version 0.7.0

cran · Jul 20, 2022 · 6884316 · 6884316
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: netassoc
 Type: Package
 Title: Inference of Species Associations from Co-Occurrence Data
-Version: 0.6.3
-Date: 2017-06-04
+Version: 0.7.0
+Date: 2022-07-20
 Author: Benjamin Blonder, Naia Morueta-Holme
-Maintainer: Benjamin Blonder <bblonder@gmail.com>
+Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
 Description: Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods. 
 License: GPL-3
 Depends: igraph, infotheo
 Imports: corpcor, huge, vegan
 NeedsCompilation: no
-Packaged: 2017-06-05 18:08:49 UTC; benjaminblonder
+Packaged: 2022-07-20 08:37:07 UTC; benjaminblonder
 Repository: CRAN
-Date/Publication: 2017-06-05 21:44:46 UTC
+Date/Publication: 2022-07-20 14:30:12 UTC
diff --git a/MD5 b/MD5
@@ -1,13 +1,13 @@
-23103a8691754dc69b42f7d56a901a59 *DESCRIPTION
+751c5ad35b48386295dd9807e29e5aef *DESCRIPTION
 5277b9b96cb92ab68ec6bc142e3b0eb4 *NAMESPACE
 c39460d085cf3ce914cf94344b1f47c3 *R/generate_nul_resample.R
 0da717e3c3000fa8d3c0549220db32c0 *R/make_netassoc_network.R
 7b95b8c6278534ba92d0d10d054c829e *R/pairwise_association.R
 e488d1659f38e75ae04bf4beadb7a723 *R/partial_correlation.R
-0ce37ad1bcd9a0de4ee01bb565d04f47 *R/plot.R
+b0f183c5bcab928a7c653cfed155e560 *R/plot.R
 e37052ada824878367e60059827bfc2f *man/make_netassoc_network.Rd
 8f11cf7649b395ffd95a9d9eb3afd309 *man/netassoc-package.Rd
 93226c98aac9dc52931e74d962f4fa5e *man/pairwise_association.Rd
 04ed50d71962306786218a6b3a336a81 *man/partial_correlation.Rd
 b533e6b2c50de93c38845bb5833d404e *man/plot_netassoc_matrix.Rd
-4f5ff85ce0e4f9ab4738fd8423da502c *man/plot_netassoc_network.Rd
+dedab9c256bdc1c9e55bb3458c925a1d *man/plot_netassoc_network.Rd
diff --git a/R/plot.R b/R/plot.R
@@ -1,6 +1,6 @@
 
 # plot network
-plot_netassoc_network <- function(network, layout = layout.fruchterman.reingold(network), 
+plot_netassoc_network <- function(network, layout = layout_nicely(network), 
                                   vertex.label = V(network)$name, 
                                   vertex.color = NA, 
                                   vertex.shape = "none",

diff --git a/man/plot_netassoc_network.Rd b/man/plot_netassoc_network.Rd
@@ -8,7 +8,7 @@ Plots species association network
 Draws a network of species associations. By default edge widths are proportional to association strength and edge color reflects association type (blue, positive; red, negative).
 }
 \usage{
-plot_netassoc_network(network, layout = layout.fruchterman.reingold(network), 
+plot_netassoc_network(network, layout = layout_nicely(network), 
   vertex.label = V(network)$name, 
   vertex.color = NA, 
   vertex.shape = "none",