From f4515e3da02c86cfae977d639540a3829dffe60f Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 11:39:35 +0200
Subject: [PATCH 1/8] Moved test_tutorials() to a testthat helper
 check_tute_rendering()

---
 NAMESPACE                         |  1 -
 R/tutorial_test.R                 | 34 -------------------------------
 man/test_tutorials.Rd             | 27 ------------------------
 tests/testthat/helper-functions.R | 21 +++++++++++++++++++
 4 files changed, 21 insertions(+), 62 deletions(-)
 delete mode 100644 R/tutorial_test.R
 delete mode 100644 man/test_tutorials.Rd

diff --git a/NAMESPACE b/NAMESPACE
index df07aa52..5faec42e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -33,7 +33,6 @@ export(test_fit)
 export(test_gof)
 export(test_permutation)
 export(test_random)
-export(test_tutorials)
 export(tidy)
 importFrom(autograph,ag_base)
 importFrom(dplyr,"%>%")
diff --git a/R/tutorial_test.R b/R/tutorial_test.R
deleted file mode 100644
index 0af38efc..00000000
--- a/R/tutorial_test.R
+++ /dev/null
@@ -1,34 +0,0 @@
-#' Test tutorials
-#'
-#' @description 
-#'   For our purposes, "testing" a tutorial means being able to 
-#'   (successfully) run `render()` on it. 
-#'   This function renders the tutorial provided in `path`. 
-#'   There is no check to see if the rendered file looks OK.
-#'   If a tutorial fails to render, then an error will be generated which will
-#'   propagate to the caller.
-#' @param path Character vector of the paths to the tutorials to be knitted.
-#' @param quiet Logical, whether to suppress messages from `render()`.
-#' @returns No return value, called for side effects.
-#' @author David Kane, see tutorial.helpers
-#' @export
-test_tutorials <- function(path, quiet = TRUE){
-  
-  stopifnot(all(file.exists(path)))
-  
-  for(i in path){
-    if(!quiet) message("Rendering: ", basename(i))
-    tryCatch({
-      rmarkdown::render(input = i, 
-                        output_dir = tempdir(),
-                        intermediates_dir = tempdir(), quiet = quiet)
-      # Note that the Debian setup on CRAN does not allow for writing files to any
-      # location other than the temporary directory, which is why we must specify
-      # tempdir() in the two dir arguments.
-      if(!quiet) message("Successfully rendered: ", basename(i))
-    }, error = function(e) {
-      stop("Failed to render ", i, ": ", e$message, call. = FALSE)
-    })
-  }
-  invisible(NULL)
-}
\ No newline at end of file
diff --git a/man/test_tutorials.Rd b/man/test_tutorials.Rd
deleted file mode 100644
index 2e36367d..00000000
--- a/man/test_tutorials.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/tutorial_test.R
-\name{test_tutorials}
-\alias{test_tutorials}
-\title{Test tutorials}
-\usage{
-test_tutorials(path, quiet = TRUE)
-}
-\arguments{
-\item{path}{Character vector of the paths to the tutorials to be knitted.}
-
-\item{quiet}{Logical, whether to suppress messages from \code{render()}.}
-}
-\value{
-No return value, called for side effects.
-}
-\description{
-For our purposes, "testing" a tutorial means being able to
-(successfully) run \code{render()} on it.
-This function renders the tutorial provided in \code{path}.
-There is no check to see if the rendered file looks OK.
-If a tutorial fails to render, then an error will be generated which will
-propagate to the caller.
-}
-\author{
-David Kane, see tutorial.helpers
-}
diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index 414f5a87..6802fba1 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -25,3 +25,24 @@ bot5 <- function(res, dec = 4){
     unname(round(res, dec))[(lr-4):lr]
   } else unname(res)[(lr-2):lr]
 }
+check_tute_rendering <- function(path, quiet = TRUE){
+  
+  stopifnot(all(file.exists(path)))
+  
+  for(i in path){
+    if(!quiet) message("Rendering: ", basename(i))
+    tryCatch({
+      rmarkdown::render(input = i, 
+                        output_dir = tempdir(),
+                        intermediates_dir = tempdir(), quiet = quiet)
+      # Note that the Debian setup on CRAN does not allow for writing files to any
+      # location other than the temporary directory, which is why we must specify
+      # tempdir() in the two dir arguments.
+      if(!quiet) message("Successfully rendered: ", basename(i))
+    }, error = function(e) {
+      stop("Failed to render ", i, ": ", e$message, call. = FALSE)
+    })
+  }
+  invisible(NULL)
+}
+

From 69bd72aad6d1c6315b18ab2ed4ff312b69735f70 Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 11:40:51 +0200
Subject: [PATCH 2/8] Fixed namespace issues

---
 R/model_distrib.R                   | 2 +-
 tests/testthat/test-model_distrib.R | 2 +-
 tests/testthat/test-model_predict.R | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/model_distrib.R b/R/model_distrib.R
index 40874cbd..7afea13a 100644
--- a/R/model_distrib.R
+++ b/R/model_distrib.R
@@ -57,7 +57,7 @@ test_distribution <- function(diff_model1, diff_model2){
 #' @export
 test_fit <- function(diff_model, diff_models){ # make into method?
   x <- diff_model
-  if(is_graph(x)) x <- as_diffusion(x)
+  if(manynet::is_graph(x)) x <- manynet::as_diffusion(x)
   y <- diff_models
   sim <- `0` <- NULL
   sims <- y %>% dplyr::select(sim, time, I)
diff --git a/tests/testthat/test-model_distrib.R b/tests/testthat/test-model_distrib.R
index 70c8b481..ca4fac83 100644
--- a/tests/testthat/test-model_distrib.R
+++ b/tests/testthat/test-model_distrib.R
@@ -7,6 +7,6 @@ test_that("test_distribution works", {
 test_that("test_fit works", {
   x <- play_diffusion(generate_random(15), transmissibility = 0.7)
   y <- play_diffusions(generate_random(15), transmissibility = 0.1, times = 40)
-  res <- test_fit(as_diffusion(x), y)
+  res <- test_fit(x, y)
   expect_output(print(res), "statistic")
 })
\ No newline at end of file
diff --git a/tests/testthat/test-model_predict.R b/tests/testthat/test-model_predict.R
index 1940ee1b..5c73ccba 100644
--- a/tests/testthat/test-model_predict.R
+++ b/tests/testthat/test-model_predict.R
@@ -1,7 +1,7 @@
 test_that("predict.netlm works", {
   networkers <- ison_networkers %>% to_subgraph(Discipline == "Sociology")
   model1 <- net_regression(weight ~ ego(Citations) + alter(Citations) + sim(Citations), 
-                        networkers, times = 10)
+                        networkers, times = 5)
   pred <- predict(model1, matrix(c(1,10,5,2),1,4))
   expect_length(pred, 1)
   expect_type(pred, "double")
@@ -11,7 +11,7 @@ test_that("predict.netlogit works", {
   networkers <- ison_networkers %>% to_subgraph(Discipline == "Sociology") %>% 
     to_unweighted()
   model1 <- net_regression(. ~ ego(Citations) + alter(Citations) + sim(Citations), 
-                        networkers, times = 10)
+                        networkers, times = 5)
   pred_link <- predict(model1, matrix(c(1,10,5,2),1,4), type = "link")
   pred_response <- predict(model1, matrix(c(1,10,5,2),1,4), type = "response")
   

From a7430c96c92f37e0c58d149d20d3e41867d3aedc Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 11:43:39 +0200
Subject: [PATCH 3/8] Added find_pkg_tutorial_paths() helper for identifying
 stocnet package tutorials

---
 tests/testthat/helper-functions.R         | 10 ++++++++++
 tests/testthat/test-tutorials_autograph.R |  2 +-
 tests/testthat/test-tutorials_manynet.R   |  6 ++----
 tests/testthat/test-tutorials_netrics.R   |  2 +-
 4 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index 6802fba1..342279c1 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -25,6 +25,16 @@ bot5 <- function(res, dec = 4){
     unname(round(res, dec))[(lr-4):lr]
   } else unname(res)[(lr-2):lr]
 }
+
+find_pkg_tutorial_paths <- function(pkg) {
+  tute_folders <- list.dirs(system.file("tutorials", package = pkg),
+                             recursive = F)
+  tute_files <- unlist(lapply(tute_folders, function(folder) {
+    list.files(folder, pattern = "*.Rmd", full.names = TRUE)
+  }))
+  tute_files
+}
+
 check_tute_rendering <- function(path, quiet = TRUE){
   
   stopifnot(all(file.exists(path)))
diff --git a/tests/testthat/test-tutorials_autograph.R b/tests/testthat/test-tutorials_autograph.R
index 2b5aeb9e..11f33c55 100644
--- a/tests/testthat/test-tutorials_autograph.R
+++ b/tests/testthat/test-tutorials_autograph.R
@@ -2,7 +2,7 @@ test_that("autograph tutorials work", {
   for(tute.dir in list.dirs(system.file("tutorials", package = "autograph"), 
                             recursive = F)){
     tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
-    expect_null(test_tutorials(tute.file))
+    expect_null(check_tute_rendering(tute.file))
   }
 })
 
diff --git a/tests/testthat/test-tutorials_manynet.R b/tests/testthat/test-tutorials_manynet.R
index d2f6e55e..3af9bf83 100644
--- a/tests/testthat/test-tutorials_manynet.R
+++ b/tests/testthat/test-tutorials_manynet.R
@@ -1,7 +1,5 @@
 test_that("manynet tutorials work", {
-  for(tute.dir in list.dirs(system.file("tutorials", package = "manynet"), 
-                            recursive = F)){
-    tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
-    expect_null(test_tutorials(tute.file))
+  for(tute in find_pkg_tutorial_paths("manynet")){
+    expect_null(check_tute_rendering(tute))
   }
 })
\ No newline at end of file
diff --git a/tests/testthat/test-tutorials_netrics.R b/tests/testthat/test-tutorials_netrics.R
index 912f638a..15b3c868 100644
--- a/tests/testthat/test-tutorials_netrics.R
+++ b/tests/testthat/test-tutorials_netrics.R
@@ -2,6 +2,6 @@ test_that("netrics tutorials work", {
   for(tute.dir in list.dirs(system.file("tutorials", package = "netrics"), 
                             recursive = F)){
     tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
-    expect_null(test_tutorials(tute.file))
+    expect_null(check_tute_rendering(tute.file))
   }
 })
\ No newline at end of file

From 6777011a22dbc75547cc36ef97db731bebd39cfb Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 11:44:27 +0200
Subject: [PATCH 4/8] Added check_tute_functions() helper for seeing whether
 the solution functions in stocnet tutorials run without error or warning

---
 tests/testthat/helper-functions.R       | 72 +++++++++++++++++++
 tests/testthat/test-tutorials_manynet.R | 10 ++-
 tests/testthat/test-tutorials_migraph.R | 94 +++++++++++++++++++++++--
 3 files changed, 169 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index 342279c1..666272af 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -56,3 +56,75 @@ check_tute_rendering <- function(path, quiet = TRUE){
   invisible(NULL)
 }
 
+check_tute_functions <- function(path, skip = "ergm\\(", quiet = TRUE){
+  tmp <- tempfile(fileext = ".R")
+  knitr::purl(
+    input  = path,
+    output = tmp,
+    quiet  = TRUE
+  )
+  exprs <- parse(tmp)  # your purled file
+  env <- new.env(parent = globalenv())
+  
+  skip_rest <- FALSE
+  is_skipped_call <- function(expr) {
+    any(grepl(skip, deparse(expr)))
+  }
+  
+  for (i in seq_along(exprs)) {
+    if (skip_rest) {
+      skip(paste("Skipping dependent expressions in", basename(path)))
+      next
+    }
+    
+    if (is_skipped_call(exprs[[i]])) {
+      skip_rest <- TRUE
+      skip(paste("Skipping slow functions in", basename(path)))
+      next
+    }
+    
+    w <- NULL
+    e <- NULL
+    m <- NULL
+    
+    not_out <- withCallingHandlers(
+      tryCatch(
+        eval(exprs[[i]], envir = env),
+        error = function(err) {
+          e <<- err
+          NULL
+        }
+      ),
+      warning = function(wrn) {
+        w <<- wrn
+        invokeRestart("muffleWarning")
+      },
+      message = function(msg) {
+        m <<- c(m, conditionMessage(msg))
+        invokeRestart("muffleMessage")
+      }
+    )
+    
+    # If there *was* a warning, check if it's a deprecated/defunct one
+    if (!is.null(w)) {
+      msg <- conditionMessage(w)
+      
+      # Only fail if it's a deprecated/defunct warning
+      if (!grepl("deprecate|defunct|moved", msg, ignore.case = TRUE)) {
+        w <- NULL
+      }
+    }
+    
+    # Now test what happened
+    expect_null(
+      e,
+      info = paste0("Error in expression ", i,
+                    " of ", basename(path), ": ", deparse(exprs[[i]]))
+    )
+    
+    expect_null(
+      w,
+      info = paste("Warning in expression", i, ":", deparse(exprs[[i]]))
+    )
+  }
+}
diff --git a/tests/testthat/test-tutorials_manynet.R b/tests/testthat/test-tutorials_manynet.R
index 3af9bf83..9d6dd37c 100644
--- a/tests/testthat/test-tutorials_manynet.R
+++ b/tests/testthat/test-tutorials_manynet.R
@@ -2,4 +2,12 @@ test_that("manynet tutorials work", {
   for(tute in find_pkg_tutorial_paths("manynet")){
     expect_null(check_tute_rendering(tute))
   }
-})
\ No newline at end of file
+})
+
+test_that("manynet tutorial code runs without warnings or errors", {
+  skip_if_not_installed("manynet", minimum_version = "2.0.2")
+  for(tute in find_pkg_tutorial_paths("manynet")){
+    expect_null(check_tute_functions(tute), 
+                info = paste("Error in tutorial", basename(tute)))
+  }
+})
diff --git a/tests/testthat/test-tutorials_migraph.R b/tests/testthat/test-tutorials_migraph.R
index 1087eeab..3246326d 100644
--- a/tests/testthat/test-tutorials_migraph.R
+++ b/tests/testthat/test-tutorials_migraph.R
@@ -1,7 +1,89 @@
-test_that("migraph tutorials work", {
-  for(tute.dir in list.dirs(system.file("tutorials", package = "migraph"), 
-                            recursive = F)){
-    tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
-    expect_null(test_tutorials(tute.file))
+# test_that("migraph tutorials render", {
+#   skip_on_cran()
+#   for(tute.dir in list.dirs(system.file("tutorials", package = "migraph"), 
+#                             recursive = F)){
+#     tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
+#     expect_null(check_tute_rendering(tute.file))
+#   }
+# })
+
+test_that("migraph tutorial code runs without warnings or errors", {
+  for(tute in find_pkg_tutorial_paths("migraph")){
+    expect_null(check_tute_functions(tute, skip = "ergm\\(|play_diffusions\\("), 
+                info = paste("Error in tutorial", basename(tute)))
   }
-})
\ No newline at end of file
+})
+
+# test_that("migraph tutorial code runs without warnings or errors", {
+#   migraph_tutes <- list.dirs(system.file("tutorials", package = "migraph"), 
+#             recursive = F)
+#   migraph_tutes <- migraph_tutes[!grepl("tutorial9", migraph_tutes)]
+#   for(tute.dir in migraph_tutes){
+#     tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
+#     tmp <- tempfile(fileext = ".R")
+#     knitr::purl(
+#       input  = tute.file,
+#       output = tmp,
+#       quiet  = TRUE
+#     )
+#     exprs <- parse(tmp)  # your purled file
+#     env <- new.env(parent = globalenv())
+#     
+#     skip_rest <- FALSE
+#     is_ergm_call <- function(expr) {
+#       any(grepl("ergm\\(", deparse(expr)))
+#     }
+#     
+#     for (i in seq_along(exprs)) {
+#       
+#       if (skip_rest) {
+#         skip(paste("Skipping dependent expressions in", basename(tute.file)))
+#         next
+#       }
+#       
+#       if (is_ergm_call(exprs[[i]])) {
+#         skip_rest <- TRUE
+#         skip(paste("Skipping ergm model in", basename(tute.file)))
+#         next
+#       }
+#       
+#       w <- NULL
+#       e <- NULL
+#       
+#       not_out <- testthat::capture_output(withCallingHandlers(
+#         tryCatch(
+#           eval(exprs[[i]], envir = env),
+#           error = function(err) {
+#             e <<- err
+#             NULL
+#           }
+#         ),
+#         warning = function(wrn) {
+#           w <<- wrn
+#           invokeRestart("muffleWarning")
+#         }
+#       ))
+#       
+#       # If there *was* a warning, check if it's a deprecated/defunct one
+#       if (!is.null(w)) {
+#         msg <- conditionMessage(w)
+#         
+#         # Only fail if it's a deprecated/defunct warning
+#         if (grepl("deprecated|defunct|moved", msg, ignore.case = TRUE)) {
+#           fail(paste(
+#             "Deprecated/defunct warning in expression", i, ":\n",
+#             deparse(exprs[[i]]), "\nMessage:", msg
+#           ))
+#         }
+#       }
+#       
+#       
+#       # Now test what happened
+#       expect_null(
+#         e,
+#         info = paste0("Error in expression ", i, 
+#                      " of ", basename(tute.file), ": ", deparse(exprs[[i]]))
+#       )
+#     }
+#   }
+# })
\ No newline at end of file

From 8157bdafcc7d21b0a38eaf2ba1995d5f1e574075 Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 11:46:16 +0200
Subject: [PATCH 5/8] Updated examples across migraph tutorials where errors
 could creep in

---
 DESCRIPTION                            |  4 ++--
 NEWS.md                                | 17 ++++++++++++++++-
 cran-comments.md                       |  2 +-
 inst/tutorials/tutorial0/tutorial0.Rmd |  2 +-
 inst/tutorials/tutorial7/diffusion.Rmd | 22 +++++++++++-----------
 inst/tutorials/tutorial8/diversity.Rmd |  3 ++-
 inst/tutorials/tutorial9/ergm.Rmd      |  2 +-
 7 files changed, 34 insertions(+), 18 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 28ff21df..7ca3a33d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: migraph
 Title: Inferential Methods for Multimodal and Other Networks 
-Version: 1.6.1
-Date: 2026-04-14
+Version: 1.6.2
+Date: 2026-04-17
 Description: A set of tools for testing networks.
    It includes functions for univariate and multivariate 
    conditional uniform graph and quadratic assignment procedure testing,
diff --git a/NEWS.md b/NEWS.md
index 612d868f..76f5a2fd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,21 @@
+# migraph 1.6.2
+
+2026-04-17
+
+## Testing
+
+- Fixed namespace issues
+
+## Tutorials
+
+- Added function testing for migraph tutorials
+- Added function testing for manynet tutorials (> v2.0.2)
+- Updated examples in solutions in migraph tutorials where errors could creep in
+- Skipped extracting some solutions in migraph where errors could creep in
+
 # migraph 1.6.1
 
-2026-04-13
+2026-04-14
 
 ## Package
 
diff --git a/cran-comments.md b/cran-comments.md
index 8d0c3374..bd6a0342 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -9,4 +9,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-- Updates to bring autograph into line with latest version of manynet (> v2.0.0)
+- Updates to improve testing length
diff --git a/inst/tutorials/tutorial0/tutorial0.Rmd b/inst/tutorials/tutorial0/tutorial0.Rmd
index a1af70dd..49f93cd7 100644
--- a/inst/tutorials/tutorial0/tutorial0.Rmd
+++ b/inst/tutorials/tutorial0/tutorial0.Rmd
@@ -127,7 +127,7 @@ Much more flexible than a high school calculator!
 It is important to note that R is case-sensitive, 
 i.e. `Print("Hello World")` will not work. Try it!
 
-```{r Print-hello-world, exercise = TRUE}
+```{r Print-hello-world, exercise = TRUE, purl=FALSE}
 Print("Hello World")
 ```
 
diff --git a/inst/tutorials/tutorial7/diffusion.Rmd b/inst/tutorials/tutorial7/diffusion.Rmd
index c5042758..68cb6907 100644
--- a/inst/tutorials/tutorial7/diffusion.Rmd
+++ b/inst/tutorials/tutorial7/diffusion.Rmd
@@ -202,7 +202,7 @@ You can start the infection in California by specifying `seeds = 5`.
 ```{r usstates-hint}
 us_diff <- play_diffusion(irps_usgeo, seeds = 5)
 plot(us_diff)
-graphr(us_diff)
+# graphr(us_diff)
 net_by_infection_complete(us_diff)
 ```
 
@@ -577,7 +577,7 @@ to indicate that in only 1/2 cases is contagion successful.
 ```{r diffusions, exercise = TRUE, fig.width=9}
 rando <- generate_random(32, 0.1)
 graphr(rando)
-plot(play_diffusions(rando, transmissibility = 0.5, times = 5, steps = 10))
+plot(play_diffusions(ison_lawfirm, transmissibility = 0.5, times = 5, steps = 10))
 ```
 
 Note that in this plot the number of new infections is not plotted
@@ -610,7 +610,7 @@ plot(play_diffusions(____, recovery = ____))
 ```
 
 ```{r sir-solution}
-plot(play_diffusions(rando, recovery = 0.2))
+plot(play_diffusions(ison_lawfirm, recovery = 0.2))
 ```
 
 What we see in these kinds of models is typically a spike in infections
@@ -624,8 +624,8 @@ which should average out these differences and make the results more reliable.
 
 ```
 
-```{r sirtimes-solution}
-plot(play_diffusions(rando, recovery = 0.2, times = 100))
+```{r sirtimes-solution, purl=FALSE}
+plot(play_diffusions(ison_lawfirm, recovery = 0.2, times = 100))
 ```
 
 ### SIRS models
@@ -642,7 +642,7 @@ Play a single diffusion so that you can see what's going on in a particular run.
 ```
 
 ```{r sirs-solution}
-plot(play_diffusion(rando, recovery = 0.2, waning = 0.05))
+plot(play_diffusion(ison_lawfirm, recovery = 0.2, waning = 0.05))
 ```
 
 <!-- # visualise diffusion within random graph -->
@@ -659,7 +659,7 @@ Depending on your particular simulation,
 there might be some variation,
 so let's run this same diffusion but multiple (100?) times.
 
-```{r sirstimes-solution, exercise.setup = "diffusions", exercise = TRUE, fig.width=9}
+```{r sirstimes-solution, exercise.setup = "diffusions", exercise = TRUE, fig.width=9, purl=FALSE}
 plot(play_diffusions(rando, recovery = 0.2, waning = 0.05, times = 100))
 ```
 
@@ -689,10 +689,10 @@ Play a single diffusion so that you can see what's going on in a particular run.
 
 ```{r seir-solution}
 set.seed(123)
-plot(play_diffusion(rando, seeds = 10, latency = 0.25, recovery = 0.2))
+plot(play_diffusion(ison_lawfirm, seeds = 10, latency = 0.75, recovery = 0.2))
 
 # visualise diffusion with latency and recovery
-graphs(play_diffusion(rando, seeds = 10, latency = 0.25, recovery = 0.2), waves = c(1,5,10))
+# graphs(play_diffusion(ison_lawfirm, seeds = 10, latency = 0.75, recovery = 0.2), waves = c(1,5,10))
 ```
 
 ## Make it stop
@@ -716,7 +716,7 @@ So how can we establish the $R_0$ here?
 We can use `net_by_reproduction()`.
 
 ```{r r0, exercise = TRUE, exercise.setup = "diffusions", fig.width=9}
-rd_diff <- play_diffusion(rando, transmissibility = 0.25, recovery = 0.05)
+rd_diff <- play_diffusion(ison_lawfirm, transmissibility = 0.25, recovery = 0.05)
 plot(rd_diff)
 # R-nought
 net_by_reproduction(rd_diff)
@@ -777,7 +777,7 @@ The unnormalised version gives the number of nodes that would need to be vaccina
 Ok, so let's try this strategy.
 
 ```{r vaccinate, exercise = TRUE, exercise.setup = "diffusions", fig.width=9}
-rd_diff_vacc <- play_diffusion(rando, transmissibility = 0.25, recovery = 0.05, 
+rd_diff_vacc <- play_diffusion(ison_lawfirm, transmissibility = 0.25, recovery = 0.05, 
                                immune = 2:9)
 plot(rd_diff_vacc)
 net_by_infection_total(rd_diff_vacc)
diff --git a/inst/tutorials/tutorial8/diversity.Rmd b/inst/tutorials/tutorial8/diversity.Rmd
index b0906e65..a9d3b1f9 100644
--- a/inst/tutorials/tutorial8/diversity.Rmd
+++ b/inst/tutorials/tutorial8/diversity.Rmd
@@ -118,7 +118,8 @@ marvel_friends
 ```
 
 ```{r friends-solution}
-marvel_friends <- to_unsigned(ison_marvel_relationships, keep = "positive")
+marvel_friends <- to_uniplex(fict_marvel, "relationship")
+marvel_friends <- to_unsigned(marvel_friends, keep = "positive")
 marvel_friends <- to_giant(marvel_friends)
 marvel_friends <- marvel_friends %>% to_subgraph(Appearances >= mean(Appearances))
 marvel_friends
diff --git a/inst/tutorials/tutorial9/ergm.Rmd b/inst/tutorials/tutorial9/ergm.Rmd
index 87c77ba3..cf7d196b 100644
--- a/inst/tutorials/tutorial9/ergm.Rmd
+++ b/inst/tutorials/tutorial9/ergm.Rmd
@@ -573,7 +573,7 @@ see  papers in e.g. *Social Networks* v.29 and *J Stat Software* v. 24.
 
 Now let's try to fit a triangle model like with the Florentine dataset above:
 
-```{r magnmark1, exercise = TRUE}
+```{r magnmark1, exercise = TRUE, purl=FALSE}
 magn.mark1 <- ergm(magnolia ~ edges + triangle)
 ```
 

From c53479a9a8e40f15bad8d352ca19129e645b2944 Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 21:20:12 +0200
Subject: [PATCH 6/8] Using check_tute_functions() for autograph and netrics
 tutorials too

---
 NEWS.md                                   |  2 +
 tests/testthat/helper-functions.R         |  3 +-
 tests/testthat/test-tutorials_autograph.R | 16 +++--
 tests/testthat/test-tutorials_migraph.R   | 74 -----------------------
 tests/testthat/test-tutorials_netrics.R   | 16 +++--
 5 files changed, 26 insertions(+), 85 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 76f5a2fd..daa98584 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,8 @@
 - Added function testing for manynet tutorials (> v2.0.2)
 - Updated examples in solutions in migraph tutorials where errors could creep in
 - Skipped extracting some solutions in migraph where errors could creep in
+- Removed `test_tutorials()` from the public API; 
+  use `run_tute()` and `extract_tute()` for supported tutorial execution and extraction workflows
 
 # migraph 1.6.1
 
diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
index 666272af..8c85a0ff 100644
--- a/tests/testthat/helper-functions.R
+++ b/tests/testthat/helper-functions.R
@@ -37,6 +37,7 @@ find_pkg_tutorial_paths <- function(pkg) {
 
 check_tute_rendering <- function(path, quiet = TRUE){
   
+  skip_if_not_installed("rmarkdown")
   stopifnot(all(file.exists(path)))
   
   for(i in path){
@@ -61,7 +62,7 @@ check_tute_functions <- function(path, skip = "ergm\\(", quiet = TRUE){
   knitr::purl(
     input  = path,
     output = tmp,
-    quiet  = TRUE
+    quiet  = quiet
   )
   exprs <- parse(tmp)  # your purled file
   env <- new.env(parent = globalenv())
diff --git a/tests/testthat/test-tutorials_autograph.R b/tests/testthat/test-tutorials_autograph.R
index 11f33c55..fa4c0700 100644
--- a/tests/testthat/test-tutorials_autograph.R
+++ b/tests/testthat/test-tutorials_autograph.R
@@ -1,8 +1,14 @@
-test_that("autograph tutorials work", {
-  for(tute.dir in list.dirs(system.file("tutorials", package = "autograph"), 
-                            recursive = F)){
-    tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
-    expect_null(check_tute_rendering(tute.file))
+# test_that("autograph tutorials work", {
+#     for(tute in find_pkg_tutorial_paths("autograph")){
+#       expect_null(check_tute_rendering(tute))
+#     }
+# })
+
+test_that("autograph tutorial code runs without warnings or errors", {
+  skip_if_not_installed("autograph", minimum_version = "1.0.0")
+  for(tute in find_pkg_tutorial_paths("autograph")){
+    expect_null(check_tute_functions(tute), 
+                info = paste("Error in tutorial", basename(tute)))
   }
 })
 
diff --git a/tests/testthat/test-tutorials_migraph.R b/tests/testthat/test-tutorials_migraph.R
index 3246326d..ee90d76d 100644
--- a/tests/testthat/test-tutorials_migraph.R
+++ b/tests/testthat/test-tutorials_migraph.R
@@ -13,77 +13,3 @@ test_that("migraph tutorial code runs without warnings or errors", {
                 info = paste("Error in tutorial", basename(tute)))
   }
 })
-
-# test_that("migraph tutorial code runs without warnings or errors", {
-#   migraph_tutes <- list.dirs(system.file("tutorials", package = "migraph"), 
-#             recursive = F)
-#   migraph_tutes <- migraph_tutes[!grepl("tutorial9", migraph_tutes)]
-#   for(tute.dir in migraph_tutes){
-#     tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
-#     tmp <- tempfile(fileext = ".R")
-#     knitr::purl(
-#       input  = tute.file,
-#       output = tmp,
-#       quiet  = TRUE
-#     )
-#     exprs <- parse(tmp)  # your purled file
-#     env <- new.env(parent = globalenv())
-#     
-#     skip_rest <- FALSE
-#     is_ergm_call <- function(expr) {
-#       any(grepl("ergm\\(", deparse(expr)))
-#     }
-#     
-#     for (i in seq_along(exprs)) {
-#       
-#       if (skip_rest) {
-#         skip(paste("Skipping dependent expressions in", basename(tute.file)))
-#         next
-#       }
-#       
-#       if (is_ergm_call(exprs[[i]])) {
-#         skip_rest <- TRUE
-#         skip(paste("Skipping ergm model in", basename(tute.file)))
-#         next
-#       }
-#       
-#       w <- NULL
-#       e <- NULL
-#       
-#       not_out <- testthat::capture_output(withCallingHandlers(
-#         tryCatch(
-#           eval(exprs[[i]], envir = env),
-#           error = function(err) {
-#             e <<- err
-#             NULL
-#           }
-#         ),
-#         warning = function(wrn) {
-#           w <<- wrn
-#           invokeRestart("muffleWarning")
-#         }
-#       ))
-#       
-#       # If there *was* a warning, check if it's a deprecated/defunct one
-#       if (!is.null(w)) {
-#         msg <- conditionMessage(w)
-#         
-#         # Only fail if it's a deprecated/defunct warning
-#         if (grepl("deprecated|defunct|moved", msg, ignore.case = TRUE)) {
-#           fail(paste(
-#             "Deprecated/defunct warning in expression", i, ":\n",
-#             deparse(exprs[[i]]), "\nMessage:", msg
-#           ))
-#         }
-#       }
-#       
-#       
-#       # Now test what happened
-#       expect_null(
-#         e,
-#         info = paste0("Error in expression ", i, 
-#                      " of ", basename(tute.file), ": ", deparse(exprs[[i]]))
-#       )
-#     }
-#   }
-# })
\ No newline at end of file
diff --git a/tests/testthat/test-tutorials_netrics.R b/tests/testthat/test-tutorials_netrics.R
index 15b3c868..0140489b 100644
--- a/tests/testthat/test-tutorials_netrics.R
+++ b/tests/testthat/test-tutorials_netrics.R
@@ -1,7 +1,13 @@
-test_that("netrics tutorials work", {
-  for(tute.dir in list.dirs(system.file("tutorials", package = "netrics"), 
-                            recursive = F)){
-    tute.file <- list.files(tute.dir, pattern = "*.Rmd", full.names = T)
-    expect_null(check_tute_rendering(tute.file))
+# test_that("netrics tutorials work", {
+#   for(tute in find_pkg_tutorial_paths("netrics")){
+#     expect_null(check_tute_rendering(tute))
+#   }
+# })
+
+test_that("netrics tutorial code runs without warnings or errors", {
+  skip_if_not_installed("netrics", minimum_version = "0.2.2")
+  for(tute in find_pkg_tutorial_paths("netrics")){
+    expect_null(check_tute_functions(tute), 
+                info = paste("Error in tutorial", basename(tute)))
   }
 })
\ No newline at end of file

From 6a31d742a9f66fb7f41c584e23b4772945e756e6 Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 21:20:35 +0200
Subject: [PATCH 7/8] Don't purl write chunks

---
 inst/tutorials/tutorial0/tutorial0.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/tutorials/tutorial0/tutorial0.Rmd b/inst/tutorials/tutorial0/tutorial0.Rmd
index 49f93cd7..d97cc8ea 100644
--- a/inst/tutorials/tutorial0/tutorial0.Rmd
+++ b/inst/tutorials/tutorial0/tutorial0.Rmd
@@ -360,7 +360,7 @@ list.files() # This tells you what files are in your working directory
 Compare the above with functions like the following, 
 which enables you to write an object out of R to some path on your hard-drive that you specify:
 
-```{r function-write, exercise = TRUE}
+```{r function-write, exercise = TRUE, purl=FALSE}
 write.csv(x = mydf, file = "~/Desktop/jamesdf.csv")
 ```
 

From fe79f87bb8e752ab92bb4637338fbfab3dc4075c Mon Sep 17 00:00:00 2001
From: James Hollway <james.hollway@graduateinstitute.ch>
Date: Fri, 17 Apr 2026 21:30:21 +0200
Subject: [PATCH 8/8] autograph tutorials only from version 1.0.1 or greater

---
 tests/testthat/test-tutorials_autograph.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-tutorials_autograph.R b/tests/testthat/test-tutorials_autograph.R
index fa4c0700..d41d50a0 100644
--- a/tests/testthat/test-tutorials_autograph.R
+++ b/tests/testthat/test-tutorials_autograph.R
@@ -5,7 +5,7 @@
 # })
 
 test_that("autograph tutorial code runs without warnings or errors", {
-  skip_if_not_installed("autograph", minimum_version = "1.0.0")
+  skip_if_not_installed("autograph", minimum_version = "1.0.1")
   for(tute in find_pkg_tutorial_paths("autograph")){
     expect_null(check_tute_functions(tute), 
                 info = paste("Error in tutorial", basename(tute)))