Merge 07cc599 into ac0a8cb

epiverse-trace · Dec 4, 2023 · bd4037a · bd4037a
2 parents ac0a8cb + 07cc599
commit bd4037a
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diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd
@@ -1,7 +1,7 @@
 ## _EpiNow2_ 
 
 ```{r lockfile-rt, include = FALSE, message = FALSE}
-renv::use("EpiNow2@1.3.4")
+renv::use("EpiNow2@1.4.0")
 ```
 
 ```{r rt-load-pkg}

diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/R0.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/R0.Rmd
@@ -1,7 +1,7 @@
 ## _R0_
 
 ```{r lockfile-rt, include = FALSE, message = FALSE}
-renv::use("R0@1.2-10")
+renv::use("R0@1.3-1")
 ```
 
 ```{r rt-load-pkg}

diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd
@@ -52,8 +52,6 @@ last_trends <- last_counts  %>%
 plot(last_trends,
   angle = 45,
   date_format = "%d %b %y",
-  color = "white",
-  fill = green_grey,
   alpha = 0.8,
   n_breaks = 12,
   nrow = n_groups,

diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd
@@ -46,128 +46,129 @@ bibliography:
 
 ```{r lockfile, include = FALSE, message = FALSE}
 renv::use(
-  "MASS@7.3-58.2",
-  "Matrix@1.5-1",
+  "MASS@7.3-59",
+  "Matrix@1.6-3",
+  "R.methodsS3@1.8.2",
+  "R.oo@1.25.0",
+  "R.utils@2.12.3",
   "R6@2.5.1",
   "RColorBrewer@1.1-3",
-  "Rcpp@1.0.10",
-  "askpass@1.1",
+  "Rcpp@1.0.11",
+  "askpass@1.2.0",
   "backports@1.4.1",
   "base64enc@0.1-3",
   "bit64@4.0.5",
   "bit@4.0.5",
-  "bslib@0.4.2",
-  "cachem@1.0.7",
+  "bslib@0.6.1",
+  "cachem@1.0.8",
   "callr@3.7.3",
   "cellranger@1.1.0",
-  "checkmate@2.1.0",
+  "checkmate@2.3.0",
   "cli@3.6.1",
   "clipr@0.8.0",
   "colorspace@2.1-0",
   "commonmark@1.9.0",
-  "cpp11@0.4.3",
+  "cpp11@0.4.7",
   "crayon@1.5.2",
-  "curl@5.0.0",
+  "curl@5.1.0",
   "data.table@1.14.8",
-  "digest@0.6.31",
+  "digest@0.6.33",
   "distcrete@1.0.3",
   "distributional@0.3.2",
-  "dplyr@1.1.1",
+  "dplyr@1.1.4",
   "ellipsis@0.3.2",
   "epiverse-trace/episoap", # nolint
   "epitrix@0.4.0",
   "epiverse-trace/epiparameter@fd250ce", # nolint 
-  "evaluate@0.20",
-  "fansi@1.0.4",
+  "evaluate@0.23",
+  "fansi@1.0.5",
   "farver@2.1.1",
   "fastmap@1.1.1",
-  "fontawesome@0.5.0",
+  "fontawesome@0.5.2",
   "forcats@1.0.0",
-  "foreign@0.8-82",
-  "fs@1.6.1",
+  "foreign@0.8-85",
+  "fs@1.6.3",
   "generics@0.1.3",
-  "ggplot2@3.4.2",
+  "ggplot2@3.4.4",
   "glue@1.6.2",
-  "grateful@0.2.0",
-  "grates@1.0.0",
-  "gtable@0.3.3",
-  "haven@2.5.2",
+  "grateful@0.2.4",
+  "grates@1.1.0",
+  "gtable@0.3.4",
+  "haven@2.5.3",
   "highr@0.10",
   "hms@1.1.3",
-  "htmltools@0.5.5",
-  "httpuv@1.6.9",
-  "httr@1.4.5",
-  "incidence2@2.0.0",
+  "htmltools@0.5.7",
+  "httpuv@1.6.12",
+  "httr@1.4.7",
+  "incidence2@2.2.1",
   "isoband@0.2.7",
   "janitor@2.2.0",
   "jquerylib@0.1.4",
-  "jsonlite@1.8.4",
+  "jsonlite@1.8.7",
   "kableExtra@1.3.4",
-  "knitr@1.42",
-  "labeling@0.4.2",
-  "later@1.3.0",
-  "lattice@0.20-45",
-  "lifecycle@1.0.3",
-  "linelist@0.0.1",
-  "lubridate@1.9.2",
+  "knitr@1.45",
+  "labeling@0.4.3",
+  "later@1.3.1",
+  "lattice@0.21-8",
+  "lifecycle@1.0.4",
+  "linelist@1.0.0",
+  "lubridate@1.9.3",
   "magrittr@2.0.3",
   "memoise@2.0.1",
-  "mgcv@1.8-41",
+  "mgcv@1.9-0",
   "mime@0.12",
   "munsell@0.5.0",
-  "nlme@3.1-162",
+  "nlme@3.1-163",
   "numDeriv@2016.8-1.1",
-  "openssl@2.0.6",
-  "openxlsx@4.2.5.2",
+  "openssl@2.1.1",
   "pillar@1.9.0",
   "pkgconfig@2.0.3",
-  "prettyunits@1.1.1",
-  "processx@3.8.0",
+  "prettyunits@1.2.0",
+  "processx@3.8.2",
   "progress@1.2.2",
-  "promises@1.2.0.1",
-  "ps@1.7.4",
-  "purrr@1.0.1",
+  "promises@1.2.1",
+  "ps@1.7.5",
+  "purrr@1.0.2",
   "rappdirs@0.3.3",
   "readr@2.1.4",
-  "readxl@1.4.2",
-  "rematch@1.0.1",
-  "remotes@2.4.2",
-  "renv@0.17.2",
-  "rio@0.5.29",
-  "rlang@1.1.0",
-  "rmarkdown@2.21",
-  "rmdformats@1.0.4",
-  "rstudioapi@0.14",
+  "readxl@1.4.3",
+  "rematch@2.0.0",
+  "remotes@2.4.2.1",
+  "renv@1.0.3",
+  "rio@1.0.1",
+  "rlang@1.1.2",
+  "rmarkdown@2.25",
+  "rstudioapi@0.15.0",
   "rvest@1.0.3",
-  "sass@0.4.5",
-  "scales@1.2.1",
+  "sass@0.4.7",
+  "scales@1.3.0",
   "selectr@0.4-2",
-  "shiny@1.7.4",
-  "snakecase@0.11.0",
-  "sodium@1.2.1",
+  "shiny@1.8.0",
+  "snakecase@0.11.1",
+  "sodium@1.3.1",
   "sourcetools@0.1.7-1",
-  "stringi@1.7.12",
-  "stringr@1.5.0",
-  "svglite@2.1.1",
-  "sys@3.4.1",
-  "systemfonts@1.0.4",
+  "stringi@1.8.2",
+  "stringr@1.5.1",
+  "svglite@2.1.2",
+  "sys@3.4.2",
+  "systemfonts@1.0.5",
   "tibble@3.2.1",
   "tidyr@1.3.0",
   "tidyselect@1.2.0",
   "timechange@0.2.0",
-  "tinytex@0.44",
-  "tzdb@0.3.0",
-  "utf8@1.2.3",
-  "vctrs@0.6.1",
-  "viridisLite@0.4.1",
-  "vroom@1.6.1",
-  "webshot@0.5.4",
-  "withr@2.5.0",
-  "xfun@0.38",
-  "xml2@1.3.3",
+  "tinytex@0.49",
+  "tzdb@0.4.0",
+  "utf8@1.2.4",
+  "vctrs@0.6.5",
+  "viridisLite@0.4.2",
+  "vroom@1.6.4",
+  "webshot@0.5.5",
+  "withr@2.5.2",
+  "writexl@1.4.2",
+  "xfun@0.41",
+  "xml2@1.3.5",
   "xtable@1.8-4",
-  "yaml@2.3.7",
-  "zip@2.2.2"
+  "yaml@2.3.7"
 )
 ```
 
@@ -451,7 +452,7 @@ i_recent <- dat_raw %>%
 ```{r}
 dat_i_day <- dat_raw %>%
   incidence("date",
-    interval = 1L,
+    interval = 1,
     counts = count_var,
     groups = group_var
   ) %>%