraph-package Man page
read.popgraph Man page
test_congruence Man page
theme_empty Man page
to_SpatialLines Man page
to_SpatialPoints Man page
to_data.frame Man page
to_html Man page
to_json Man page
to_kml Man page
to_matrix Man page
to_pgraph Man page
upiga Man page
write_popgraph Man page

Files

inst
inst/tests
inst/tests/test-popgraph.R
inst/tests/test-to_json.R
inst/tests/test-to_kml.R
inst/tests/test-ops_popgraph.R
inst/tests/test-to_matrix.R
inst/tests/test-overlay_popgraph.R
inst/tests/test-to_html.R
inst/tests/test-to_pgraph.R
inst/tests/test-as_popgraph.R
inst/tests/test-congruence_topology.R
inst/tests/test-to_SpatialLines.R
inst/tests/test-write_popgraph.R
inst/tests/test-read_popgraph.R
inst/tests/test-to_SpatialPoints.R
inst/tests/test-decorate_popgraph.R
inst/tests/test-bootstrap_popgraph.R
inst/tests/test-test_congruence.R
inst/extdata
inst/extdata/d3footer.html
inst/extdata/lopho.pgraph
inst/extdata/arapat_pops.rda
inst/extdata/arapat_mv.rda
inst/extdata/d3header.html
tests
tests/run-testthat-popgraph.R
NAMESPACE
NEWS
data
data/upiga.rda
data/lopho.rda
data/baja.rda
data/alt.rda
R
R/to_data.frame.R
R/geom_edgeset.R
R/geom_edgelabels.R
R/centroid_variance.R
R/theme_empty.R
R/test_congruence.R
R/to_kml.R
R/to_SpatialLines.R
R/as_popgraph.R
R/centroid_distance.R
R/to_pgraph.R
R/to_html.R
R/to_json.R
R/write_popgraph.R
R/permute_popgraph.R
R/geom_nodeset.R
R/overlay_popgraph.R
R/ops_popgraph.R
R/to_SpatialPoints.R
R/congruence_topology.R
R/to_matrix.R
R/popgraph-package.R
R/decorate_graph.R
R/popgraph.R
R/read_popgraph.R
vignettes
vignettes/Popgraph.tex
MD5
DESCRIPTION
man
man/popgraph-operator-minus.Rd
man/popgraph-package.Rd
man/geom_edgelabels.Rd
man/to_data.frame.Rd
man/lopho.Rd
man/congruence_topology.Rd
man/permute_popgraph.Rd
man/arapat_mv.Rd
man/to_SpatialLines.Rd
man/geom_edgeset.Rd
man/baja.Rd
man/centroid_variance.Rd
man/to_pgraph.Rd
man/decorate_graph.Rd
man/geom_nodeset.Rd
man/overlay_popgraph.Rd
man/to_html.Rd
man/centroid_distance.Rd
man/to_json.Rd
man/test_congruence.Rd
man/to_kml.Rd
man/write_popgraph.Rd
man/as.popgraph.Rd
man/upiga.Rd
man/popgraph.Rd
man/theme_empty.Rd
man/arapat_pop.Rd
man/to_SpatialPoints.Rd
man/to_matrix.Rd
man/read.popgraph.Rd
man/alt.Rd
popgraph documentation built on April 14, 2017, 9:58 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.