From b7b16cb18343a6038b59a3711115bc69c81fb7dd Mon Sep 17 00:00:00 2001
From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com>
Date: Tue, 14 Jan 2025 09:15:20 +0100
Subject: [PATCH 1/2] update packages in lockfile

---
 renv.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/renv.lock b/renv.lock
index 158e8ba..c65ac9b 100644
--- a/renv.lock
+++ b/renv.lock
@@ -45,9 +45,9 @@
     },
     "ape": {
       "Package": "ape",
-      "Version": "5.8",
+      "Version": "5.8-1",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "Rcpp",
@@ -60,7 +60,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "16b5ff4dff0ead9ea955f62f794b1535"
+      "Hash": "54e5b03e928da23e75dc5bb633648d27"
     },
     "codetools": {
       "Package": "codetools",

From 8d7739d9c859d3eb2e005561105a3439f8e535b0 Mon Sep 17 00:00:00 2001
From: Niklas Hohmann <67792281+NiklasHohmann@users.noreply.github.com>
Date: Tue, 14 Jan 2025 09:45:39 +0100
Subject: [PATCH 2/2] expand figure 5 to include recovery probability

---
 code/examples.R | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/code/examples.R b/code/examples.R
index 851948c..4e96592 100644
--- a/code/examples.R
+++ b/code/examples.R
@@ -75,7 +75,7 @@ dev.off()
 #### Figure 5 ####
 # effect of water depth on fossil abundance
 pdf(file = "figs/fig5.pdf")
-par(mfrow = c(1,2))
+par(mfrow = c(2,2))
 gc = approxfun(scenarioA$t_myr, scenarioA$wd_m[,"12km"])
 niche = snd_niche(opt = 100, tol = 30, cutoff_val = 0) # define niche with optimum at 100 m
 plot(scenarioA$t_myr, gc(scenarioA$t_myr),
@@ -85,6 +85,24 @@ plot(scenarioA$t_myr, gc(scenarioA$t_myr),
      ylab = "Water depth [m]",
      main = "Water Depth on the Proximal Slope")
 
+plot(x = scenarioA$t_myr, 
+     y = niche(gc(scenarioA$t_myr)),
+     type = "l",
+     lwd = 3,
+     xlab = "Time [Myr]",
+     ylab = "Recovery probability",
+     main = "Niche in Time Domain")
+
+r = list(t = scenarioA$t_myr, y = niche(gc(scenarioA$t_myr)))  |> time_to_strat(adm12)
+
+plot(x = r$h[!is.na(r$h)],
+     y = r$y[!is.na(r$h)],
+     type = "l",
+     lwd = 3,
+     xlab = "Stratigraphic position [m]",
+     ylab = "Recovery probability",
+     main = "Niche in Stratigraphic Domain")
+
 p3(rate = rolo, min_time(adm12), max_time(adm12)) |>
   apply_niche(niche, gc) |>
   time_to_strat(adm12, destructive = TRUE) |>