From 768efe15dbd5c0ee934a4470ec2cf9b417438863 Mon Sep 17 00:00:00 2001
From: Jim Thorson <50178738+James-Thorson-NOAA@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:51:50 -0700
Subject: [PATCH] removing phylosignal for now

---
 DESCRIPTION     |  5 ++---
 R/phylosem.R    | 13 -------------
 man/phylosem.Rd | 13 -------------
 3 files changed, 2 insertions(+), 29 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 57b6e3a..9c226fd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: phylosem
 Type: Package
 Title: Phylogenetic Structural Equation Model
-Version: 1.0.0
-Date: 2023-08-15
+Version: 1.0.1
+Date: 2023-09-18
 Authors@R: 
     c(person(given = "James",
              family = "Thorson",
@@ -24,7 +24,6 @@ Depends:
     TMB,
     R (>= 4.0.0),
 Suggests:
-    phylosignal,
     DiagrammeR,
     semPlot,
     phytools,
diff --git a/R/phylosem.R b/R/phylosem.R
index f85b319..645b1b5 100644
--- a/R/phylosem.R
+++ b/R/phylosem.R
@@ -161,19 +161,6 @@
 #'                    nodeLabels = myplot@Vars$name )
 #' }
 #'
-#' # Plot using phylosignal
-#' if( require(phylosignal) ){
-#'   dotplot( my_phylo4d )
-#'   gridplot( my_phylo4d )
-#'
-#'   # Cluster based on phylogeny and traits
-#'   gC = graphClust( my_phylo4d,
-#'                  lim.phylo = 5,
-#'                  lim.trait = 5,
-#'                  scale.lim = FALSE)
-#'   plot(gC, which = "graph", ask = FALSE)
-#' }
-#'
 #' @useDynLib phylosem, .registration = TRUE
 #' @export
 phylosem <-
diff --git a/man/phylosem.Rd b/man/phylosem.Rd
index 6e24784..9126d8f 100644
--- a/man/phylosem.Rd
+++ b/man/phylosem.Rd
@@ -152,19 +152,6 @@ if( require(semPlot) ){
                    nodeLabels = myplot@Vars$name )
 }
 
-# Plot using phylosignal
-if( require(phylosignal) ){
-  dotplot( my_phylo4d )
-  gridplot( my_phylo4d )
-
-  # Cluster based on phylogeny and traits
-  gC = graphClust( my_phylo4d,
-                 lim.phylo = 5,
-                 lim.trait = 5,
-                 scale.lim = FALSE)
-  plot(gC, which = "graph", ask = FALSE)
-}
-
 }
 \references{
 **Introducing the package, its features, and comparison with other software