diff --git a/.Rbuildignore b/.Rbuildignore
index 8a8a9deb..802417e3 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -12,3 +12,5 @@
 ^scripts$
 ^\.appveyor\.yml$
 ^doc$
+^created\.xml$
+^expected\.xml$
diff --git a/DESCRIPTION b/DESCRIPTION
index b9690882..816dc468 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: beautier
 Title: 'BEAUti' from R
-Version: 2.5.2
+Version: 2.6
 Authors@R: c(
   person("Richèl J.C.", "Bilderbeek", email = "richel@richelbilderbeek.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1107-7049")),
   person("Joëlle", "Barido-Sottani", role = "rev", comment = "Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209"),
diff --git a/NEWS.md b/NEWS.md
index e674e2cf..fe3081bd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,24 @@
 
 Newest versions at top.
 
+## beautier 2.6 (2021-05-22)
+
+### NEW FEATURES
+
+ * None
+
+### MINOR IMPROVEMENTS
+
+ * Make sure that no files are created in `~/.cache`
+
+### BUG FIXES
+
+ * None
+
+### DEPRECATED AND DEFUNCT
+
+ * None
+
 ## beautier 2.5.2 (2021-05-22)
 
 ### NEW FEATURES
diff --git a/R/beautier.R b/R/beautier.R
index 6c0e8be2..ff260f95 100644
--- a/R/beautier.R
+++ b/R/beautier.R
@@ -13,7 +13,7 @@
 #' input_filename <- get_fasta_filename()
 #'
 #' # The file created by beautier, a BEAST2 input file
-#' output_filename <- tempfile()
+#' output_filename <- get_beautier_tempfilename()
 #'
 #' # Use the default BEAUti settings to create a BEAST2 input file
 #' create_beast2_input_file_from_model(
@@ -21,6 +21,7 @@
 #'   output_filename,
 #'   inference_model = create_inference_model()
 #' )
+#' file.remove(output_filename)
 #' @seealso
 #' These are packages associated with \code{beautier}:
 #' \itemize{
diff --git a/R/create_beast2_input_file.R b/R/create_beast2_input_file.R
index f8c4e211..997009de 100644
--- a/R/create_beast2_input_file.R
+++ b/R/create_beast2_input_file.R
@@ -6,12 +6,13 @@
 #' input_filename <- get_fasta_filename()
 #'
 #' # The file created by beautier, a BEAST2 input file
-#' output_filename <- tempfile(pattern = "beast2", fileext = ".xml")
+#' output_filename <- get_beautier_tempfilename()
 #'
 #' create_beast2_input_file(
 #'   input_filename,
 #'   output_filename
 #' )
+#' file.remove(output_filename)
 #' @author Richèl J.C. Bilderbeek
 #' @seealso
 #'   Use \link{create_beast2_input_file_from_model} to do the same with an
diff --git a/R/create_beast2_input_file_from_model.R b/R/create_beast2_input_file_from_model.R
index fa2de802..6a94825c 100644
--- a/R/create_beast2_input_file_from_model.R
+++ b/R/create_beast2_input_file_from_model.R
@@ -4,11 +4,13 @@
 #' @seealso use \link{create_beast2_input_from_model} to
 #' get the BEAST2 input file as text
 #' @examples
+#' output_filename <- get_beautier_tempfilename()
 #' create_beast2_input_file_from_model(
 #'   input_filename = get_fasta_filename(),
-#'   output_filename = tempfile(),
+#'   output_filename = output_filename,
 #'   inference_model = create_inference_model()
 #' )
+#' file.remove(output_filename)
 #' @author Richèl J.C. Bilderbeek
 #' @seealso
 #' See \code{\link{create_site_model}} for examples with
diff --git a/R/create_clock_model.R b/R/create_clock_model.R
index 09187aca..e8065245 100644
--- a/R/create_clock_model.R
+++ b/R/create_clock_model.R
@@ -15,25 +15,25 @@
 #'   model, see \code{\link{create_strict_clock_model}}.
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   rln_clock_model <- create_rln_clock_model()
+#' rln_clock_model <- create_rln_clock_model()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = rln_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = rln_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   strict_clock_model <- create_strict_clock_model()
+#' strict_clock_model <- create_strict_clock_model()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = strict_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = strict_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #' @export
 create_clock_model <- function(
   name,
@@ -80,27 +80,27 @@ create_clock_model <- function(
 #' @return a relaxed log-normal clock_model
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   rln_clock_model <- create_rln_clock_model()
+#' rln_clock_model <- create_rln_clock_model()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = rln_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = rln_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   rln_clock_model_exp <- create_rln_clock_model(
-#'     mean_rate_prior_distr = create_exp_distr()
-#'   )
+#' rln_clock_model_exp <- create_rln_clock_model(
+#'   mean_rate_prior_distr = create_exp_distr()
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = rln_clock_model_exp
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = rln_clock_model_exp
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rln_clock_model create_clock_model_rln
 #' @export create_rln_clock_model create_clock_model_rln
 create_rln_clock_model <- create_clock_model_rln <- function(
@@ -139,30 +139,30 @@ create_rln_clock_model <- create_clock_model_rln <- function(
 #' @return a strict clock_model
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   strict_clock_model <- create_strict_clock_model(
-#'     clock_rate_param = 1.0,
-#'     clock_rate_distr = create_uniform_distr()
-#'   )
+#' strict_clock_model <- create_strict_clock_model(
+#'   clock_rate_param = 1.0,
+#'   clock_rate_distr = create_uniform_distr()
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = strict_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = strict_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   strict_clock_model_gamma <- create_strict_clock_model(
-#'     clock_rate_distr = create_gamma_distr()
-#'   )
+#' strict_clock_model_gamma <- create_strict_clock_model(
+#'   clock_rate_distr = create_gamma_distr()
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = strict_clock_model_gamma
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = strict_clock_model_gamma
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_strict_clock_model create_clock_model_strict
 #' @export create_strict_clock_model create_clock_model_strict
 create_strict_clock_model <- create_clock_model_strict <- function(
diff --git a/R/create_distr.R b/R/create_distr.R
index 4260f5a7..652db838 100644
--- a/R/create_distr.R
+++ b/R/create_distr.R
@@ -33,18 +33,18 @@
 #'   and \code{\link{create_uniform_distr}}
 #'   for examples how to use those distributions
 #' @examples
-#'   # Use any distribution
-#'   distr <- create_beta_distr()
+#' # Use any distribution
+#' distr <- create_beta_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @author Richèl J.C. Bilderbeek
 #' @export
 create_distr <- function(
@@ -100,17 +100,17 @@ create_distr <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   beta_distr <- create_beta_distr()
+#' beta_distr <- create_beta_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = beta_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = beta_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_beta_distr create_distr_beta
 #' @export create_beta_distr create_distr_beta
 create_beta_distr <- create_distr_beta <- function(
@@ -163,17 +163,17 @@ create_beta_distr <- create_distr_beta <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   exp_distr <- create_exp_distr()
+#' exp_distr <- create_exp_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = exp_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = exp_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_exp_distr create_distr_exp
 #' @export create_exp_distr create_distr_exp
 create_exp_distr <- create_distr_exp <- function(
@@ -215,22 +215,22 @@ create_exp_distr <- create_distr_exp <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   gamma_distr <- create_gamma_distr(
-#'      alpha = 0.05,
-#'      beta = 10.0
-#'   )
+#' gamma_distr <- create_gamma_distr(
+#'    alpha = 0.05,
+#'    beta = 10.0
+#' )
 #'
-#'   gtr_site_model <- create_gtr_site_model(
-#'     rate_ac_prior_distr = gamma_distr
-#'   )
+#' gtr_site_model <- create_gtr_site_model(
+#'   rate_ac_prior_distr = gamma_distr
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = gtr_site_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = gtr_site_model
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_gamma_distr create_distr_gamma
 #' @export create_gamma_distr create_distr_gamma
 create_gamma_distr <- create_distr_gamma <- function(
@@ -288,17 +288,17 @@ create_gamma_distr <- create_distr_gamma <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   inv_gamma_distr <- create_inv_gamma_distr()
+#' inv_gamma_distr <- create_inv_gamma_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = inv_gamma_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = inv_gamma_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_inv_gamma_distr create_distr_inv_gamma
 #' @export create_inv_gamma_distr create_distr_inv_gamma
 create_inv_gamma_distr <- create_distr_inv_gamma <- function(
@@ -349,17 +349,17 @@ create_inv_gamma_distr <- create_distr_inv_gamma <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   laplace_distr <- create_laplace_distr()
+#' laplace_distr <- create_laplace_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = laplace_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = laplace_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_laplace_distr create_distr_laplace
 #' @export create_laplace_distr create_distr_laplace
 create_laplace_distr <- create_distr_laplace <- function(
@@ -411,17 +411,17 @@ create_laplace_distr <- create_distr_laplace <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   log_normal_distr <- create_log_normal_distr()
+#' log_normal_distr <- create_log_normal_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = log_normal_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = log_normal_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_log_normal_distr create_distr_log_normal
 #' @export create_log_normal_distr create_distr_log_normal
 create_log_normal_distr <- create_distr_log_normal <- function(
@@ -473,17 +473,17 @@ create_log_normal_distr <- create_distr_log_normal <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   normal_distr <- create_normal_distr()
+#' normal_distr <- create_normal_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = normal_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = normal_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_normal_distr create_distr_normal
 #' @export create_normal_distr create_distr_normal
 create_normal_distr <- create_distr_normal <- function(
@@ -527,17 +527,17 @@ create_normal_distr <- create_distr_normal <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   one_div_x_distr <- create_one_div_x_distr()
+#' one_div_x_distr <- create_one_div_x_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = one_div_x_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = one_div_x_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_one_div_x_distr create_distr_one_div_x
 #' @export create_one_div_x_distr create_distr_one_div_x
 create_one_div_x_distr <- create_distr_one_div_x <- function(
@@ -566,17 +566,17 @@ create_one_div_x_distr <- create_distr_one_div_x <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   poisson_distr <- create_poisson_distr()
+#' poisson_distr <- create_poisson_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = poisson_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = poisson_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_poisson_distr create_distr_poisson
 #' @export create_poisson_distr create_distr_poisson
 create_poisson_distr <- create_distr_poisson <- function(
@@ -611,17 +611,17 @@ create_poisson_distr <- create_distr_poisson <- function(
 #'   of all supported distributions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   uniform_distr <- create_uniform_distr()
+#' uniform_distr <- create_uniform_distr()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = uniform_distr
-#'     )
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = uniform_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_uniform_distr create_distr_uniform
 #' @export create_uniform_distr create_distr_uniform
 create_uniform_distr <- create_distr_uniform <- function(
diff --git a/R/create_gamma_site_model.R b/R/create_gamma_site_model.R
index 5146ba99..f22769e5 100644
--- a/R/create_gamma_site_model.R
+++ b/R/create_gamma_site_model.R
@@ -20,17 +20,17 @@
 #' @seealso Use \code{\link{create_gamma_site_model}}
 #'   to create a gamma site model
 #' @examples
-#'   gamma_site_model <- create_gamma_site_model(prop_invariant = 0.5)
+#' gamma_site_model <- create_gamma_site_model(prop_invariant = 0.5)
 #'
-#'   site_model <- create_hky_site_model(gamma_site_model = gamma_site_model)
+#' site_model <- create_hky_site_model(gamma_site_model = gamma_site_model)
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = site_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = site_model
+#' )
+#' file.remove(beast2_input_file)
 #' @author Richèl J.C. Bilderbeek
 #' @export
 create_gamma_site_model <- function(
diff --git a/R/create_inference_model.R b/R/create_inference_model.R
index fb33ae37..c05c5467 100644
--- a/R/create_inference_model.R
+++ b/R/create_inference_model.R
@@ -17,11 +17,13 @@
 #'   mcmc = create_mcmc(chain_length = 50000, store_every = 1000)
 #' )
 #'
+#' output_filename <- get_beautier_tempfilename()
 #' create_beast2_input_file_from_model(
 #'   input_filename = get_fasta_filename(),
-#'   output_filename = tempfile(fileext = ".xml"),
+#'   output_filename = output_filename,
 #'   inference_model = inference_model
 #' )
+#' file.remove(beast2_input_file)
 #' @export
 create_inference_model <- function(
   site_model = beautier::create_jc69_site_model(),
diff --git a/R/create_mcmc.R b/R/create_mcmc.R
index 6d47671e..f0785f08 100644
--- a/R/create_mcmc.R
+++ b/R/create_mcmc.R
@@ -24,16 +24,16 @@
 #' Use \code{\link{rename_mcmc_filenames}} to rename the filenames in an MCMC.
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'
 #' # Create an MCMC chain with 50 states
 #' mcmc <- create_mcmc(chain_length = 50000, store_every = 1000)
 #'
-#' beast2_input_file <- tempfile()
+#' beast2_input_file <- get_beautier_tempfilename()
 #' create_beast2_input_file(
 #'   get_fasta_filename(),
 #'   beast2_input_file,
 #'   mcmc = mcmc
 #' )
+#' file.remove(beast2_input_file)
 #' @export
 create_mcmc <- function(
   chain_length = 10000000,
diff --git a/R/create_mcmc_nested_sampling.R b/R/create_mcmc_nested_sampling.R
index 5e2fffd2..76dc28b1 100644
--- a/R/create_mcmc_nested_sampling.R
+++ b/R/create_mcmc_nested_sampling.R
@@ -17,21 +17,21 @@
 #'   with, among others, a short MCMC chain length.
 #' Use \code{\link{check_ns_mcmc}} to check that an NS MCMC object is valid.
 #' @examples
-#'   mcmc <- create_ns_mcmc(
-#'     chain_length = 1e7,
-#'     store_every = 1000,
-#'     particle_count = 1,
-#'     sub_chain_length = 1000,
-#'     epsilon = 1e-12
-#'   )
+#' mcmc <- create_ns_mcmc(
+#'   chain_length = 1e7,
+#'   store_every = 1000,
+#'   particle_count = 1,
+#'   sub_chain_length = 1000,
+#'   epsilon = 1e-12
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     get_fasta_filename(),
-#'     beast2_input_file,
-#'     mcmc = mcmc
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   get_fasta_filename(),
+#'   beast2_input_file,
+#'   mcmc = mcmc
+#' )
+#' file.remove(beast2_input_file)
 #' @references
 #'   * [1] Patricio Maturana Russel, Brendon J Brewer, Steffen Klaere,
 #'     Remco R Bouckaert; Model Selection and Parameter Inference in
diff --git a/R/create_param.R b/R/create_param.R
index ee5c3e7c..4674942c 100644
--- a/R/create_param.R
+++ b/R/create_param.R
@@ -23,24 +23,24 @@
 #' @return a parameter
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create an alpha parameter
-#'   alpha_param <- create_alpha_param()
+#' # Create an alpha parameter
+#' alpha_param <- create_alpha_param()
 #'
-#'   # Use the parameter in a distribution
-#'   beta_distr <- create_beta_distr(
-#'     alpha = alpha_param
-#'   )
+#' # Use the parameter in a distribution
+#' beta_distr <- create_beta_distr(
+#'   alpha = alpha_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = beta_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = beta_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @export
 create_param <- function(
   name,
@@ -85,24 +85,24 @@ create_param <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   alpha_param <- create_alpha_param()
+#' # Create the parameter
+#' alpha_param <- create_alpha_param()
 #'
-#'   # Use the parameter in a distribution
-#'   beta_distr <- create_beta_distr(
-#'     alpha = alpha_param
-#'   )
+#' # Use the parameter in a distribution
+#' beta_distr <- create_beta_distr(
+#'   alpha = alpha_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = beta_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = beta_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_alpha_param create_param_alpha
 #' @export create_alpha_param create_param_alpha
 create_alpha_param <- create_param_alpha <- function(
@@ -131,24 +131,24 @@ create_alpha_param <- create_param_alpha <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   beta_param <- create_beta_param()
+#' # Create the parameter
+#' beta_param <- create_beta_param()
 #'
-#'   # Use the parameter in a distribution
-#'   gamma_distr <- create_gamma_distr(
-#'     beta = beta_param
-#'   )
+#' # Use the parameter in a distribution
+#' gamma_distr <- create_gamma_distr(
+#'   beta = beta_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = gamma_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = gamma_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_beta_param create_param_beta
 #' @export create_beta_param create_param_beta
 create_beta_param <- create_param_beta <- function(
@@ -172,23 +172,23 @@ create_beta_param <- create_param_beta <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   clock_rate_param <- create_clock_rate_param(
-#'     id = "anthus_aco", value = 1.0
-#'   )
+#' clock_rate_param <- create_clock_rate_param(
+#'   id = "anthus_aco", value = 1.0
+#' )
 #'
-#'   # Use the parameter in a clock model
-#'   strict_clock_model <- create_strict_clock_model(
-#'     clock_rate_param = clock_rate_param
-#'   )
+#' # Use the parameter in a clock model
+#' strict_clock_model <- create_strict_clock_model(
+#'   clock_rate_param = clock_rate_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     clock_model = strict_clock_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   clock_model = strict_clock_model
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_clock_rate_param create_param_clock_rate
 #' @export create_clock_rate_param create_param_clock_rate
 create_clock_rate_param <- create_param_clock_rate <- function(
@@ -254,24 +254,24 @@ create_kappa_2_param <- create_param_kappa_2 <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   lambda_param <- create_lambda_param()
+#' # Create the parameter
+#' lambda_param <- create_lambda_param()
 #'
-#'   # Use the parameter in a distribution
-#'   poisson_distr <- create_poisson_distr(
-#'     lambda = lambda_param
-#'   )
+#' # Use the parameter in a distribution
+#' poisson_distr <- create_poisson_distr(
+#'   lambda = lambda_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = poisson_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = poisson_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_lambda_param create_param_lambda
 #' @export create_lambda_param create_param_lambda
 create_lambda_param <- create_param_lambda <- function(
@@ -295,24 +295,24 @@ create_lambda_param <- create_param_lambda <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   m_param <- create_m_param()
+#' # Create the parameter
+#' m_param <- create_m_param()
 #'
-#'   # Use the parameter in a distribution
-#'   log_normal_distr <- create_log_normal_distr(
-#'     m = m_param
-#'   )
+#' # Use the parameter in a distribution
+#' log_normal_distr <- create_log_normal_distr(
+#'   m = m_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = log_normal_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = log_normal_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_m_param create_param_m
 #' @export create_m_param create_param_m
 create_m_param <- create_param_m <- function(
@@ -339,24 +339,24 @@ create_m_param <- create_param_m <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   mean_param <- create_mean_param(value = 1.0)
+#' # Create the parameter
+#' mean_param <- create_mean_param(value = 1.0)
 #'
-#'   # Use the parameter in a distribution
-#'   exp_distr <- create_exp_distr(
-#'     mean = mean_param
-#'   )
+#' # Use the parameter in a distribution
+#' exp_distr <- create_exp_distr(
+#'   mean = mean_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = exp_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = exp_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_mean_param create_param_mean
 #' @export create_mean_param create_param_mean
 create_mean_param <- create_param_mean <- function(
@@ -381,24 +381,24 @@ create_mean_param <- create_param_mean <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   mu_param <- create_mu_param()
+#' # Create the parameter
+#' mu_param <- create_mu_param()
 #'
-#'   # Use the parameter in a distribution
-#'   laplace_distr <- create_laplace_distr(
-#'     mu = mu_param
-#'   )
+#' # Use the parameter in a distribution
+#' laplace_distr <- create_laplace_distr(
+#'   mu = mu_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = laplace_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = laplace_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_mu_param create_param_mu
 #' @export create_mu_param create_param_mu
 create_mu_param <- create_param_mu <- function(
@@ -420,19 +420,19 @@ create_mu_param <- create_param_mu <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create parameter
-#'   rate_ac_param <- create_rate_ac_param(value = 1, estimate = FALSE)
+#' # Create parameter
+#' rate_ac_param <- create_rate_ac_param(value = 1, estimate = FALSE)
 #'
-#'   # Use the parameter to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = create_gtr_site_model(
-#'       rate_ac_param = rate_ac_param
-#'     )
+#' # Use the parameter to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = create_gtr_site_model(
+#'     rate_ac_param = rate_ac_param
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rate_ac_param create_param_rate_ac
 #' @export create_rate_ac_param create_param_rate_ac
 create_rate_ac_param <- create_param_rate_ac <- function(
@@ -457,19 +457,19 @@ create_rate_ac_param <- create_param_rate_ac <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create parameter
-#'   rate_ag_param <- create_rate_ag_param(value = 1, estimate = FALSE)
+#' # Create parameter
+#' rate_ag_param <- create_rate_ag_param(value = 1, estimate = FALSE)
 #'
-#'   # Use the parameter to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = create_gtr_site_model(
-#'       rate_ag_param = rate_ag_param
-#'     )
+#' # Use the parameter to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = create_gtr_site_model(
+#'     rate_ag_param = rate_ag_param
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rate_ag_param create_param_rate_ag
 #' @export create_rate_ag_param create_param_rate_ag
 create_rate_ag_param <- create_param_rate_ag <- function(
@@ -494,19 +494,19 @@ create_rate_ag_param <- create_param_rate_ag <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create parameter
-#'   rate_at_param <- create_rate_at_param(value = 1, estimate = FALSE)
+#' # Create parameter
+#' rate_at_param <- create_rate_at_param(value = 1, estimate = FALSE)
 #'
-#'   # Use the parameter to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = create_gtr_site_model(
-#'       rate_at_param = rate_at_param
-#'     )
+#' # Use the parameter to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = create_gtr_site_model(
+#'     rate_at_param = rate_at_param
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rate_at_param create_param_rate_at
 #' @export create_rate_at_param create_param_rate_at
 create_rate_at_param <- create_param_rate_at <- function(
@@ -531,19 +531,19 @@ create_rate_at_param <- create_param_rate_at <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create parameter
-#'   rate_cg_param <- create_rate_cg_param(value = 1, estimate = FALSE)
+#' # Create parameter
+#' rate_cg_param <- create_rate_cg_param(value = 1, estimate = FALSE)
 #'
-#'   # Use the parameter to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = create_gtr_site_model(
-#'       rate_cg_param = rate_cg_param
-#'     )
+#' # Use the parameter to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = create_gtr_site_model(
+#'     rate_cg_param = rate_cg_param
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rate_cg_param create_param_rate_cg
 #' @export create_rate_cg_param create_param_rate_cg
 create_rate_cg_param <- create_param_rate_cg <- function(
@@ -568,19 +568,19 @@ create_rate_cg_param <- create_param_rate_cg <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create parameter
-#'   rate_ct_param <- create_rate_ct_param(value = 1)
+#' # Create parameter
+#' rate_ct_param <- create_rate_ct_param(value = 1)
 #'
-#'   # Use the parameter to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = create_gtr_site_model(
-#'       rate_ct_param = rate_ct_param
-#'     )
+#' # Use the parameter to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = create_gtr_site_model(
+#'     rate_ct_param = rate_ct_param
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rate_ct_param create_param_rate_ct
 #' @export create_rate_ct_param create_param_rate_ct
 create_rate_ct_param <- create_param_rate_ct <- function(
@@ -604,19 +604,19 @@ create_rate_ct_param <- create_param_rate_ct <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create parameter
-#'   rate_gt_param <- create_rate_gt_param(value = 1, estimate = FALSE)
+#' # Create parameter
+#' rate_gt_param <- create_rate_gt_param(value = 1, estimate = FALSE)
 #'
-#'   # Use the parameter to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = create_gtr_site_model(
-#'       rate_gt_param = rate_gt_param
-#'     )
+#' # Use the parameter to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = create_gtr_site_model(
+#'     rate_gt_param = rate_gt_param
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_rate_gt_param create_param_rate_gt
 #' @export create_rate_gt_param create_param_rate_gt
 create_rate_gt_param <- create_param_rate_gt <- function(
@@ -643,24 +643,24 @@ create_rate_gt_param <- create_param_rate_gt <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   s_param <- create_s_param()
+#' # Create the parameter
+#' s_param <- create_s_param()
 #'
-#'   # Use the parameter in a distribution
-#'   log_normal_distr <- create_log_normal_distr(
-#'     s = s_param
-#'   )
+#' # Use the parameter in a distribution
+#' log_normal_distr <- create_log_normal_distr(
+#'   s = s_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = log_normal_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = log_normal_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_s_param create_param_s
 #' @export create_s_param create_param_s
 create_s_param <- create_param_s <- function(
@@ -689,24 +689,24 @@ create_s_param <- create_param_s <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   scale_param <- create_scale_param()
+#' # Create the parameter
+#' scale_param <- create_scale_param()
 #'
-#'   # Use the parameter in a distribution
-#'   laplace_distr <- create_laplace_distr(
-#'     scale = scale_param
-#'   )
+#' # Use the parameter in a distribution
+#' laplace_distr <- create_laplace_distr(
+#'   scale = scale_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = laplace_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = laplace_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_scale_param create_param_scale
 #' @export create_scale_param create_param_scale
 create_scale_param <- create_param_scale <- function(
@@ -731,24 +731,24 @@ create_scale_param <- create_param_scale <- function(
 #'   of all parameters that can be created
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   # Create the parameter
-#'   sigma_param <- create_sigma_param()
+#' # Create the parameter
+#' sigma_param <- create_sigma_param()
 #'
-#'   # Use the parameter in a distribution
-#'   normal_distr <- create_normal_distr(
-#'     sigma = sigma_param
-#'   )
+#' # Use the parameter in a distribution
+#' normal_distr <- create_normal_distr(
+#'   sigma = sigma_param
+#' )
 #'
-#'   # Use the distribution to create a BEAST2 input file
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior(
-#'       birth_rate_distr = normal_distr
-#'     )
+#' # Use the distribution to create a BEAST2 input file
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior(
+#'     birth_rate_distr = normal_distr
 #'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_sigma_param create_param_sigma
 #' @export create_sigma_param create_param_sigma
 create_sigma_param <- create_param_sigma <- function(
diff --git a/R/create_site_model.R b/R/create_site_model.R
index 20b8cd4d..c07111ca 100644
--- a/R/create_site_model.R
+++ b/R/create_site_model.R
@@ -24,36 +24,40 @@
 #' input_filename <- get_fasta_filename()
 #'
 #' # GTR
-#' output_filename <- tempfile(pattern = "example_gtr", fileext = ".xml")
+#' output_filename <- get_beautier_tempfilename()
 #' create_beast2_input_file(
 #'   input_filename = input_filename,
 #'   output_filename = output_filename,
 #'   site_model = create_gtr_site_model()
 #' )
+#' file.remove(output_filename)
 #'
 #' # HKY
-#' output_filename <- tempfile(pattern = "example_hky", fileext = ".xml")
+#' output_filename <- get_beautier_tempfilename()
 #' create_beast2_input_file(
 #'   input_filename = input_filename,
 #'   output_filename = output_filename,
 #'   site_model = create_hky_site_model()
 #' )
+#' file.remove(output_filename)
 #'
 #' # JC69
-#' output_filename <- tempfile(pattern = "example_jc69", fileext = ".xml")
+#' output_filename <- get_beautier_tempfilename()
 #' create_beast2_input_file(
 #'   input_filename = input_filename,
 #'   output_filename = output_filename,
 #'   site_model = create_jc69_site_model()
 #' )
+#' file.remove(output_filename)
 #'
 #' # TN93
-#' output_filename <- tempfile(pattern = "example_tn93", fileext = ".xml")
+#' output_filename <- get_beautier_tempfilename()
 #' create_beast2_input_file(
 #'   input_filename = input_filename,
 #'   output_filename = output_filename,
 #'   site_model = create_tn93_site_model()
 #' )
+#' file.remove(output_filename)
 #' @export
 create_site_model <- function(
   name,
@@ -128,22 +132,22 @@ create_site_model <- function(
 #' @return a GTR site_model
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   gtr_site_model <- create_gtr_site_model(
-#'     rate_ac_param = 1.2,
-#'     rate_ag_param = 2.3,
-#'     rate_at_param = 3.4,
-#'     rate_cg_param = 4.5,
-#'     rate_ct_param = 5.6,
-#'     rate_gt_param = 6.7
-#'  )
+#' gtr_site_model <- create_gtr_site_model(
+#'   rate_ac_param = 1.2,
+#'   rate_ag_param = 2.3,
+#'   rate_at_param = 3.4,
+#'   rate_cg_param = 4.5,
+#'   rate_ct_param = 5.6,
+#'   rate_gt_param = 6.7
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     site_model = gtr_site_model
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   site_model = gtr_site_model
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_gtr_site_model create_site_model_gtr
 #' @export create_gtr_site_model create_site_model_gtr
 create_gtr_site_model <- create_site_model_gtr <- function(
@@ -233,12 +237,13 @@ create_gtr_site_model <- create_site_model_gtr <- function(
 #' @author Richèl J.C. Bilderbeek
 #' @examples
 #'  hky_site_model <- create_hky_site_model()
-#'
+#'  output_filename <- get_beautier_tempfilename()
 #'  create_beast2_input_file(
 #'    input_filename = get_fasta_filename(),
-#'    output_filename = tempfile(pattern = "beast", fileext = ".xml"),
+#'    output_filename = output_filename,
 #'    site_model = hky_site_model
 #'  )
+#' file.remove(output_filename)
 #' @aliases create_hky_site_model create_site_model_hky
 #' @export create_hky_site_model create_site_model_hky
 create_hky_site_model <- create_site_model_hky <- function(
@@ -268,11 +273,13 @@ create_hky_site_model <- create_site_model_hky <- function(
 #' @examples
 #'  jc69_site_model <- create_jc69_site_model()
 #'
+#'  output_filename <- get_beautier_tempfilename()
 #'  create_beast2_input_file(
 #'    input_filename = get_fasta_filename(),
-#'    output_filename = tempfile(pattern = "beast", fileext = ".xml"),
+#'    output_filename = output_filename,
 #'    site_model = jc69_site_model
 #'  )
+#' file.remove(output_filename)
 #' @aliases create_jc69_site_model create_site_model_jc69
 #' @export create_jc69_site_model create_site_model_jc69
 create_jc69_site_model <- create_site_model_jc69 <- function(
@@ -316,11 +323,13 @@ create_jc69_site_model <- create_site_model_jc69 <- function(
 #'    kappa_2_param = 2.0
 #'  )
 #'
+#'  output_filename <- get_beautier_tempfilename()
 #'  create_beast2_input_file(
 #'    input_filename = get_fasta_filename(),
-#'    output_filename = tempfile(pattern = "beast", fileext = ".xml"),
+#'    output_filename = output_filename,
 #'    site_model = tn93_site_model
 #'  )
+#' file.remove(output_filename)
 #' @aliases create_tn93_site_model create_site_model_tn93
 #' @export create_tn93_site_model create_site_model_tn93
 create_tn93_site_model <- create_site_model_tn93 <- function(
diff --git a/R/create_temp_screenlog_filename.R b/R/create_temp_screenlog_filename.R
index 73272dae..3b8eb322 100644
--- a/R/create_temp_screenlog_filename.R
+++ b/R/create_temp_screenlog_filename.R
@@ -4,9 +4,8 @@
 #' @export
 create_temp_screenlog_filename <- function() {
   normalizePath(
-    tempfile(
+    get_beautier_tempfilename(
       pattern = "screenlog_",
-      tmpdir = rappdirs::user_cache_dir(),
       fileext = ".csv"
     ),
     mustWork = FALSE
diff --git a/R/create_temp_tracelog_filename.R b/R/create_temp_tracelog_filename.R
index e7021ae8..acf3de08 100644
--- a/R/create_temp_tracelog_filename.R
+++ b/R/create_temp_tracelog_filename.R
@@ -4,9 +4,8 @@
 #' @export
 create_temp_tracelog_filename <- function() {
   normalizePath(
-    tempfile(
+    get_beautier_tempfilename(
       pattern = "tracelog_",
-      tmpdir = rappdirs::user_cache_dir(),
       fileext = ".log"
     ),
     mustWork = FALSE
diff --git a/R/create_temp_treelog_filename.R b/R/create_temp_treelog_filename.R
index c5d6a842..144e5152 100644
--- a/R/create_temp_treelog_filename.R
+++ b/R/create_temp_treelog_filename.R
@@ -4,9 +4,8 @@
 #' @export
 create_temp_treelog_filename <- function() {
   normalizePath(
-    tempfile(
+    get_beautier_tempfilename(
       pattern = "treelog_",
-      tmpdir = rappdirs::user_cache_dir(),
       fileext = ".trees"
     ),
     mustWork = FALSE
diff --git a/R/create_test_inference_model.R b/R/create_test_inference_model.R
index 320d2361..8d012d9a 100644
--- a/R/create_test_inference_model.R
+++ b/R/create_test_inference_model.R
@@ -14,12 +14,13 @@
 #' @examples
 #' inference_model <- create_test_inference_model()
 #'
-#' beast2_input_file <- tempfile(fileext = ".xml")
+#' beast2_input_file <- get_beautier_tempfilename()
 #' create_beast2_input_file_from_model(
 #'   get_fasta_filename(),
 #'   beast2_input_file,
 #'   inference_model = inference_model
 #' )
+#' file.remove(beast2_input_file)
 #' @export
 create_test_inference_model <- function(
   site_model = beautier::create_jc69_site_model(),
diff --git a/R/create_test_mcmc.R b/R/create_test_mcmc.R
index 621d0ded..0576ce11 100644
--- a/R/create_test_mcmc.R
+++ b/R/create_test_mcmc.R
@@ -8,12 +8,13 @@
 #' # Create an MCMC chain with 50 states
 #' mcmc <- create_test_mcmc()
 #'
-#' beast2_input_file <- tempfile(fileext = ".xml")
+#' beast2_input_file <- get_beautier_tempfilename()
 #' create_beast2_input_file(
 #'   get_fasta_filename(),
 #'   beast2_input_file,
 #'   mcmc = mcmc
 #' )
+#' file.remove(beast2_input_file)
 #' @export
 create_test_mcmc <- function(
   chain_length = 3000,
diff --git a/R/create_test_ns_mcmc.R b/R/create_test_ns_mcmc.R
index b716a7f6..1a50bfbe 100644
--- a/R/create_test_ns_mcmc.R
+++ b/R/create_test_ns_mcmc.R
@@ -8,16 +8,14 @@
 #' @seealso Use \code{\link{create_ns_mcmc}} to create a default
 #' nested sampling MCMC
 #' @examples
-#'
 #' mcmc <- create_test_ns_mcmc()
-#'
-#' beast2_input_file <- tempfile(fileext = ".xml")
-#'
+#' beast2_input_file <- get_beautier_tempfilename()
 #' create_beast2_input_file(
 #'   get_fasta_filename(),
 #'   beast2_input_file,
 #'   mcmc = mcmc
 #' )
+#' file.remove(beast2_input_file)
 #' @author Richèl J.C. Bilderbeek
 #' @export
 create_test_ns_mcmc <- function(
diff --git a/R/create_tree_prior.R b/R/create_tree_prior.R
index 63fef7c4..6cc36348 100644
--- a/R/create_tree_prior.R
+++ b/R/create_tree_prior.R
@@ -20,45 +20,45 @@
 #'   for more examples using those functions
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_bd_tree_prior()
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_bd_tree_prior()
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_beautier_path("test_output_6.fas"),
-#'     beast2_input_file,
-#'     tree_prior = create_cbs_tree_prior()
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_beautier_path("test_output_6.fas"),
+#'   beast2_input_file,
+#'   tree_prior = create_cbs_tree_prior()
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_ccp_tree_prior()
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_ccp_tree_prior()
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_cep_tree_prior()
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_cep_tree_prior()
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = create_yule_tree_prior()
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = create_yule_tree_prior()
+#' )
+#' file.remove(beast2_input_file)
 #' @export
 create_tree_prior <- function(
   name,
@@ -100,27 +100,27 @@ create_tree_prior <- function(
 #'   its FASTA filename using \code{\link{get_alignment_id}}
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   bd_tree_prior <- create_bd_tree_prior()
+#' bd_tree_prior <- create_bd_tree_prior()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = bd_tree_prior
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = bd_tree_prior
+#' )
+#' file.remove(beast2_input_file)
 #'
-#'   bd_tree_prior_exp <- create_bd_tree_prior(
-#'     birth_rate_distr = create_exp_distr()
-#'   )
+#' bd_tree_prior_exp <- create_bd_tree_prior(
+#'   birth_rate_distr = create_exp_distr()
+#' )
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = bd_tree_prior_exp
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = bd_tree_prior_exp
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_bd_tree_prior create_tree_prior_bd
 #' @export create_bd_tree_prior create_tree_prior_bd
 create_bd_tree_prior <- create_tree_prior_bd <- function(
@@ -143,15 +143,15 @@ create_bd_tree_prior <- create_tree_prior_bd <- function(
 #'   its FASTA filename using \code{\link{get_alignment_id}}
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   cbs_tree_prior <- create_cbs_tree_prior()
+#' cbs_tree_prior <- create_cbs_tree_prior()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_beautier_path("test_output_6.fas"),
-#'     beast2_input_file,
-#'     tree_prior = cbs_tree_prior
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_beautier_path("test_output_6.fas"),
+#'   beast2_input_file,
+#'   tree_prior = cbs_tree_prior
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_cbs_tree_prior create_tree_prior_cbs
 #' @export create_cbs_tree_prior create_tree_prior_cbs
 create_cbs_tree_prior <- create_tree_prior_cbs <- function(
@@ -176,15 +176,15 @@ create_cbs_tree_prior <- create_tree_prior_cbs <- function(
 #'   its FASTA filename using \code{\link{get_alignment_id}}
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   ccp_tree_prior <- create_ccp_tree_prior()
+#' ccp_tree_prior <- create_ccp_tree_prior()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = ccp_tree_prior
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = ccp_tree_prior
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_ccp_tree_prior create_tree_prior_ccp
 #' @export create_ccp_tree_prior create_tree_prior_ccp
 create_ccp_tree_prior <- create_tree_prior_ccp <- function(
@@ -211,15 +211,15 @@ create_ccp_tree_prior <- create_tree_prior_ccp <- function(
 #'   its FASTA filename using \code{\link{get_alignment_id}}
 #' @author Richèl J.C. Bilderbeek
 #' @examples
-#'   cep_tree_prior <- create_cep_tree_prior()
+#' cep_tree_prior <- create_cep_tree_prior()
 #'
-#'   beast2_input_file <- tempfile(fileext = ".xml")
-#'   create_beast2_input_file(
-#'     input_filename = get_fasta_filename(),
-#'     beast2_input_file,
-#'     tree_prior = cep_tree_prior
-#'   )
-#'   testit::assert(file.exists(beast2_input_file))
+#' beast2_input_file <- get_beautier_tempfilename()
+#' create_beast2_input_file(
+#'   input_filename = get_fasta_filename(),
+#'   beast2_input_file,
+#'   tree_prior = cep_tree_prior
+#' )
+#' file.remove(beast2_input_file)
 #' @aliases create_cep_tree_prior create_tree_prior_cep
 #' @export create_cep_tree_prior create_tree_prior_cep
 create_cep_tree_prior <- create_tree_prior_cep <- function(
@@ -251,12 +251,13 @@ create_cep_tree_prior <- create_tree_prior_cep <- function(
 #' @examples
 #'  yule_tree_prior <- create_yule_tree_prior()
 #'
-#'  beast2_input_file <- tempfile(fileext = ".xml")
+#'  beast2_input_file <- get_beautier_tempfilename()
 #'  create_beast2_input_file(
 #'    input_filename = get_fasta_filename(),
 #'    beast2_input_file,
 #'    tree_prior = yule_tree_prior
 #' )
+#' file.remove(beast2_input_file)
 #' @aliases create_yule_tree_prior create_tree_prior_yule
 #' @export create_yule_tree_prior create_tree_prior_yule
 create_yule_tree_prior <- create_tree_prior_yule <- function(
diff --git a/R/get_beautier_tempfilename.R b/R/get_beautier_tempfilename.R
index 2e31f23d..52201c10 100644
--- a/R/get_beautier_tempfilename.R
+++ b/R/get_beautier_tempfilename.R
@@ -1,11 +1,14 @@
 #' Get a temporary filename
 #'
-#' Get a temporary filename, similar to \linky{tempfile},
+#' Get a temporary filename, similar to \link{tempfile},
 #' except that it always writes to a temporary folder
 #' named \link{beautier}.
 #' @note this function is added to make sure no temporary
 #' cache files are left undeleted
-#' @inheritParams tempfile
+#' @param pattern	a non-empty character vector
+#'   giving the initial part of the name.
+#' @param fileext	a non-empty character vector
+#'   giving the file extension
 #' @return name for a temporary file
 #' @export
 get_beautier_tempfilename <- function(
diff --git a/R/get_remove_hex_fun.R b/R/get_remove_hex_fun.R
index 529d3df3..2da66b8f 100644
--- a/R/get_remove_hex_fun.R
+++ b/R/get_remove_hex_fun.R
@@ -5,7 +5,8 @@
 #' where \code{/home/john/.cache} is the location to a temporary folder
 #' (on Linux) and \code{tracelog_82c5888db98.log} the filename.
 #' The filename ends with a hex string (as is common for temporary files,
-#' as \link{tempfile} does so). Because \link{beautier} puts an underscore
+#' as \link{tempfile} does so).
+#' Because \link{beautier} puts an underscore
 #' between the filename description (\code{tracelog}) and the hex
 #' string, this function removes both.
 #'
diff --git a/R/get_test_filenames.R b/R/get_test_filenames.R
index 07f4b002..b2363aa6 100644
--- a/R/get_test_filenames.R
+++ b/R/get_test_filenames.R
@@ -1,13 +1,15 @@
 #' Get the path of a FASTA file used in testing
 #' @return the path of a FASTA file used in testing
 #' @examples
-#'   filename <- beautier::get_fasta_filename()
-#'   testit::assert(file.exists(filename))
+#' input_filename <- beautier::get_fasta_filename()
+#' output_filename <- get_beautier_tempfilename()
 #'
-#'   create_beast2_input_file(
-#'     input_filename = filename,
-#'     output_filename = tempfile(pattern = "beast", fileext = ".xml")
-#'   )
+#' create_beast2_input_file(
+#'   input_filename = input_filename,
+#'   output_filename = output_filename
+#' )
+#'
+#' file.remove(output_filename)
 #' @author Richèl J.C. Bilderbeek
 #' @export
 get_fasta_filename <- function() {
diff --git a/doc/demo.R b/doc/demo.R
index c9d01c05..dfb75d40 100644
--- a/doc/demo.R
+++ b/doc/demo.R
@@ -14,7 +14,7 @@ fasta_filename <- get_beautier_path("test_output_0.fas")
 image(ape::read.FASTA(fasta_filename))
 
 ## ----create_output_filename---------------------------------------------------
-output_filename <- tempfile(pattern = "beast2", fileext = ".xml")
+output_filename <- get_beautier_tempfilename(pattern = "beast2", fileext = ".xml")
 output_filename
 
 ## ----create_beast2_input_file-------------------------------------------------
diff --git a/man/beautier.Rd b/man/beautier.Rd
index 674ed8f3..df0169de 100644
--- a/man/beautier.Rd
+++ b/man/beautier.Rd
@@ -19,7 +19,7 @@ features of BEAST2 that \code{beautier} supports.
 input_filename <- get_fasta_filename()
 
 # The file created by beautier, a BEAST2 input file
-output_filename <- tempfile()
+output_filename <- get_beautier_tempfilename()
 
 # Use the default BEAUti settings to create a BEAST2 input file
 create_beast2_input_file_from_model(
@@ -27,6 +27,7 @@ create_beast2_input_file_from_model(
   output_filename,
   inference_model = create_inference_model()
 )
+file.remove(output_filename)
 }
 \seealso{
 These are packages associated with \code{beautier}:
diff --git a/man/create_alpha_param.Rd b/man/create_alpha_param.Rd
index f3d9b933..da00c66e 100644
--- a/man/create_alpha_param.Rd
+++ b/man/create_alpha_param.Rd
@@ -28,24 +28,24 @@ and inverse-gamma distribution
 It cannot be estimated (as a hyper parameter) yet.
 }
 \examples{
-  # Create the parameter
-  alpha_param <- create_alpha_param()
+# Create the parameter
+alpha_param <- create_alpha_param()
 
-  # Use the parameter in a distribution
-  beta_distr <- create_beta_distr(
-    alpha = alpha_param
-  )
+# Use the parameter in a distribution
+beta_distr <- create_beta_distr(
+  alpha = alpha_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = beta_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = beta_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_bd_tree_prior.Rd b/man/create_bd_tree_prior.Rd
index 3a91c475..4a396019 100644
--- a/man/create_bd_tree_prior.Rd
+++ b/man/create_bd_tree_prior.Rd
@@ -27,27 +27,27 @@ a Birth-Death tree_prior
 Create a Birth-Death tree prior
 }
 \examples{
-  bd_tree_prior <- create_bd_tree_prior()
+bd_tree_prior <- create_bd_tree_prior()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = bd_tree_prior
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = bd_tree_prior
+)
+file.remove(beast2_input_file)
 
-  bd_tree_prior_exp <- create_bd_tree_prior(
-    birth_rate_distr = create_exp_distr()
-  )
+bd_tree_prior_exp <- create_bd_tree_prior(
+  birth_rate_distr = create_exp_distr()
+)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = bd_tree_prior_exp
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = bd_tree_prior_exp
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 An alignment ID can be extracted from
diff --git a/man/create_beast2_input_file.Rd b/man/create_beast2_input_file.Rd
index 11902472..7cd54ad1 100644
--- a/man/create_beast2_input_file.Rd
+++ b/man/create_beast2_input_file.Rd
@@ -84,12 +84,13 @@ Create a BEAST2 input file
 input_filename <- get_fasta_filename()
 
 # The file created by beautier, a BEAST2 input file
-output_filename <- tempfile(pattern = "beast2", fileext = ".xml")
+output_filename <- get_beautier_tempfilename()
 
 create_beast2_input_file(
   input_filename,
   output_filename
 )
+file.remove(output_filename)
 }
 \seealso{
 Use \link{create_beast2_input_file_from_model} to do the same with an
diff --git a/man/create_beast2_input_file_from_model.Rd b/man/create_beast2_input_file_from_model.Rd
index f492b568..14605cc8 100644
--- a/man/create_beast2_input_file_from_model.Rd
+++ b/man/create_beast2_input_file_from_model.Rd
@@ -32,11 +32,13 @@ nothing
 Create a BEAST2 input file from an inference model
 }
 \examples{
+output_filename <- get_beautier_tempfilename()
 create_beast2_input_file_from_model(
   input_filename = get_fasta_filename(),
-  output_filename = tempfile(),
+  output_filename = output_filename,
   inference_model = create_inference_model()
 )
+file.remove(output_filename)
 }
 \seealso{
 use \link{create_beast2_input_from_model} to
diff --git a/man/create_beta_distr.Rd b/man/create_beta_distr.Rd
index 0cbf26dc..9dffca2d 100644
--- a/man/create_beta_distr.Rd
+++ b/man/create_beta_distr.Rd
@@ -45,17 +45,17 @@ a beta distribution
 Create a beta distribution
 }
 \examples{
-  beta_distr <- create_beta_distr()
+beta_distr <- create_beta_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = beta_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = beta_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_beta_param.Rd b/man/create_beta_param.Rd
index f2190791..bbabaf2c 100644
--- a/man/create_beta_param.Rd
+++ b/man/create_beta_param.Rd
@@ -28,24 +28,24 @@ and inverse-gamma distribution
 It cannot be estimated (as a hyper parameter) yet.
 }
 \examples{
-  # Create the parameter
-  beta_param <- create_beta_param()
+# Create the parameter
+beta_param <- create_beta_param()
 
-  # Use the parameter in a distribution
-  gamma_distr <- create_gamma_distr(
-    beta = beta_param
-  )
+# Use the parameter in a distribution
+gamma_distr <- create_gamma_distr(
+  beta = beta_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = gamma_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = gamma_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_cbs_tree_prior.Rd b/man/create_cbs_tree_prior.Rd
index 177021c0..002a6e14 100644
--- a/man/create_cbs_tree_prior.Rd
+++ b/man/create_cbs_tree_prior.Rd
@@ -22,15 +22,15 @@ a Coalescent Bayesian Skyline tree_prior
 Create a Coalescent Bayesian Skyline tree prior
 }
 \examples{
-  cbs_tree_prior <- create_cbs_tree_prior()
+cbs_tree_prior <- create_cbs_tree_prior()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_beautier_path("test_output_6.fas"),
-    beast2_input_file,
-    tree_prior = cbs_tree_prior
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_beautier_path("test_output_6.fas"),
+  beast2_input_file,
+  tree_prior = cbs_tree_prior
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 An alignment ID can be extracted from
diff --git a/man/create_ccp_tree_prior.Rd b/man/create_ccp_tree_prior.Rd
index c25fb8c8..ae46506a 100644
--- a/man/create_ccp_tree_prior.Rd
+++ b/man/create_ccp_tree_prior.Rd
@@ -23,15 +23,15 @@ a Coalescent Constant Population tree_prior
 Create a Coalescent Constant Population tree prior
 }
 \examples{
-  ccp_tree_prior <- create_ccp_tree_prior()
+ccp_tree_prior <- create_ccp_tree_prior()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = ccp_tree_prior
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = ccp_tree_prior
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 An alignment ID can be extracted from
diff --git a/man/create_cep_tree_prior.Rd b/man/create_cep_tree_prior.Rd
index 316df2ae..c8dd4247 100644
--- a/man/create_cep_tree_prior.Rd
+++ b/man/create_cep_tree_prior.Rd
@@ -27,15 +27,15 @@ a Coalescent Exponential Population tree_prior
 Create a Coalescent Exponential Population tree prior
 }
 \examples{
-  cep_tree_prior <- create_cep_tree_prior()
+cep_tree_prior <- create_cep_tree_prior()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = cep_tree_prior
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = cep_tree_prior
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 An alignment ID can be extracted from
diff --git a/man/create_clock_model.Rd b/man/create_clock_model.Rd
index 27d2c8f3..65c05bd0 100644
--- a/man/create_clock_model.Rd
+++ b/man/create_clock_model.Rd
@@ -26,25 +26,25 @@ Prefer using the named function
   and \code{\link{create_strict_clock_model}}
 }
 \examples{
-  rln_clock_model <- create_rln_clock_model()
+rln_clock_model <- create_rln_clock_model()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    clock_model = rln_clock_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  clock_model = rln_clock_model
+)
+file.remove(beast2_input_file)
 
-  strict_clock_model <- create_strict_clock_model()
+strict_clock_model <- create_strict_clock_model()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    clock_model = strict_clock_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  clock_model = strict_clock_model
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 An alignment ID can be extracted from
diff --git a/man/create_clock_rate_param.Rd b/man/create_clock_rate_param.Rd
index 720870ab..af3c64a9 100644
--- a/man/create_clock_rate_param.Rd
+++ b/man/create_clock_rate_param.Rd
@@ -24,23 +24,23 @@ Create a parameter called \code{clock_rate},
 It cannot be estimated (as a hyper parameter) yet.
 }
 \examples{
-  clock_rate_param <- create_clock_rate_param(
-    id = "anthus_aco", value = 1.0
-  )
+clock_rate_param <- create_clock_rate_param(
+  id = "anthus_aco", value = 1.0
+)
 
-  # Use the parameter in a clock model
-  strict_clock_model <- create_strict_clock_model(
-    clock_rate_param = clock_rate_param
-  )
+# Use the parameter in a clock model
+strict_clock_model <- create_strict_clock_model(
+  clock_rate_param = clock_rate_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    clock_model = strict_clock_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  clock_model = strict_clock_model
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_distr.Rd b/man/create_distr.Rd
index 5c1baba0..ff04c813 100644
--- a/man/create_distr.Rd
+++ b/man/create_distr.Rd
@@ -55,18 +55,18 @@ See
   for examples how to use those distributions
 }
 \examples{
-  # Use any distribution
-  distr <- create_beta_distr()
+# Use any distribution
+distr <- create_beta_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_exp_distr.Rd b/man/create_exp_distr.Rd
index 46358243..555215b9 100644
--- a/man/create_exp_distr.Rd
+++ b/man/create_exp_distr.Rd
@@ -29,17 +29,17 @@ an exponential distribution
 Create an exponential distribution
 }
 \examples{
-  exp_distr <- create_exp_distr()
+exp_distr <- create_exp_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = exp_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = exp_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_gamma_distr.Rd b/man/create_gamma_distr.Rd
index fb56a5d4..bc97dd83 100644
--- a/man/create_gamma_distr.Rd
+++ b/man/create_gamma_distr.Rd
@@ -41,22 +41,22 @@ a gamma distribution
 Create a gamma distribution
 }
 \examples{
-  gamma_distr <- create_gamma_distr(
-     alpha = 0.05,
-     beta = 10.0
-  )
+gamma_distr <- create_gamma_distr(
+   alpha = 0.05,
+   beta = 10.0
+)
 
-  gtr_site_model <- create_gtr_site_model(
-    rate_ac_prior_distr = gamma_distr
-  )
+gtr_site_model <- create_gtr_site_model(
+  rate_ac_prior_distr = gamma_distr
+)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = gtr_site_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = gtr_site_model
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_gamma_site_model.Rd b/man/create_gamma_site_model.Rd
index 71591069..001e0302 100644
--- a/man/create_gamma_site_model.Rd
+++ b/man/create_gamma_site_model.Rd
@@ -42,17 +42,17 @@ a gamma site model
 Create a gamma site model, part of a site model
 }
 \examples{
-  gamma_site_model <- create_gamma_site_model(prop_invariant = 0.5)
+gamma_site_model <- create_gamma_site_model(prop_invariant = 0.5)
 
-  site_model <- create_hky_site_model(gamma_site_model = gamma_site_model)
+site_model <- create_hky_site_model(gamma_site_model = gamma_site_model)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    site_model = site_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  site_model = site_model
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 Use \code{\link{create_gamma_site_model}}
diff --git a/man/create_gtr_site_model.Rd b/man/create_gtr_site_model.Rd
index ffa8371c..5104f3fa 100644
--- a/man/create_gtr_site_model.Rd
+++ b/man/create_gtr_site_model.Rd
@@ -91,22 +91,22 @@ a GTR site_model
 Create a GTR site model
 }
 \examples{
-  gtr_site_model <- create_gtr_site_model(
-    rate_ac_param = 1.2,
-    rate_ag_param = 2.3,
-    rate_at_param = 3.4,
-    rate_cg_param = 4.5,
-    rate_ct_param = 5.6,
-    rate_gt_param = 6.7
- )
+gtr_site_model <- create_gtr_site_model(
+  rate_ac_param = 1.2,
+  rate_ag_param = 2.3,
+  rate_at_param = 3.4,
+  rate_cg_param = 4.5,
+  rate_ct_param = 5.6,
+  rate_gt_param = 6.7
+)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = gtr_site_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = gtr_site_model
+)
+file.remove(beast2_input_file)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_hky_site_model.Rd b/man/create_hky_site_model.Rd
index 58ce8742..1cdd86d9 100644
--- a/man/create_hky_site_model.Rd
+++ b/man/create_hky_site_model.Rd
@@ -41,12 +41,13 @@ Create an HKY site model
 }
 \examples{
  hky_site_model <- create_hky_site_model()
-
+ output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
-   output_filename = tempfile(pattern = "beast", fileext = ".xml"),
+   output_filename = output_filename,
    site_model = hky_site_model
  )
+file.remove(output_filename)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_inference_model.Rd b/man/create_inference_model.Rd
index 0c3449af..ea0bed7b 100644
--- a/man/create_inference_model.Rd
+++ b/man/create_inference_model.Rd
@@ -55,11 +55,13 @@ inference_model <- create_inference_model(
   mcmc = create_mcmc(chain_length = 50000, store_every = 1000)
 )
 
+output_filename <- get_beautier_tempfilename()
 create_beast2_input_file_from_model(
   input_filename = get_fasta_filename(),
-  output_filename = tempfile(fileext = ".xml"),
+  output_filename = output_filename,
   inference_model = inference_model
 )
+file.remove(beast2_input_file)
 }
 \seealso{
 Use \link{create_test_inference_model} to create an inference model
diff --git a/man/create_inv_gamma_distr.Rd b/man/create_inv_gamma_distr.Rd
index ef23af9c..a875fb59 100644
--- a/man/create_inv_gamma_distr.Rd
+++ b/man/create_inv_gamma_distr.Rd
@@ -41,17 +41,17 @@ an inverse-gamma distribution
 Create an inverse-gamma distribution
 }
 \examples{
-  inv_gamma_distr <- create_inv_gamma_distr()
+inv_gamma_distr <- create_inv_gamma_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = inv_gamma_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = inv_gamma_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_jc69_site_model.Rd b/man/create_jc69_site_model.Rd
index dffd3ed7..f19e7c78 100644
--- a/man/create_jc69_site_model.Rd
+++ b/man/create_jc69_site_model.Rd
@@ -23,11 +23,13 @@ Create a JC69 site model
 \examples{
  jc69_site_model <- create_jc69_site_model()
 
+ output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
-   output_filename = tempfile(pattern = "beast", fileext = ".xml"),
+   output_filename = output_filename,
    site_model = jc69_site_model
  )
+file.remove(output_filename)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_lambda_param.Rd b/man/create_lambda_param.Rd
index bf7eab75..bcd83ba5 100644
--- a/man/create_lambda_param.Rd
+++ b/man/create_lambda_param.Rd
@@ -23,24 +23,24 @@ this parameter is used in a Poisson distribution
   (as returned by \code{\link{create_poisson_distr}})
 }
 \examples{
-  # Create the parameter
-  lambda_param <- create_lambda_param()
+# Create the parameter
+lambda_param <- create_lambda_param()
 
-  # Use the parameter in a distribution
-  poisson_distr <- create_poisson_distr(
-    lambda = lambda_param
-  )
+# Use the parameter in a distribution
+poisson_distr <- create_poisson_distr(
+  lambda = lambda_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = poisson_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = poisson_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_laplace_distr.Rd b/man/create_laplace_distr.Rd
index 66346338..bc835323 100644
--- a/man/create_laplace_distr.Rd
+++ b/man/create_laplace_distr.Rd
@@ -41,17 +41,17 @@ a Laplace distribution
 Create a Laplace distribution
 }
 \examples{
-  laplace_distr <- create_laplace_distr()
+laplace_distr <- create_laplace_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = laplace_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = laplace_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_log_normal_distr.Rd b/man/create_log_normal_distr.Rd
index dab26e73..355a38c6 100644
--- a/man/create_log_normal_distr.Rd
+++ b/man/create_log_normal_distr.Rd
@@ -41,17 +41,17 @@ a log-normal distribution
 Create a log-normal distribution
 }
 \examples{
-  log_normal_distr <- create_log_normal_distr()
+log_normal_distr <- create_log_normal_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = log_normal_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = log_normal_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_m_param.Rd b/man/create_m_param.Rd
index 612c8357..eecd484e 100644
--- a/man/create_m_param.Rd
+++ b/man/create_m_param.Rd
@@ -24,24 +24,24 @@ this parameter is used in a log-normal distribution
   It cannot be estimated (as a hyper parameter) yet.
 }
 \examples{
-  # Create the parameter
-  m_param <- create_m_param()
+# Create the parameter
+m_param <- create_m_param()
 
-  # Use the parameter in a distribution
-  log_normal_distr <- create_log_normal_distr(
-    m = m_param
-  )
+# Use the parameter in a distribution
+log_normal_distr <- create_log_normal_distr(
+  m = m_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = log_normal_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = log_normal_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_mcmc.Rd b/man/create_mcmc.Rd
index fd35b60c..bbf07c49 100644
--- a/man/create_mcmc.Rd
+++ b/man/create_mcmc.Rd
@@ -59,16 +59,16 @@ There are four things that can be saved:
    how to specify the filename
 }
 \examples{
-
 # Create an MCMC chain with 50 states
 mcmc <- create_mcmc(chain_length = 50000, store_every = 1000)
 
-beast2_input_file <- tempfile()
+beast2_input_file <- get_beautier_tempfilename()
 create_beast2_input_file(
   get_fasta_filename(),
   beast2_input_file,
   mcmc = mcmc
 )
+file.remove(beast2_input_file)
 }
 \seealso{
 Use \code{\link{create_test_mcmc}} to create a short regular MCMC,
diff --git a/man/create_mean_param.Rd b/man/create_mean_param.Rd
index 4d8fdde3..d5b3a205 100644
--- a/man/create_mean_param.Rd
+++ b/man/create_mean_param.Rd
@@ -26,24 +26,24 @@ this parameter is used in an exponential distribution
   It cannot be estimated (as a hyper parameter) yet.
 }
 \examples{
-  # Create the parameter
-  mean_param <- create_mean_param(value = 1.0)
+# Create the parameter
+mean_param <- create_mean_param(value = 1.0)
 
-  # Use the parameter in a distribution
-  exp_distr <- create_exp_distr(
-    mean = mean_param
-  )
+# Use the parameter in a distribution
+exp_distr <- create_exp_distr(
+  mean = mean_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = exp_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = exp_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_mu_param.Rd b/man/create_mu_param.Rd
index 81507dd0..4c50c159 100644
--- a/man/create_mu_param.Rd
+++ b/man/create_mu_param.Rd
@@ -24,24 +24,24 @@ this parameter is used in a Laplace distribution
   It cannot be estimated (as a hyper parameter) yet.
 }
 \examples{
-  # Create the parameter
-  mu_param <- create_mu_param()
+# Create the parameter
+mu_param <- create_mu_param()
 
-  # Use the parameter in a distribution
-  laplace_distr <- create_laplace_distr(
-    mu = mu_param
-  )
+# Use the parameter in a distribution
+laplace_distr <- create_laplace_distr(
+  mu = mu_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = laplace_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = laplace_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_normal_distr.Rd b/man/create_normal_distr.Rd
index 157b14ce..07a2e84b 100644
--- a/man/create_normal_distr.Rd
+++ b/man/create_normal_distr.Rd
@@ -41,17 +41,17 @@ a normal distribution
 Create an normal distribution
 }
 \examples{
-  normal_distr <- create_normal_distr()
+normal_distr <- create_normal_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = normal_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = normal_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_ns_mcmc.Rd b/man/create_ns_mcmc.Rd
index 1e7241f8..52fa52fa 100644
--- a/man/create_ns_mcmc.Rd
+++ b/man/create_ns_mcmc.Rd
@@ -56,21 +56,21 @@ In this context, \code{chain_length} is only an upper bound
 to the length of that run.
 }
 \examples{
-  mcmc <- create_ns_mcmc(
-    chain_length = 1e7,
-    store_every = 1000,
-    particle_count = 1,
-    sub_chain_length = 1000,
-    epsilon = 1e-12
-  )
+mcmc <- create_ns_mcmc(
+  chain_length = 1e7,
+  store_every = 1000,
+  particle_count = 1,
+  sub_chain_length = 1000,
+  epsilon = 1e-12
+)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    mcmc = mcmc
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  mcmc = mcmc
+)
+file.remove(beast2_input_file)
 }
 \references{
 * [1] Patricio Maturana Russel, Brendon J Brewer, Steffen Klaere,
diff --git a/man/create_one_div_x_distr.Rd b/man/create_one_div_x_distr.Rd
index f5592c98..f75ba5fc 100644
--- a/man/create_one_div_x_distr.Rd
+++ b/man/create_one_div_x_distr.Rd
@@ -24,17 +24,17 @@ a 1/x distribution
 Create a 1/x distribution
 }
 \examples{
-  one_div_x_distr <- create_one_div_x_distr()
+one_div_x_distr <- create_one_div_x_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = one_div_x_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = one_div_x_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_param.Rd b/man/create_param.Rd
index fc6b46a7..6be11d75 100644
--- a/man/create_param.Rd
+++ b/man/create_param.Rd
@@ -45,24 +45,24 @@ Prefer using the
   and \code{\link{create_sigma_param}}
 }
 \examples{
-  # Create an alpha parameter
-  alpha_param <- create_alpha_param()
+# Create an alpha parameter
+alpha_param <- create_alpha_param()
 
-  # Use the parameter in a distribution
-  beta_distr <- create_beta_distr(
-    alpha = alpha_param
-  )
+# Use the parameter in a distribution
+beta_distr <- create_beta_distr(
+  alpha = alpha_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = beta_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = beta_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_poisson_distr.Rd b/man/create_poisson_distr.Rd
index a62df7a0..94756231 100644
--- a/man/create_poisson_distr.Rd
+++ b/man/create_poisson_distr.Rd
@@ -29,17 +29,17 @@ a Poisson distribution
 Create a Poisson distribution
 }
 \examples{
-  poisson_distr <- create_poisson_distr()
+poisson_distr <- create_poisson_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = poisson_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = poisson_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_rate_ac_param.Rd b/man/create_rate_ac_param.Rd
index 008ce57e..0c2043e2 100644
--- a/man/create_rate_ac_param.Rd
+++ b/man/create_rate_ac_param.Rd
@@ -25,19 +25,19 @@ a parameter called 'rate AC'
 Create a parameter called 'rate AC'
 }
 \examples{
-  # Create parameter
-  rate_ac_param <- create_rate_ac_param(value = 1, estimate = FALSE)
+# Create parameter
+rate_ac_param <- create_rate_ac_param(value = 1, estimate = FALSE)
 
-  # Use the parameter to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = create_gtr_site_model(
-      rate_ac_param = rate_ac_param
-    )
+# Use the parameter to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = create_gtr_site_model(
+    rate_ac_param = rate_ac_param
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_rate_ag_param.Rd b/man/create_rate_ag_param.Rd
index 60fe5e79..46d95f91 100644
--- a/man/create_rate_ag_param.Rd
+++ b/man/create_rate_ag_param.Rd
@@ -25,19 +25,19 @@ a parameter called 'rate AG'
 Create a parameter called 'rate AG'
 }
 \examples{
-  # Create parameter
-  rate_ag_param <- create_rate_ag_param(value = 1, estimate = FALSE)
+# Create parameter
+rate_ag_param <- create_rate_ag_param(value = 1, estimate = FALSE)
 
-  # Use the parameter to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = create_gtr_site_model(
-      rate_ag_param = rate_ag_param
-    )
+# Use the parameter to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = create_gtr_site_model(
+    rate_ag_param = rate_ag_param
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_rate_at_param.Rd b/man/create_rate_at_param.Rd
index 98d1b2e0..84628c6e 100644
--- a/man/create_rate_at_param.Rd
+++ b/man/create_rate_at_param.Rd
@@ -25,19 +25,19 @@ a parameter called 'rate AT'
 Create a parameter called 'rate AT'
 }
 \examples{
-  # Create parameter
-  rate_at_param <- create_rate_at_param(value = 1, estimate = FALSE)
+# Create parameter
+rate_at_param <- create_rate_at_param(value = 1, estimate = FALSE)
 
-  # Use the parameter to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = create_gtr_site_model(
-      rate_at_param = rate_at_param
-    )
+# Use the parameter to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = create_gtr_site_model(
+    rate_at_param = rate_at_param
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_rate_cg_param.Rd b/man/create_rate_cg_param.Rd
index e29f1f28..de95d1de 100644
--- a/man/create_rate_cg_param.Rd
+++ b/man/create_rate_cg_param.Rd
@@ -25,19 +25,19 @@ a parameter called 'rate CG'
 Create a parameter called 'rate CG'
 }
 \examples{
-  # Create parameter
-  rate_cg_param <- create_rate_cg_param(value = 1, estimate = FALSE)
+# Create parameter
+rate_cg_param <- create_rate_cg_param(value = 1, estimate = FALSE)
 
-  # Use the parameter to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = create_gtr_site_model(
-      rate_cg_param = rate_cg_param
-    )
+# Use the parameter to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = create_gtr_site_model(
+    rate_cg_param = rate_cg_param
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_rate_ct_param.Rd b/man/create_rate_ct_param.Rd
index 69e4dc6a..2215881f 100644
--- a/man/create_rate_ct_param.Rd
+++ b/man/create_rate_ct_param.Rd
@@ -22,19 +22,19 @@ a parameter called 'rate CT'
 Create a parameter called 'rate CT'
 }
 \examples{
-  # Create parameter
-  rate_ct_param <- create_rate_ct_param(value = 1)
+# Create parameter
+rate_ct_param <- create_rate_ct_param(value = 1)
 
-  # Use the parameter to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = create_gtr_site_model(
-      rate_ct_param = rate_ct_param
-    )
+# Use the parameter to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = create_gtr_site_model(
+    rate_ct_param = rate_ct_param
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_rate_gt_param.Rd b/man/create_rate_gt_param.Rd
index e9066c6b..06abec7d 100644
--- a/man/create_rate_gt_param.Rd
+++ b/man/create_rate_gt_param.Rd
@@ -25,19 +25,19 @@ a parameter called 'rate GT'
 Create a parameter called 'rate GT'
 }
 \examples{
-  # Create parameter
-  rate_gt_param <- create_rate_gt_param(value = 1, estimate = FALSE)
+# Create parameter
+rate_gt_param <- create_rate_gt_param(value = 1, estimate = FALSE)
 
-  # Use the parameter to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    site_model = create_gtr_site_model(
-      rate_gt_param = rate_gt_param
-    )
+# Use the parameter to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  site_model = create_gtr_site_model(
+    rate_gt_param = rate_gt_param
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_rln_clock_model.Rd b/man/create_rln_clock_model.Rd
index cabe99e8..2da206d5 100644
--- a/man/create_rln_clock_model.Rd
+++ b/man/create_rln_clock_model.Rd
@@ -52,27 +52,27 @@ a relaxed log-normal clock_model
 Create a relaxed log-normal clock model
 }
 \examples{
-  rln_clock_model <- create_rln_clock_model()
+rln_clock_model <- create_rln_clock_model()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    clock_model = rln_clock_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  clock_model = rln_clock_model
+)
+file.remove(beast2_input_file)
 
-  rln_clock_model_exp <- create_rln_clock_model(
-    mean_rate_prior_distr = create_exp_distr()
-  )
+rln_clock_model_exp <- create_rln_clock_model(
+  mean_rate_prior_distr = create_exp_distr()
+)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    clock_model = rln_clock_model_exp
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  clock_model = rln_clock_model_exp
+)
+file.remove(beast2_input_file)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_s_param.Rd b/man/create_s_param.Rd
index 236c89e1..b5abc0d9 100644
--- a/man/create_s_param.Rd
+++ b/man/create_s_param.Rd
@@ -28,24 +28,24 @@ this parameter is used in a log-normal distribution
   (as returned by \code{\link{create_log_normal_distr}})
 }
 \examples{
-  # Create the parameter
-  s_param <- create_s_param()
+# Create the parameter
+s_param <- create_s_param()
 
-  # Use the parameter in a distribution
-  log_normal_distr <- create_log_normal_distr(
-    s = s_param
-  )
+# Use the parameter in a distribution
+log_normal_distr <- create_log_normal_distr(
+  s = s_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = log_normal_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = log_normal_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_scale_param.Rd b/man/create_scale_param.Rd
index 343950db..86362cac 100644
--- a/man/create_scale_param.Rd
+++ b/man/create_scale_param.Rd
@@ -23,24 +23,24 @@ this parameter is used in a Laplace distribution
   (as returned by \code{\link{create_laplace_distr}})
 }
 \examples{
-  # Create the parameter
-  scale_param <- create_scale_param()
+# Create the parameter
+scale_param <- create_scale_param()
 
-  # Use the parameter in a distribution
-  laplace_distr <- create_laplace_distr(
-    scale = scale_param
-  )
+# Use the parameter in a distribution
+laplace_distr <- create_laplace_distr(
+  scale = scale_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = laplace_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = laplace_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_sigma_param.Rd b/man/create_sigma_param.Rd
index d3cbbd75..df7fa072 100644
--- a/man/create_sigma_param.Rd
+++ b/man/create_sigma_param.Rd
@@ -23,24 +23,24 @@ this parameter is used in a normal distribution
   (as returned by \code{\link{create_normal_distr}})
 }
 \examples{
-  # Create the parameter
-  sigma_param <- create_sigma_param()
+# Create the parameter
+sigma_param <- create_sigma_param()
 
-  # Use the parameter in a distribution
-  normal_distr <- create_normal_distr(
-    sigma = sigma_param
-  )
+# Use the parameter in a distribution
+normal_distr <- create_normal_distr(
+  sigma = sigma_param
+)
 
-  # Use the distribution to create a BEAST2 input file
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = normal_distr
-    )
+# Use the distribution to create a BEAST2 input file
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = normal_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_param}} contains a list
diff --git a/man/create_site_model.Rd b/man/create_site_model.Rd
index 40827616..a05ea38f 100644
--- a/man/create_site_model.Rd
+++ b/man/create_site_model.Rd
@@ -36,36 +36,40 @@ Prefer using the
 input_filename <- get_fasta_filename()
 
 # GTR
-output_filename <- tempfile(pattern = "example_gtr", fileext = ".xml")
+output_filename <- get_beautier_tempfilename()
 create_beast2_input_file(
   input_filename = input_filename,
   output_filename = output_filename,
   site_model = create_gtr_site_model()
 )
+file.remove(output_filename)
 
 # HKY
-output_filename <- tempfile(pattern = "example_hky", fileext = ".xml")
+output_filename <- get_beautier_tempfilename()
 create_beast2_input_file(
   input_filename = input_filename,
   output_filename = output_filename,
   site_model = create_hky_site_model()
 )
+file.remove(output_filename)
 
 # JC69
-output_filename <- tempfile(pattern = "example_jc69", fileext = ".xml")
+output_filename <- get_beautier_tempfilename()
 create_beast2_input_file(
   input_filename = input_filename,
   output_filename = output_filename,
   site_model = create_jc69_site_model()
 )
+file.remove(output_filename)
 
 # TN93
-output_filename <- tempfile(pattern = "example_tn93", fileext = ".xml")
+output_filename <- get_beautier_tempfilename()
 create_beast2_input_file(
   input_filename = input_filename,
   output_filename = output_filename,
   site_model = create_tn93_site_model()
 )
+file.remove(output_filename)
 }
 \seealso{
 See \code{\link{create_gtr_site_model}} for more examples
diff --git a/man/create_strict_clock_model.Rd b/man/create_strict_clock_model.Rd
index 474ad282..c4634f56 100644
--- a/man/create_strict_clock_model.Rd
+++ b/man/create_strict_clock_model.Rd
@@ -31,30 +31,30 @@ a strict clock_model
 Create a strict clock model
 }
 \examples{
-  strict_clock_model <- create_strict_clock_model(
-    clock_rate_param = 1.0,
-    clock_rate_distr = create_uniform_distr()
-  )
+strict_clock_model <- create_strict_clock_model(
+  clock_rate_param = 1.0,
+  clock_rate_distr = create_uniform_distr()
+)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    clock_model = strict_clock_model
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  clock_model = strict_clock_model
+)
+file.remove(beast2_input_file)
 
-  strict_clock_model_gamma <- create_strict_clock_model(
-    clock_rate_distr = create_gamma_distr()
-  )
+strict_clock_model_gamma <- create_strict_clock_model(
+  clock_rate_distr = create_gamma_distr()
+)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    get_fasta_filename(),
-    beast2_input_file,
-    clock_model = strict_clock_model_gamma
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  get_fasta_filename(),
+  beast2_input_file,
+  clock_model = strict_clock_model_gamma
+)
+file.remove(beast2_input_file)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_test_inference_model.Rd b/man/create_test_inference_model.Rd
index 0447d7d8..eb759b1f 100644
--- a/man/create_test_inference_model.Rd
+++ b/man/create_test_inference_model.Rd
@@ -52,12 +52,13 @@ to be used in testing.
 \examples{
 inference_model <- create_test_inference_model()
 
-beast2_input_file <- tempfile(fileext = ".xml")
+beast2_input_file <- get_beautier_tempfilename()
 create_beast2_input_file_from_model(
   get_fasta_filename(),
   beast2_input_file,
   inference_model = inference_model
 )
+file.remove(beast2_input_file)
 }
 \seealso{
 Use \link{create_inference_model} to create a
diff --git a/man/create_test_mcmc.Rd b/man/create_test_mcmc.Rd
index 0034b35e..3f1226a3 100644
--- a/man/create_test_mcmc.Rd
+++ b/man/create_test_mcmc.Rd
@@ -48,12 +48,13 @@ Create an MCMC configuration for testing.
 # Create an MCMC chain with 50 states
 mcmc <- create_test_mcmc()
 
-beast2_input_file <- tempfile(fileext = ".xml")
+beast2_input_file <- get_beautier_tempfilename()
 create_beast2_input_file(
   get_fasta_filename(),
   beast2_input_file,
   mcmc = mcmc
 )
+file.remove(beast2_input_file)
 }
 \seealso{
 Use \code{\link{create_mcmc}} to create a default BEAST2 MCMC
diff --git a/man/create_test_ns_mcmc.Rd b/man/create_test_ns_mcmc.Rd
index 85a70128..146a2ca7 100644
--- a/man/create_test_ns_mcmc.Rd
+++ b/man/create_test_ns_mcmc.Rd
@@ -51,16 +51,14 @@ an MCMC object
 Create an NS MCMC object for testing
 }
 \examples{
-
 mcmc <- create_test_ns_mcmc()
-
-beast2_input_file <- tempfile(fileext = ".xml")
-
+beast2_input_file <- get_beautier_tempfilename()
 create_beast2_input_file(
   get_fasta_filename(),
   beast2_input_file,
   mcmc = mcmc
 )
+file.remove(beast2_input_file)
 }
 \seealso{
 Use \code{\link{create_ns_mcmc}} to create a default
diff --git a/man/create_tn93_site_model.Rd b/man/create_tn93_site_model.Rd
index e3a92509..9100217c 100644
--- a/man/create_tn93_site_model.Rd
+++ b/man/create_tn93_site_model.Rd
@@ -59,11 +59,13 @@ Create a TN93 site model
    kappa_2_param = 2.0
  )
 
+ output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
-   output_filename = tempfile(pattern = "beast", fileext = ".xml"),
+   output_filename = output_filename,
    site_model = tn93_site_model
  )
+file.remove(output_filename)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/create_tree_prior.Rd b/man/create_tree_prior.Rd
index ac45e7b1..b977d1a3 100644
--- a/man/create_tree_prior.Rd
+++ b/man/create_tree_prior.Rd
@@ -30,45 +30,45 @@ Prefer the use the named functions
   instead
 }
 \examples{
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_bd_tree_prior()
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_bd_tree_prior()
+)
+file.remove(beast2_input_file)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_beautier_path("test_output_6.fas"),
-    beast2_input_file,
-    tree_prior = create_cbs_tree_prior()
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_beautier_path("test_output_6.fas"),
+  beast2_input_file,
+  tree_prior = create_cbs_tree_prior()
+)
+file.remove(beast2_input_file)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_ccp_tree_prior()
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_ccp_tree_prior()
+)
+file.remove(beast2_input_file)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_cep_tree_prior()
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_cep_tree_prior()
+)
+file.remove(beast2_input_file)
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior()
-  )
-  testit::assert(file.exists(beast2_input_file))
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior()
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 See
diff --git a/man/create_uniform_distr.Rd b/man/create_uniform_distr.Rd
index 13b0e680..1ea27068 100644
--- a/man/create_uniform_distr.Rd
+++ b/man/create_uniform_distr.Rd
@@ -24,17 +24,17 @@ a uniform distribution
 Create a uniform distribution
 }
 \examples{
-  uniform_distr <- create_uniform_distr()
+uniform_distr <- create_uniform_distr()
 
-  beast2_input_file <- tempfile(fileext = ".xml")
-  create_beast2_input_file(
-    input_filename = get_fasta_filename(),
-    beast2_input_file,
-    tree_prior = create_yule_tree_prior(
-      birth_rate_distr = uniform_distr
-    )
+beast2_input_file <- get_beautier_tempfilename()
+create_beast2_input_file(
+  input_filename = get_fasta_filename(),
+  beast2_input_file,
+  tree_prior = create_yule_tree_prior(
+    birth_rate_distr = uniform_distr
   )
-  testit::assert(file.exists(beast2_input_file))
+)
+file.remove(beast2_input_file)
 }
 \seealso{
 the function \code{\link{create_distr}} shows an overview
diff --git a/man/create_yule_tree_prior.Rd b/man/create_yule_tree_prior.Rd
index c4fb8767..ba25e124 100644
--- a/man/create_yule_tree_prior.Rd
+++ b/man/create_yule_tree_prior.Rd
@@ -25,12 +25,13 @@ Create a Yule tree prior
 \examples{
  yule_tree_prior <- create_yule_tree_prior()
 
- beast2_input_file <- tempfile(fileext = ".xml")
+ beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = yule_tree_prior
 )
+file.remove(beast2_input_file)
 }
 \seealso{
 An alignment ID can be extracted from
diff --git a/man/get_beautier_tempfilename.Rd b/man/get_beautier_tempfilename.Rd
index 6a142006..4e258c6a 100644
--- a/man/get_beautier_tempfilename.Rd
+++ b/man/get_beautier_tempfilename.Rd
@@ -6,11 +6,18 @@
 \usage{
 get_beautier_tempfilename(pattern = "file", fileext = "")
 }
+\arguments{
+\item{pattern}{a non-empty character vector
+giving the initial part of the name.}
+
+\item{fileext}{a non-empty character vector
+giving the file extension}
+}
 \value{
 name for a temporary file
 }
 \description{
-Get a temporary filename, similar to \linky{tempfile},
+Get a temporary filename, similar to \link{tempfile},
 except that it always writes to a temporary folder
 named \link{beautier}.
 }
diff --git a/man/get_fasta_filename.Rd b/man/get_fasta_filename.Rd
index f28eb480..19cac7dc 100644
--- a/man/get_fasta_filename.Rd
+++ b/man/get_fasta_filename.Rd
@@ -13,13 +13,15 @@ the path of a FASTA file used in testing
 Get the path of a FASTA file used in testing
 }
 \examples{
-  filename <- beautier::get_fasta_filename()
-  testit::assert(file.exists(filename))
+input_filename <- beautier::get_fasta_filename()
+output_filename <- get_beautier_tempfilename()
 
-  create_beast2_input_file(
-    input_filename = filename,
-    output_filename = tempfile(pattern = "beast", fileext = ".xml")
-  )
+create_beast2_input_file(
+  input_filename = input_filename,
+  output_filename = output_filename
+)
+
+file.remove(output_filename)
 }
 \author{
 Richèl J.C. Bilderbeek
diff --git a/man/get_remove_hex_fun.Rd b/man/get_remove_hex_fun.Rd
index 556c6bfb..bff5572b 100644
--- a/man/get_remove_hex_fun.Rd
+++ b/man/get_remove_hex_fun.Rd
@@ -12,7 +12,8 @@ such as \code{/home/john/.cache/tracelog_82c5888db98.log} (on Linux),
 where \code{/home/john/.cache} is the location to a temporary folder
 (on Linux) and \code{tracelog_82c5888db98.log} the filename.
 The filename ends with a hex string (as is common for temporary files,
-as \link{tempfile} does so). Because \link{beautier} puts an underscore
+as \link{tempfile} does so).
+Because \link{beautier} puts an underscore
 between the filename description (\code{tracelog}) and the hex
 string, this function removes both.
 }
diff --git a/scripts/issue_105.R b/scripts/issue_105.R
index 1e228354..27d7619e 100644
--- a/scripts/issue_105.R
+++ b/scripts/issue_105.R
@@ -1,9 +1,9 @@
 # Test if treelog$filename really creates that file
 library(beautier)
 
-tracelog_filename <- tempfile()
-screenlog_filename <- tempfile()
-treelog_filename <- tempfile()
+tracelog_filename <- get_beautier_tempfilename()
+screenlog_filename <- get_beautier_tempfilename()
+treelog_filename <- get_beautier_tempfilename()
 
 testit::assert(!file.exists(tracelog_filename))
 testit::assert(!file.exists(screenlog_filename))
@@ -26,7 +26,7 @@ inference_model <- beautier::create_inference_model(
   )
 )
 
-beast2_input_filename <- tempfile()
+beast2_input_filename <- get_beautier_tempfilename()
 
 create_beast2_input_file_from_model(
   input_filename = get_fasta_filename(),
@@ -34,7 +34,7 @@ create_beast2_input_file_from_model(
   inference_model = inference_model
 )
 
-new_wd <- tempfile()
+new_wd <- get_beautier_tempfilename()
 dir.create(new_wd, recursive = TRUE)
 setwd(new_wd)
 
diff --git a/tests/testthat/test-compare_lines.R b/tests/testthat/test-compare_lines.R
index 9038891c..b9f47e01 100644
--- a/tests/testthat/test-compare_lines.R
+++ b/tests/testthat/test-compare_lines.R
@@ -7,8 +7,8 @@ test_that("compare all", {
       lines = readLines(beautier::get_beautier_path("bd_2_4.xml")),
       expected = readLines(beautier::get_beautier_path("bd_2_4.xml")),
       section = NA,
-      created_lines_filename = tempfile(),
-      expected_lines_filename = tempfile()
+      created_lines_filename = get_beautier_tempfilename(),
+      expected_lines_filename = get_beautier_tempfilename()
     )
   )
 })
@@ -20,8 +20,8 @@ test_that("compare state", {
       lines = readLines(beautier::get_beautier_path("bd_2_4.xml")),
       expected = readLines(beautier::get_beautier_path("bd_2_4.xml")),
       section = "state",
-      created_lines_filename = tempfile(),
-      expected_lines_filename = tempfile()
+      created_lines_filename = get_beautier_tempfilename(),
+      expected_lines_filename = get_beautier_tempfilename()
     )
   )
 })
@@ -33,8 +33,8 @@ test_that("compare operators", {
       lines = readLines(beautier::get_beautier_path("bd_2_4.xml")),
       expected = readLines(beautier::get_beautier_path("bd_2_4.xml")),
       section = "operators",
-      created_lines_filename = tempfile(),
-      expected_lines_filename = tempfile()
+      created_lines_filename = get_beautier_tempfilename(),
+      expected_lines_filename = get_beautier_tempfilename()
     )
   )
 })
diff --git a/tests/testthat/test-create_beast2_input_file.R b/tests/testthat/test-create_beast2_input_file.R
index 4a8cdfbc..542dcdd8 100644
--- a/tests/testthat/test-create_beast2_input_file.R
+++ b/tests/testthat/test-create_beast2_input_file.R
@@ -2,7 +2,7 @@ context("create_beast2_input_file")
 
 test_that("use", {
 
-  output_filename <- tempfile()
+  output_filename <- get_beautier_tempfilename()
   testit::assert(!file.exists(output_filename))
 
   expect_silent(
@@ -17,7 +17,7 @@ test_that("use", {
 
 test_that("abuse", {
 
-  output_filename <- tempfile()
+  output_filename <- get_beautier_tempfilename()
 
   # input_filenames
   expect_error(
@@ -80,7 +80,9 @@ test_that("abuse", {
   expect_silent(
     create_beast2_input_file(
       input_filename = get_fasta_filename(),
-      output_filename = file.path(tempfile(), "1", "2", "beast2.xml")
+      output_filename = file.path(
+        get_beautier_tempfilename(), "1", "2", "beast2.xml"
+      )
     )
   )
 
diff --git a/tests/testthat/test-create_beast2_input_file_from_model.R b/tests/testthat/test-create_beast2_input_file_from_model.R
index 30bbace3..ec7f992d 100644
--- a/tests/testthat/test-create_beast2_input_file_from_model.R
+++ b/tests/testthat/test-create_beast2_input_file_from_model.R
@@ -1,6 +1,6 @@
 test_that("use", {
 
-  output_filename <- tempfile()
+  output_filename <- get_beautier_tempfilename()
   testit::assert(!file.exists(output_filename))
 
   expect_silent(
@@ -15,7 +15,7 @@ test_that("use", {
 
 test_that("abuse", {
 
-  output_filename <- tempfile()
+  output_filename <- get_beautier_tempfilename()
 
   # input_filenames
   expect_error(