diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd
index 573a5bf9..5e03f931 100644
--- a/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd
@@ -53,7 +53,7 @@ renv::use(
   "R.utils@2.12.3",
   "R6@2.5.1",
   "RColorBrewer@1.1-3",
-  "Rcpp@1.0.11",
+  "Rcpp@1.0.12",
   "askpass@1.2.0",
   "backports@1.4.1",
   "base64enc@0.1-3",
@@ -61,61 +61,60 @@ renv::use(
   "bit@4.0.5",
   "bslib@0.6.1",
   "cachem@1.0.8",
-  "callr@3.7.3",
+  "callr@3.7.5",
   "cellranger@1.1.0",
-  "checkmate@2.3.0",
-  "cli@3.6.1",
+  "checkmate@2.3.1",
+  "cli@3.6.2",
   "clipr@0.8.0",
   "colorspace@2.1-0",
-  "commonmark@1.9.0",
+  "commonmark@1.9.1",
   "cpp11@0.4.7",
   "crayon@1.5.2",
-  "curl@5.1.0",
+  "curl@5.2.1",
   "data.table@1.14.8",
-  "digest@0.6.33",
+  "digest@0.6.35",
   "distcrete@1.0.3",
   "distributional@0.3.2",
   "dplyr@1.1.4",
   "ellipsis@0.3.2",
   "epiverse-trace/episoap", # nolint
-  "epitrix@0.4.0",
   "epiverse-trace/epiparameter@328706e", # nolint 
   "evaluate@0.23",
-  "fansi@1.0.5",
+  "fansi@1.0.6",
   "farver@2.1.1",
   "fastmap@1.1.1",
   "fontawesome@0.5.2",
   "forcats@1.0.0",
-  "foreign@0.8-85",
+  "foreign@0.8-86",
   "fs@1.6.3",
   "generics@0.1.3",
   "ggplot2@3.5.0",
-  "glue@1.6.2",
+  "glue@1.7.0",
   "grateful@0.2.4",
   "grates@1.1.0",
   "gtable@0.3.4",
-  "haven@2.5.3",
+  "haven@2.5.4",
   "highr@0.10",
   "hms@1.1.3",
   "htmltools@0.5.7",
-  "httpuv@1.6.12",
+  "httpuv@1.6.14",
   "httr@1.4.7",
   "incidence2@2.2.3",
   "isoband@0.2.7",
   "janitor@2.2.0",
   "jquerylib@0.1.4",
-  "jsonlite@1.8.7",
+  "jsonlite@1.8.8",
   "kableExtra@1.3.4",
   "knitr@1.45",
   "labeling@0.4.3",
-  "later@1.3.1",
+  "later@1.3.2",
   "lattice@0.21-8",
   "lifecycle@1.0.4",
-  "linelist@1.0.0",
+  "linelist@1.1.0",
   "lubridate@1.9.3",
   "magrittr@2.0.3",
   "memoise@2.0.1",
-  "mgcv@1.9-0",
+  "mgcv@1.9-1",
   "mime@0.12",
   "munsell@0.5.0",
   "nlme@3.1-163",
@@ -124,10 +123,10 @@ renv::use(
   "pillar@1.9.0",
   "pkgconfig@2.0.3",
   "prettyunits@1.2.0",
-  "processx@3.8.2",
-  "progress@1.2.2",
+  "processx@3.8.4",
+  "progress@1.2.3",
   "promises@1.2.1",
-  "ps@1.7.5",
+  "ps@1.7.6",
   "purrr@1.0.2",
   "rappdirs@0.3.3",
   "readr@2.1.4",
@@ -136,39 +135,38 @@ renv::use(
   "remotes@2.4.2.1",
   "renv@1.0.3",
   "rio@1.0.1",
-  "rlang@1.1.2",
-  "rmarkdown@2.25",
+  "rlang@1.1.3",
+  "rmarkdown@2.26",
   "rstudioapi@0.15.0",
-  "rvest@1.0.3",
-  "sass@0.4.7",
+  "rvest@1.0.4",
+  "sass@0.4.9",
   "scales@1.3.0",
   "selectr@0.4-2",
   "shiny@1.8.0",
   "snakecase@0.11.1",
-  "sodium@1.3.1",
   "sourcetools@0.1.7-1",
-  "stringi@1.8.2",
+  "stringi@1.8.3",
   "stringr@1.5.1",
-  "svglite@2.1.2",
+  "svglite@2.1.3",
   "sys@3.4.2",
-  "systemfonts@1.0.5",
+  "systemfonts@1.0.6",
   "tibble@3.2.1",
   "tidyr@1.3.0",
   "tidyselect@1.2.0",
   "timechange@0.2.0",
-  "tinytex@0.49",
+  "tinytex@0.50",
   "tzdb@0.4.0",
   "utf8@1.2.4",
   "vctrs@0.6.5",
   "viridisLite@0.4.2",
-  "vroom@1.6.4",
+  "vroom@1.6.5",
   "webshot@0.5.5",
-  "withr@2.5.2",
+  "withr@3.0.0",
   "writexl@1.4.2",
-  "xfun@0.41",
-  "xml2@1.3.5",
+  "xfun@0.42",
+  "xml2@1.3.6",
   "xtable@1.8-4",
-  "yaml@2.3.7"
+  "yaml@2.3.8"
 )
 ```