Minor tweak of tutorial

PaulRegular · Jan 31, 2025 · a69755d · a69755d
1 parent d2f1de2
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Showing 3 changed files with 13 additions and 8 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 0.1.6
-Date: 2023-09-18 14:42:04 UTC
-SHA: 28daf1f7c21db3a333d9752661e1771ca4d259bb
+Date: 2023-09-18 20:13:26 UTC
+SHA: d2f1de207dc4ba178aa883cc440cf0d1512289b9
diff --git a/SimSurvey.Rproj b/SimSurvey.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: b80f9c1a-b225-47ef-bc29-3c521134f26c
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

diff --git a/tutorial/tutorial.Rmd b/tutorial/tutorial.Rmd
@@ -262,10 +262,12 @@ dat <- as_tibble(survey$setdet) %>%
 
 ## Make mesh and fit geostatistical model to survey data
 mesh <- sdmTMB::make_mesh(dat, xy_cols = c("x", "y"), cutoff = 20)
-fit <- sdmTMB(N ~ 0 + as.factor(year) + offset,
+fit <- sdmTMB(N ~ 0 + as.factor(year),
+              offset = dat$offset,
+              mesh = mesh,
               data = dat,
-              family = nbinom2(link = "log"), spde = mesh,
-              include_spatial = TRUE, time = "year")
+              family = nbinom2(link = "log"), 
+              time = "year")
 
 ## Expand grid data for predictions
 grid_dat <- as_tibble(select(survey$grid_xy, x, y, depth)) %>% distinct()
@@ -328,10 +330,12 @@ dat <- as_tibble(survey$setdet) %>%
 
 ## Make mesh and fit geostatistical model to survey data
 mesh <- sdmTMB::make_mesh(dat, xy_cols = c("x", "y"), cutoff = 20)
-fit <- sdmTMB(N ~ 0 + as.factor(year) + offset,
+fit <- sdmTMB(N ~ 0 + as.factor(year),
+              offset = dat$offset,
+              mesh = mesh,
               data = dat,
-              family = nbinom2(link = "log"), spde = mesh,
-              include_spatial = TRUE, time = "year")
+              family = nbinom2(link = "log"),
+              time = "year")
 
 ## Expand grid data for predictions
 grid_dat <- as_tibble(select(survey$grid_xy, x, y, depth)) %>% distinct()