popgraph: 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.

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

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

Functions

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 Man page
popgraph-package Man page
read.popgraph Man page
test_congruence Man page
theme_empty 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
to_SpatialLines Man page
to_SpatialPoints 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

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

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

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