From aa2a5bcb59e170f9cf6e40af61ac341873698fbc Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 Dec 2023 12:13:11 +0100 Subject: [PATCH 1/2] Update lockfiles --- .../skeleton/rmdchunks/EpiNow2.Rmd | 2 +- .../skeleton/rmdchunks/R0.Rmd | 2 +- .../transmissibility/skeleton/skeleton.Rmd | 147 +++++++++--------- 3 files changed, 76 insertions(+), 75 deletions(-) diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiNow2.Rmd index e89e14f..828360a 100644 --- 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 index 7ac0834..26629b3 100644 --- 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/skeleton.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd index 06f26cb..57d8bb1 100644 --- 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" ) ``` From 07cc599fcbd745bd2896555d7cc3d29999f3dc55 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 Dec 2023 14:01:59 +0100 Subject: [PATCH 2/2] Fix breaking change --- .../templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd | 2 -- inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd index 654dbac..44cd846 100644 --- 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 index 57d8bb1..7bbdadb 100644 --- a/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/transmissibility/skeleton/skeleton.Rmd @@ -452,7 +452,7 @@ i_recent <- dat_raw %>% ```{r} dat_i_day <- dat_raw %>% incidence("date", - interval = 1L, + interval = 1, counts = count_var, groups = group_var ) %>%