Last updated: 2026-08-31

Checks: 7 0

Knit directory: covid_script/

This reproducible R Markdown analysis was created with workflowr (version 1.7.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20260831)

The command set.seed(20260831) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

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File paths: relative

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Repository version: 9b2893c

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The results in this page were generated with repository version 9b2893c. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .DS_Store
    Ignored:    analysis/assets/
    Ignored:    output/
    Ignored:    renv/library/
    Ignored:    renv/staging/
    Ignored:    scratch/
    Ignored:    tmp/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/figure_01.Rmd) and HTML (docs/figure_01.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html b47130b Ziang Zhang 2026-08-31 build: refresh published site provenance
html e5925a4 Ziang Zhang 2026-08-31 build: publish workflowr analysis site
Rmd 083fcf3 Ziang Zhang 2026-08-31 fix: improve publication site readability
Rmd e87ff80 Ziang Zhang 2026-08-31 feat: add publication workflowr website

Figure 1

Figure 1. Illustration of the Seasonally Adaptive Mortality Model (SAMM) fitted to the elderly population (aged 80+) in the Netherlands. Shown are the overall mortality counts and modelled expected counts (A), inferred long-term trend (B), and the adaptive seasonal component (C). Data up to January 2020 (vertical dashed line) were used to train the model, and forecasts from the model beyond 2020 show increasingly broad credible regions.
Download editable PDF

Reproducible code

The reporting script reads the completed model summary and writes both PDF and PNG output. It is displayed here but is not executed during website generation.

#!/usr/bin/env Rscript

suppressPackageStartupMessages({
  library(here)
  library(readr)
})

source(here::here("R", "reporting.R"))
source(here::here("R", "figures.R"))

arguments <- reporting_arguments(list(
  input = here::here(
    "output",
    "reporting",
    "inputs",
    "figure_01_model_illustration.rds"
  ),
  output = here::here(
    "output",
    "figures",
    "figure_01_model_illustration.pdf"
  )
))

reporting_require_files(arguments$input, "Figure 1 input")
rendered <- render_figure_01(readRDS(arguments$input), arguments$output)
message("Rendered Figure 1: ", paste(rendered, collapse = ", "))

sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3     cli_3.6.6       knitr_1.50      rlang_1.2.0    
 [5] xfun_0.55       stringi_1.8.9   otel_0.2.0      renv_1.1.5     
 [9] promises_1.5.0  jsonlite_2.0.0  workflowr_1.7.2 glue_1.8.1     
[13] rprojroot_2.1.1 git2r_0.36.2    htmltools_0.5.9 httpuv_1.6.16  
[17] sass_0.4.10     rmarkdown_2.30  evaluate_1.0.5  jquerylib_0.1.4
[21] tibble_3.3.0    fastmap_1.2.0   yaml_2.3.12     lifecycle_1.0.5
[25] whisker_0.4.1   stringr_1.6.0   compiler_4.5.1  fs_1.6.6       
[29] Rcpp_1.1.1-1.1  pkgconfig_2.0.3 here_1.0.2      later_1.4.4    
[33] digest_0.6.39   R6_2.6.1        pillar_1.11.1   magrittr_2.0.5 
[37] bslib_0.9.0     tools_4.5.1     cachem_1.1.0