Vignette rebuild and source files

rafalopespx · rafalopespx · commit 153b11a9584a · 2025-09-20T00:16:20.000-04:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,17 +26,22 @@ Imports:
     tidyr,
     tibble
 Suggests: 
-    INLA (>= 22.5.3),
+    INLA (>= 23.01.31),
     ggplot2,
-    knitr,
     rmarkdown,
+    knitr,
     vroom,
     parallel,
     lubridate,
-    lme4, sn,
-    stringr
+    lme4,
+    sn,
+    sp,
+    stringr,
+    fmesher (>= 0.5.0),
+    testthat (>= 3.0.0)
 LazyData: true
+BuildVignettes: true
+VignetteBuilder: knitr
 Additional_repositories: 
     https://inla.r-inla-download.org/R/stable/
-VignetteBuilder: knitr
 Config/testthat/edition: 3
diff --git a/README.Rmd b/README.Rmd
@@ -18,6 +18,7 @@ library(badger)
 `r badger::badge_license(url = "https://github.com/covid19br/nowcaster/blob/main/LICENSE.md")`
 `r badger::badge_lifecycle(stage = "experimental")`
 [![R-CMD-check](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml)
+[![CRAN status](https://www.r-pkg.org/badges/version/nowcaster)](https://CRAN.R-project.org/package=nowcaster)
 <!-- badges: end -->
 
 `nowcaster` is an R package for “nowcasting” epidemiological time-series on individual level data.
diff --git a/README.md b/README.md
@@ -3,14 +3,17 @@
 
 <!-- badges: start -->
 
-[![CRAN
-checks](https://badges.cranchecks.info/summary/nowcaster.svg)](https://cran.r-project.org/web/checks/check_results_nowcaster.html)
-[![Dependencies](https://tinyverse.netlify.com/badge/nowcaster)](https://cran.r-project.org/package=nowcaster)
+<!-- [![CRAN checks](https://badges.cranchecks.info/summary/nowcaster.svg)](https://cran.r-project.org/web/checks/check_results_nowcaster.html) -->
+
+<!-- [![Dependencies](https://tinyverse.netlify.com/badge/nowcaster)](https://cran.r-project.org/package=nowcaster) -->
+
 `badger::badge_devel(color = "blue", pkg = "nowcaster")` [![License: GPL
 (\>=
 3)](https://img.shields.io/badge/license-GPL%20(%3E=%203)-blue.svg)](https://github.com/covid19br/nowcaster/blob/main/LICENSE.md)
 [![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/covid19br/nowcaster/actions/workflows/R-CMD-check.yaml)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/nowcaster)](https://CRAN.R-project.org/package=nowcaster)
 <!-- badges: end -->
 
 `nowcaster` is an R package for “nowcasting” epidemiological time-series
@@ -25,6 +28,18 @@ model to the time steps of delay between onset date of the event,
 death) and the date of report (*i.e.*, date of notification of the case
 or death).
 
+## Installing
+
+After have a proper `INLA` installation to install `nowcaster` package
+simply run the code below in R:
+
+``` r
+devtools::install_github("https://github.com/covid19br/nowcaster")
+```
+
+If you have any problem installing, please refer to next section on the
+dependencies of the package.
+
 ## Dependencies
 
 `nowcaster` is based on the
@@ -54,19 +69,6 @@ If you want more detail on other possible installations of `INLA`,
 please refer to the official
 [page](https://www.r-inla.org/download-install) of the package.
 
-
-## Installing
-
-After have a proper `INLA` installation to install `nowcaster` package
-simply run the code below in R:
-
-``` r
-devtools::install_github("https://github.com/covid19br/nowcaster")
-```
-
-If you have any problem installing, please refer to next section on the
-dependencies of the package.
-
 ## Similar Initiatives
 
 There are other alternative packages, that can produce nowcasting
diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,15 @@
+citHeader("To cite nowcaster in publications use:")
+
+bibentry(
+  bibtype  = "Article",
+  title="A Modelling approach for correcting reporting delays in disease surveillance data",
+  author="Bastos, Leonardo S and Economou, Theodoros and Gomes, Marcelo FC and Villela, Daniel AM and Coelho, Flavio C and Cruz, Oswaldo G and Stoner, Oliver and Bailey, Trevor and Codeço, Claudia T",
+  journal="Statistics in medicine",
+  year="2019",
+  volume="38",
+  number="22",
+  pages="4363--4377",
+  publisher="Wiley Online Library",
+  doi      ="https://doi.org/10.1002/sim.8303"
+)
+
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(nowcaster)
+
+test_check("nowcaster")
diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R
@@ -0,0 +1,7 @@
+test_that("setup-INLA", {
+  if (requireNamespace("INLA", quietly = TRUE)) {
+    INLA::inla.setOption(fmesher.evolution = 2L)
+    INLA::inla.setOption(fmesher.evolution.warn = TRUE)
+    INLA::inla.setOption(fmesher.evolution.verbosity = "warn")
+  }
+})
diff --git a/vignettes/articles/1_structured_data.Rmd b/vignettes/articles/1_structured_data.Rmd
@@ -25,6 +25,11 @@ if(requireNamespace("INLA", quietly = T)){
   if(packageVersion("INLA") >= "22.5.3"){knitr::opts_chunk$set(eval = T)}
   else{knitr::opts_chunk$set(eval = F)}
 }
+if (requireNamespace("INLA", quietly = TRUE)) {
+  INLA::inla.setOption(fmesher.evolution = 2L)
+  INLA::inla.setOption(fmesher.evolution.warn = TRUE)
+  INLA::inla.setOption(fmesher.evolution.verbosity = "warn")
+}
 ```
 
 ## TL;DR
diff --git a/vignettes/articles/2_nowcasting_importance.Rmd b/vignettes/articles/2_nowcasting_importance.Rmd
@@ -25,6 +25,11 @@ if(requireNamespace("INLA", quietly = T)){
   if(packageVersion("INLA") >= "22.5.3"){knitr::opts_chunk$set(eval = T)}
   else{knitr::opts_chunk$set(eval = F)}
 }
+if (requireNamespace("INLA", quietly = TRUE)) {
+  INLA::inla.setOption(fmesher.evolution = 2L)
+  INLA::inla.setOption(fmesher.evolution.warn = TRUE)
+  INLA::inla.setOption(fmesher.evolution.verbosity = "warn")
+}
 ```
 
 ## TL;DR
diff --git a/vignettes/articles/3_forecasting.Rmd b/vignettes/articles/3_forecasting.Rmd
@@ -25,6 +25,11 @@ if(requireNamespace("INLA", quietly = T)){
   if(packageVersion("INLA") >= "22.5.3"){knitr::opts_chunk$set(eval = T)}
   else{knitr::opts_chunk$set(eval = F)}
 }
+if (requireNamespace("INLA", quietly = TRUE)) {
+  INLA::inla.setOption(fmesher.evolution = 2L)
+  INLA::inla.setOption(fmesher.evolution.warn = TRUE)
+  INLA::inla.setOption(fmesher.evolution.verbosity = "warn")
+}
 ```
 
 ## TL;DR
diff --git a/vignettes/nowcaster.Rmd b/vignettes/nowcaster.Rmd
@@ -25,6 +25,11 @@ if(requireNamespace("INLA", quietly = T)){
   if(packageVersion("INLA") >= "22.5.3"){knitr::opts_chunk$set(eval = T)}
   else{knitr::opts_chunk$set(eval = F)}
 }
+if (requireNamespace("INLA", quietly = TRUE)) {
+  INLA::inla.setOption(fmesher.evolution = 2L)
+  INLA::inla.setOption(fmesher.evolution.warn = TRUE)
+  INLA::inla.setOption(fmesher.evolution.verbosity = "warn")
+}
 ```
 
 ## First example on LazyData
