Last updated: 2026-08-31
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Knit directory: covid_script/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
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| region_set | geography | people_vaccinated_per_hundred | vaccination_group | estimand_age_group | initial | alpha | delta | omicron |
|---|---|---|---|---|---|---|---|---|
| Europe | BE | 63.15 | high | 60-79 | M: 0.132; F: 0.105 | M: 0.137; F: 0.098 | M: 0.167; F: 0.110 | M: 0.085; F: 0.091 |
| Europe | IT | 58.79 | high | 60-79 | M: 0.172; F: 0.107 | M: 0.286; F: 0.188 | M: 0.087; F: 0.104 | M: 0.055; F: 0.063 |
| Europe | FI | 58.28 | high | 60-79 | M: 0.014; F: 0.043 | M: 0.035; F: 0.001 | M: 0.106; F: 0.079 | M: 0.111; F: 0.134 |
| Europe | HU | 55.05 | high | 60-79 | M: -0.000; F: 0.037 | M: 0.317; F: 0.305 | M: 0.203; F: 0.221 | M: -0.017; F: -0.001 |
| Europe | ES | 54.56 | high | 60-79 | M: 0.242; F: 0.237 | M: 0.158; F: 0.180 | M: 0.122; F: 0.126 | M: 0.095; F: 0.158 |
| Europe | AT | 53.48 | high | 60-79 | M: 0.012; F: 0.003 | M: 0.109; F: 0.072 | M: 0.120; F: 0.108 | M: 0.026; F: 0.007 |
| Europe | DK | 53.29 | high | 60-79 | M: -0.020; F: 0.008 | M: -0.022; F: 0.000 | M: 0.058; F: 0.080 | M: -0.014; F: 0.036 |
| Europe | PT | 53.12 | high | 60-79 | M: 0.077; F: 0.111 | M: 0.218; F: 0.207 | M: 0.058; F: 0.109 | M: 0.071; F: 0.117 |
| Europe | RS | 39.21 | low | 60-79 | M: 0.102; F: 0.079 | M: 0.480; F: 0.405 | M: 0.468; F: 0.601 | M: -0.018; F: 0.057 |
| Europe | HR | 36.94 | low | 60-79 | M: 0.043; F: 0.091 | M: 0.315; F: 0.334 | M: 0.369; F: 0.405 | M: 0.101; F: 0.154 |
| Europe | SK | 36.55 | low | 60-79 | M: 0.031; F: 0.043 | M: 0.493; F: 0.513 | M: 0.277; F: 0.407 | M: 0.008; F: 0.023 |
| Europe | LV | 33.98 | low | 60-79 | M: 0.037; F: 0.046 | M: 0.227; F: 0.226 | M: 0.351; F: 0.390 | M: 0.109; F: 0.088 |
| Europe | RO | 24.05 | low | 60-79 | M: 0.093; F: 0.093 | M: 0.322; F: 0.357 | M: 0.386; F: 0.614 | M: -0.037; F: 0.017 |
| Europe | BG | 14.18 | low | 60-79 | M: 0.026; F: 0.048 | M: 0.546; F: 0.562 | M: 0.541; F: 0.738 | M: 0.037; F: 0.055 |
| Europe | AM | 2.10 | low | 60-79 | M: 0.240; F: 0.174 | M: 0.651; F: 0.589 | M: 0.579; F: 0.833 | M: 0.232; F: 0.165 |
| United States | Massachusetts | 70.52 | high | 65-84 | M: 0.220; F: 0.229 | M: 0.109; F: 0.074 | M: 0.114; F: 0.148 | M: 0.059; F: 0.089 |
| United States | Connecticut | 67.10 | high | 65-84 | M: 0.215; F: 0.275 | M: 0.124; F: 0.141 | M: 0.094; F: 0.132 | M: 0.016; F: 0.110 |
| United States | New Mexico | 63.02 | high | 65-84 | M: 0.089; F: 0.184 | M: 0.272; F: 0.284 | M: 0.294; F: 0.348 | M: 0.074; F: 0.153 |
| United States | New Jersey | 62.95 | high | 65-84 | M: 0.402; F: 0.359 | M: 0.233; F: 0.170 | M: 0.076; F: 0.136 | M: 0.032; F: 0.071 |
| United States | Pennsylvania | 62.87 | high | 65-84 | M: 0.127; F: 0.139 | M: 0.244; F: 0.194 | M: 0.243; F: 0.230 | M: 0.080; F: 0.100 |
| United States | Maryland | 62.03 | high | 65-84 | M: 0.204; F: 0.181 | M: 0.172; F: 0.151 | M: 0.114; F: 0.113 | M: 0.054; F: 0.039 |
| United States | Tennessee | 41.75 | low | 65-84 | M: 0.121; F: 0.124 | M: 0.203; F: 0.222 | M: 0.251; F: 0.324 | M: 0.052; F: 0.135 |
| United States | Alabama | 40.03 | low | 65-84 | M: 0.168; F: 0.184 | M: 0.263; F: 0.235 | M: 0.227; F: 0.256 | M: 0.040; F: 0.084 |
| United States | Idaho | 39.60 | low | 65-84 | M: 0.068; F: 0.076 | M: 0.150; F: 0.117 | M: 0.349; F: 0.355 | M: 0.053; F: 0.091 |
| United States | Louisiana | 38.50 | low | 65-84 | M: 0.295; F: 0.275 | M: 0.215; F: 0.148 | M: 0.267; F: 0.237 | M: 0.078; F: 0.064 |
| United States | Mississippi | 36.27 | low | 65-84 | M: 0.208; F: 0.240 | M: 0.219; F: 0.235 | M: 0.190; F: 0.290 | M: 0.026; F: 0.114 |
#!/usr/bin/env Rscript
suppressPackageStartupMessages({
library(dplyr)
library(here)
library(readr)
library(tidyr)
})
source(here::here("R", "reporting.R"))
source(here::here("R", "tables.R"))
arguments <- reporting_arguments(list(
europe_wave = here::here("output", "results", "europe", "wave_summary.csv"),
us_wave = here::here("output", "results", "us", "wave_summary.csv"),
europe_vaccination = here::here(
"output",
"data",
"europe",
"vaccination_membership.csv"
),
us_vaccination = here::here(
"output",
"data",
"us",
"vaccination_membership.csv"
),
output = here::here("output", "tables", "table_01_wave_pscores.csv")
))
inputs <- unlist(arguments[c(
"europe_wave",
"us_wave",
"europe_vaccination",
"us_vaccination"
)])
reporting_require_files(inputs, "Table 1 input")
table <- build_table_01(
readr::read_csv(arguments$europe_wave, show_col_types = FALSE),
readr::read_csv(arguments$us_wave, show_col_types = FALSE),
readr::read_csv(arguments$europe_vaccination, show_col_types = FALSE),
readr::read_csv(arguments$us_vaccination, show_col_types = FALSE)
)
html_output <- sub("\\.csv$", ".html", arguments$output, ignore.case = TRUE)
written <- write_table_01(table, arguments$output, html_output)
message("Rendered Table 1: ", paste(written, 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