This repository,
wildfires_school_exposure,
contains reproducible code for our open-access JAMA Network Open
research letter, “Quantifying exposure to wildfire smoke among
school-aged children in California, 2006 –
2021”,
which uses publicly-available school enrollment data from the
NCES and wildfire PM2.5
estimates
to quantify the number of student-days of wildfire smoke exposure among
California kids. The full citation is:
Velásquez EE, Benmarhnia T, Casey JA, Aguilera R, Kiang MV. Quantifying exposure to wildfire smoke among school-aged children in California, 2006 - 2021. JAMA Network Open. 2023;6(4):e235863. doi: 10.1001/jamanetworkopen.2023.5863
For interested readers, an invited commentary was published along side the letter.
All code can be found in the ./code folder and must be run in order.
The first few lines of each code file contains a brief description of
the tasks related to that file. Numeric representation of our figures
can be found in the ./output folder. Figures are in the ./plots
folder. The table was generated using rmarkdown and both source and
output are in the ./rmds folder.
Due to file size limitations on Github, the files in ./data and
./data_raw are not in this repository. They must be downloaded from
OSF and then decompressed into the root directory
or can be downloaded by running ./code/00_get_data_files.R.
- Rosana Aguilera
- Tarik Benmarhnia
(
: benmarhnia-lab |
: @tbenmarhnia)
- Joan A Casey
(
- Mathew V Kiang
(
- Esther E Velásquez (
We use renv for package
management but below we also post the relevant session information to
ensure full reproducibility. As stated above, data files are publicly
available but must be downloaded from OSF due to
file size constraints on Github. Run ./code/00_get_data_files.R to
download and unzip the relevant data files.
> sessioninfo::session_info()
─ Session info ─────────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os macOS 13.2.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2023-02-26
rstudio 2022.07.2+576 Spotted Wakerobin (desktop)
pandoc 2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
─ Packages ─────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.1.0)
backports 1.4.1 2021-12-13 [2] CRAN (R 4.1.1)
broom 0.7.11 2022-01-03 [2] CRAN (R 4.1.1)
bslib 0.3.1 2021-10-06 [2] CRAN (R 4.1.1)
cachem 1.0.6 2021-08-19 [2] CRAN (R 4.1.1)
cellranger 1.1.0 2016-07-27 [2] CRAN (R 4.1.0)
cli 3.4.0 2022-09-08 [1] CRAN (R 4.1.1)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.1.2)
colorspace 2.0-2 2021-06-24 [2] CRAN (R 4.1.1)
config * 0.3.1 2020-12-17 [2] CRAN (R 4.1.0)
crayon 1.4.2 2021-10-29 [2] CRAN (R 4.1.1)
DBI 1.1.2 2021-12-20 [2] CRAN (R 4.1.1)
dbplyr 2.1.1 2021-04-06 [2] CRAN (R 4.1.0)
digest 0.6.29 2021-12-01 [2] CRAN (R 4.1.1)
doParallel * 1.0.17 2022-02-07 [2] CRAN (R 4.1.1)
dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.1.1)
ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.1.0)
evaluate 0.14 2019-05-28 [2] CRAN (R 4.1.0)
fansi 1.0.0 2022-01-10 [2] CRAN (R 4.1.1)
fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.1.0)
fontawesome 0.2.2 2021-07-02 [2] CRAN (R 4.1.0)
forcats * 0.5.1 2021-01-27 [2] CRAN (R 4.1.1)
foreach * 1.5.2 2022-02-02 [2] CRAN (R 4.1.1)
fs * 1.5.2 2021-12-08 [2] CRAN (R 4.1.1)
furrr * 0.2.3 2021-06-25 [2] CRAN (R 4.1.0)
future * 1.29.0 2022-11-06 [1] CRAN (R 4.1.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.1)
ggplot2 * 3.3.5 2021-06-25 [2] CRAN (R 4.1.1)
ggsci * 2.9 2018-05-14 [2] CRAN (R 4.1.1)
globals 0.16.1 2022-08-28 [1] CRAN (R 4.1.1)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.1)
gtable 0.3.0 2019-03-25 [2] CRAN (R 4.1.1)
haven 2.4.3 2021-08-04 [2] CRAN (R 4.1.1)
here * 1.0.1 2020-12-13 [2] CRAN (R 4.1.0)
hms 1.1.1 2021-09-26 [2] CRAN (R 4.1.1)
htmltools 0.5.2 2021-08-25 [2] CRAN (R 4.1.1)
httpuv 1.6.5 2022-01-05 [2] CRAN (R 4.1.1)
httr 1.4.4 2022-08-17 [1] CRAN (R 4.1.1)
ineq * 0.2-13 2014-07-21 [1] CRAN (R 4.1.0)
iterators * 1.0.14 2022-02-05 [2] CRAN (R 4.1.1)
janitor * 2.1.0 2021-01-05 [2] CRAN (R 4.1.0)
jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.1.0)
jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.1.1)
knitr * 1.37 2021-12-16 [2] CRAN (R 4.1.1)
later 1.3.0 2021-08-18 [2] CRAN (R 4.1.1)
lifecycle 1.0.1 2021-09-24 [2] CRAN (R 4.1.1)
listenv 0.8.0 2019-12-05 [2] CRAN (R 4.1.0)
lubridate 1.8.0 2021-10-07 [2] CRAN (R 4.1.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.1)
mime 0.12 2021-09-28 [2] CRAN (R 4.1.1)
miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.1.0)
modelr 0.1.8 2020-05-19 [2] CRAN (R 4.1.0)
munsell 0.5.0 2018-06-12 [2] CRAN (R 4.1.0)
parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.1.1)
patchwork * 1.1.1 2020-12-17 [2] CRAN (R 4.1.1)
pillar 1.6.4 2021-10-18 [2] CRAN (R 4.1.1)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.0)
prefixer 0.1.5.9000 2022-11-04 [1] Github (dreamRs/prefixer@e43f934)
promises 1.2.0.1 2021-02-11 [2] CRAN (R 4.1.0)
purrr * 0.3.4 2020-04-17 [2] CRAN (R 4.1.0)
R6 2.5.1 2021-08-19 [2] CRAN (R 4.1.1)
Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.1.1)
readr * 2.1.1 2021-11-30 [2] CRAN (R 4.1.1)
readxl 1.3.1 2019-03-13 [2] CRAN (R 4.1.0)
renv 0.15.4 2022-03-03 [1] CRAN (R 4.1.1)
reprex 2.0.1 2021-08-05 [2] CRAN (R 4.1.1)
rlang 1.0.5 2022-08-31 [1] CRAN (R 4.1.1)
rmarkdown 2.11 2021-09-14 [2] CRAN (R 4.1.1)
rprojroot 2.0.2 2020-11-15 [2] CRAN (R 4.1.0)
rstudioapi 0.13 2020-11-12 [2] CRAN (R 4.1.0)
rvest 1.0.2 2021-10-16 [2] CRAN (R 4.1.1)
sass 0.4.2 2022-07-16 [1] CRAN (R 4.1.1)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.1.1)
sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.1.1)
shiny * 1.7.1 2021-10-02 [2] CRAN (R 4.1.1)
shinyWidgets 0.7.4 2022-10-05 [1] CRAN (R 4.1.1)
snakecase 0.11.0 2019-05-25 [2] CRAN (R 4.1.0)
stringi 1.7.6 2021-11-29 [2] CRAN (R 4.1.1)
stringr * 1.4.0 2019-02-10 [2] CRAN (R 4.1.1)
tibble * 3.1.6 2021-11-07 [2] CRAN (R 4.1.1)
tidyr * 1.1.4 2021-09-27 [2] CRAN (R 4.1.1)
tidyselect 1.1.1 2021-04-30 [2] CRAN (R 4.1.0)
tidyverse * 1.3.1 2021-04-15 [2] CRAN (R 4.1.0)
tzdb 0.2.0 2021-10-27 [2] CRAN (R 4.1.1)
usmap 0.6.0 2022-02-27 [2] CRAN (R 4.1.1)
usmapdata 0.1.0 2022-02-09 [2] CRAN (R 4.1.1)
utf8 1.2.2 2021-07-24 [2] CRAN (R 4.1.0)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.1)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.1)
xfun 0.29 2021-12-14 [2] CRAN (R 4.1.1)
xml2 1.3.3 2021-11-30 [2] CRAN (R 4.1.1)
xtable 1.8-4 2019-04-21 [2] CRAN (R 4.1.0)
yaml 2.3.7 2023-01-23 [1] CRAN (R 4.1.1)
zipzcta * 0.0.0.9000 2022-08-08 [1] Github (jjchern/zipzcta@11e241b)
[1] /Users/mvk/Library/R/arm64/4.1/library
[2] /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 13.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] furrr_0.2.3 future_1.29.0 janitor_2.1.0 fs_1.5.2
[5] config_0.3.1 doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2
[9] ggsci_2.9 patchwork_1.1.1 knitr_1.37 ineq_0.2-13
[13] zipzcta_0.0.0.9000 here_1.0.1 forcats_0.5.1 stringr_1.4.0
[17] dplyr_1.0.10 purrr_0.3.4 readr_2.1.1 tidyr_1.1.4
[21] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 shiny_1.7.1
loaded via a namespace (and not attached):
[1] lubridate_1.8.0 fontawesome_0.2.2 httr_1.4.4
[4] rprojroot_2.0.2 tools_4.1.2 backports_1.4.1
[7] bslib_0.3.1 utf8_1.2.2 R6_2.5.1
[10] DBI_1.1.2 colorspace_2.0-2 withr_2.5.0
[13] tidyselect_1.1.1 compiler_4.1.2 cli_3.4.0
[16] rvest_1.0.2 xml2_1.3.3 sass_0.4.2
[19] scales_1.2.1 digest_0.6.29 rmarkdown_2.11
[22] pkgconfig_2.0.3 htmltools_0.5.2 sessioninfo_1.2.2
[25] parallelly_1.32.1 prefixer_0.1.5.9000 dbplyr_2.1.1
[28] fastmap_1.1.0 rlang_1.0.5 readxl_1.3.1
[31] rstudioapi_0.13 jquerylib_0.1.4 generics_0.1.3
[34] jsonlite_1.8.4 magrittr_2.0.3 usmap_0.6.0
[37] Rcpp_1.0.8.3 munsell_0.5.0 fansi_1.0.0
[40] lifecycle_1.0.1 stringi_1.7.6 yaml_2.3.7
[43] snakecase_0.11.0 grid_4.1.2 listenv_0.8.0
[46] promises_1.2.0.1 crayon_1.4.2 miniUI_0.1.1.1
[49] haven_2.4.3 hms_1.1.1 pillar_1.6.4
[52] codetools_0.2-18 reprex_2.0.1 glue_1.6.2
[55] evaluate_0.14 usmapdata_0.1.0 renv_0.15.4
[58] modelr_0.1.8 vctrs_0.4.1 tzdb_0.2.0
[61] httpuv_1.6.5 cellranger_1.1.0 gtable_0.3.0
[64] assertthat_0.2.1 cachem_1.0.6 xfun_0.29
[67] mime_0.12 xtable_1.8-4 broom_0.7.11
[70] later_1.3.0 globals_0.16.1 shinyWidgets_0.7.4
[73] ellipsis_0.3.2