From 38c5a21c003dbdfcb1a86bada90079907c32b9ca Mon Sep 17 00:00:00 2001
From: ualvaro <alvaro.uzaheta@gess.ethz.ch>
Date: Mon, 2 Sep 2024 21:47:26 +0200
Subject: [PATCH] Update deprecated functions in the vignettes

---
 .github/workflows/R-CMD-check.yml    | 2 +-
 .github/workflows/prchecks.yml       | 2 +-
 .github/workflows/test-coverage.yaml | 2 +-
 DESCRIPTION                          | 1 +
 NEWS.md                              | 1 +
 vignettes/teaching1.Rmd.orig         | 6 +++---
 vignettes/teaching2.Rmd.orig         | 6 +++---
 7 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 210d4cf..8505458 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -41,7 +41,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache_version: 2
+          cache-version: 2
           extra-packages: any::rcmdcheck
           needs: check
 
diff --git a/.github/workflows/prchecks.yml b/.github/workflows/prchecks.yml
index 4283d03..d3d063c 100644
--- a/.github/workflows/prchecks.yml
+++ b/.github/workflows/prchecks.yml
@@ -35,7 +35,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache_version: 2
+          cache-version: 2
           extra-packages: |
             any::pkgbuild
             any::lintr
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 3947965..cbee7ac 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -23,7 +23,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache_version: 2
+          cache-version: 2
           extra-packages: any::covr
           needs: coverage
 
diff --git a/DESCRIPTION b/DESCRIPTION
index 229e77f..2ffad12 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,6 +56,7 @@ Suggests:
     ggraph,
     migraph,
     manynet,
+    patchwork,
     broom,
     lmtest
 VignetteBuilder: knitr 
diff --git a/NEWS.md b/NEWS.md
index c3b7901..4b3b6df 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,6 @@
 # goldfish 1.6.9
 
+* Update deprecated functions in the vignettes from `manynet`.
 * Solve issue on `Makevars.in` file that produced a note when check as CRAN. 
 
 # goldfish 1.6.8
diff --git a/vignettes/teaching1.Rmd.orig b/vignettes/teaching1.Rmd.orig
index 6e982ee..eacfdd4 100644
--- a/vignettes/teaching1.Rmd.orig
+++ b/vignettes/teaching1.Rmd.orig
@@ -249,7 +249,7 @@ library(ggraph)
 library(migraph)
 # The network at the beginning
 callNetworkBgn <- as.matrix(callNetwork)
-autographr(callNetworkBgn, labels = FALSE, layout = "fr")
+graphr(callNetworkBgn, labels = FALSE, layout = "fr")
 
 # The network at half time
 callNetworkHlf <- as.matrix(
@@ -259,7 +259,7 @@ callNetworkHlf <- as.matrix(
   as_igraph() |>
   add_node_attribute("floor", actors$floor)
 
-autographr(callNetworkHlf, labels = FALSE, layout = "fr") +
+graphr(callNetworkHlf, labels = FALSE, layout = "fr") +
   geom_node_point(aes(color = as.factor(floor)), size = 2, show.legend = FALSE)
 
 # The network at the end
@@ -267,7 +267,7 @@ callNetworkEnd <- as.matrix(callNetwork, time = max(calls$time) + 1) |>
   as_igraph() |>
   add_node_attribute("floor", actors$floor)
 
-autographr(callNetworkEnd, labels = FALSE, layout = "fr") +
+graphr(callNetworkEnd, labels = FALSE, layout = "fr") +
   geom_node_point(aes(color = as.factor(floor)), size = 2, show.legend = FALSE)
 
 
diff --git a/vignettes/teaching2.Rmd.orig b/vignettes/teaching2.Rmd.orig
index 6b14cc6..6b7c3dd 100644
--- a/vignettes/teaching2.Rmd.orig
+++ b/vignettes/teaching2.Rmd.orig
@@ -243,15 +243,15 @@ endNet <- as.matrix(bilatnet, time = as.numeric(as.POSIXct("1970-01-01"))) |>
   add_node_attribute("gdp", endStates$gdp)
 
 # logical value indicating if states where present and with agreements
-isStateActiveStart <- startStates$present & node_degree(startNet) > 0
-isStateActiveEnd <- endStates$present & node_degree(endNet) > 0
+isStateActiveStart <- startStates$present & node_deg(startNet) > 0
+isStateActiveEnd <- endStates$present & node_deg(endNet) > 0
 isStateActive <- isStateActiveStart | isStateActiveEnd
 
 # subset networks to active states
 startNet <- delete_nodes(startNet, !isStateActive)
 endNet <- delete_nodes(endNet, !isStateActive)
 
-autographs(list(startNet, endNet), layout = "fr")
+graphs(list(startNet, endNet), layout = "fr")
 ```
 
 What can we observe?