version 0.6.3

cran · Jun 5, 2017 · 3c55434 · 3c55434
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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: 0.6.2
-Date: 2015-11-23
+Version: 0.6.3
+Date: 2017-06-04
 Author: Benjamin Blonder, Naia Morueta-Holme
 Maintainer: Benjamin Blonder <bblonder@gmail.com>
 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: rags2ridges, corpcor, huge, vegan
+Imports: corpcor, huge, vegan
 NeedsCompilation: no
-Packaged: 2015-11-23 21:40:00 UTC; benjaminblonder
+Packaged: 2017-06-05 18:08:49 UTC; benjaminblonder
 Repository: CRAN
-Date/Publication: 2015-11-24 07:46:52
+Date/Publication: 2017-06-05 21:44:46 UTC
diff --git a/MD5 b/MD5
@@ -1,13 +1,13 @@
-cb225004cdc2bce35851bc7b34149c24 *DESCRIPTION
-9f25089fefe79e2a8c12e30938a3fd6d *NAMESPACE
+23103a8691754dc69b42f7d56a901a59 *DESCRIPTION
+5277b9b96cb92ab68ec6bc142e3b0eb4 *NAMESPACE
 c39460d085cf3ce914cf94344b1f47c3 *R/generate_nul_resample.R
 0da717e3c3000fa8d3c0549220db32c0 *R/make_netassoc_network.R
 7b95b8c6278534ba92d0d10d054c829e *R/pairwise_association.R
-19a162e0145463d76e3b70b479c5d452 *R/partial_correlation.R
+e488d1659f38e75ae04bf4beadb7a723 *R/partial_correlation.R
 0ce37ad1bcd9a0de4ee01bb565d04f47 *R/plot.R
 e37052ada824878367e60059827bfc2f *man/make_netassoc_network.Rd
 8f11cf7649b395ffd95a9d9eb3afd309 *man/netassoc-package.Rd
 93226c98aac9dc52931e74d962f4fa5e *man/pairwise_association.Rd
-21095f107a35447ed412eb29de5e3bb3 *man/partial_correlation.Rd
+04ed50d71962306786218a6b3a336a81 *man/partial_correlation.Rd
 b533e6b2c50de93c38845bb5833d404e *man/plot_netassoc_matrix.Rd
 4f5ff85ce0e4f9ab4738fd8423da502c *man/plot_netassoc_network.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,6 @@
 export(plot_netassoc_network, make_netassoc_network, partial_correlation, plot_netassoc_matrix, pairwise_association)
 import(igraph)
-importFrom(rags2ridges, optPenalty.LOOCVauto)
+#importFrom(rags2ridges, optPenalty.LOOCVauto)
 importFrom(corpcor, decompose.invcov)
 importFrom(corpcor, invcov.shrink)
 importFrom(vegan, permatfull)

diff --git a/R/netassoc.R b/R/netassoc.R
diff --git a/R/partial_correlation.R b/R/partial_correlation.R
@@ -10,11 +10,6 @@ partial_correlation <- function(mat, method, verbose=FALSE)
     # use auto-selected lambda shrinkage parameter
     invcov <- corpcor::invcov.shrink(t(mat), verbose=verbose)
   }
-  else if (method=="ridge")
-  {
-    # use auto-selected lambda penalty parameter based on approximate leave one out cross validation
-    invcov <- rags2ridges::optPenalty.LOOCVauto(t(mat), lambdaMin=1e-3,lambdaMax=1e4)$optPrec
-  }
   else if (method=="exact")
   {
     # estimate inverse covariance from 
@@ -34,4 +29,10 @@ partial_correlation <- function(mat, method, verbose=FALSE)
   }
 
   return(pcor)
-}
+}
+
+#else if (method=="ridge")
+#{
+#  # use auto-selected lambda penalty parameter based on approximate leave one out cross validation
+#  invcov <- rags2ridges::optPenalty.LOOCVauto(t(mat), lambdaMin=1e-3,lambdaMax=1e4)$optPrec
+#}