This repository,
parental_death,
contains reproducible code for manuscript, “Youth experiencing parental
death due to drug poisoning and firearm violence in the US, 1999 -
2020”, which uses publicly-available multiple causes of death data from
January 1, 1990, through December 31, 2020, from the National Center
for Health Statistics to
quantify the number of children experiencing parental death due to drugs
and firearms. The full citation is:
Schlüter B-S, Alburez-Gutierrez D, Bibbins-Domingo K, Alexander M, Kiang MV, “Youth experiencing parental death due to drug poisoning and firearm violence in the US, 1999 - 2020.” JAMA. Published online May 4, 2024. doi: 10.1001/jama.2024.8391
Question. What are the estimated rates of US youth (younger than 18 years) who have lost a parent due to drug poisoning or firearms?
Findings. In this cross-sectional study of the US population using publicly available data from 1990 through 2020, between 1999 and 2020, an estimated 1.19 million US youth had a parent die by drug poisoning or firearms. In 2020, drugs and firearms caused 23% of all parental deaths compared with 12% in 1999, and Black youth experienced a disproportionate burden, mainly due to firearm deaths of fathers.
Meaning. Results of this modeling study suggest that US youth are at high and increasing risk of experiencing parental death by drugs or firearms.
All code can be found in the ./codes 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 ./outputs/data_public folder. Figures are in the
./outputs/figures folder. The table was generated using Excel with
data in ./outputs/tables/table_data_manuscript.xlsx created with code
./codes/05_numbers_text.R.
While JAMA Network journals do not provide updated acknowledgements for identifying errors, we do want to publicly acknowledge and thank those who carefully read the manuscript and identify mistakes.
We thank Dr. Ashton Verdery for identifying an error in the Table of the manuscript. Four cells were mistakenly duplicated. This error does not appear in the code-generated version of the table, so we believe it was a copy and paste error.
Separately, one cell in the Table had the 95% confidence interval values reversed (i.e., the lower bound was on the right and the upper bound was on the left) but was otherwise numerically correct.
A corrected manuscript with the revised Table and a correction notice have been published.
- Diego Alburez-Gutierrez
- Monica Alexander
- Kirsten Bibbins-Domingo
- Mathew V Kiang
- Benjamin-Samuel Schlüter
We use publicly available data and provide code that will download
and/or munge these data as necessary. For full reproducibility, we also
provide all of our simulation
files,
which will allow for exact reproduction of our results. These files are
stores on the Harvard
Dataverse;
however, due to limitations on file size, we split each of the (>5GB)
simulation files into 10 smaller chunks and provide code to recombine
them (./codes/00_combine_sim_files.R). If you wish to fully reproduce
our results, use the 00 code file to download the files noting that
they take up approximately 55GB of space and require ~16GB of RAM (each
file) to recombine.
We use renv for package
management but below we also post the relevant session information to
ensure full reproducibility.
> sessioninfo::session_info()
- Session info -------------------------------------------------------
setting value
version R version 4.1.3 (2022-03-10)
os Windows 10 x64 (build 19044)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz Europe/Paris
date 2023-11-27
rstudio 2023.09.1+494 Desert Sunflower (desktop)
pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
- Packages -----------------------------------------------------------
! package * version date (UTC) lib source
P askpass 1.2.0 2023-09-03 [?] CRAN (R 4.1.3)
P cellranger 1.1.0 2016-07-27 [?] CRAN (R 4.1.3)
P cli 3.6.1 2023-03-23 [?] CRAN (R 4.1.3)
P colorspace 2.1-0 2023-01-23 [?] CRAN (R 4.1.3)
P digest 0.6.33 2023-07-07 [?] CRAN (R 4.1.3)
P dplyr * 1.1.4 2023-11-17 [?] CRAN (R 4.1.3)
P evaluate 0.23 2023-11-01 [?] CRAN (R 4.1.3)
P fansi 1.0.5 2023-10-08 [?] CRAN (R 4.1.3)
P fastmap 1.1.1 2023-02-24 [?] CRAN (R 4.1.3)
P forcats * 1.0.0 2023-01-29 [?] CRAN (R 4.1.3)
P generics 0.1.3 2022-07-05 [?] CRAN (R 4.1.3)
P ggplot2 * 3.4.4 2023-10-12 [?] CRAN (R 4.1.3)
P glue 1.6.2 2022-02-24 [?] CRAN (R 4.1.3)
P gtable 0.3.4 2023-08-21 [?] CRAN (R 4.1.3)
P here * 1.0.1 2020-12-13 [?] CRAN (R 4.1.3)
P hms 1.1.3 2023-03-21 [?] CRAN (R 4.1.3)
P htmltools 0.5.7 2023-11-03 [?] CRAN (R 4.1.3)
P httr 1.4.7 2023-08-15 [?] CRAN (R 4.1.3)
P knitr 1.45 2023-10-30 [?] CRAN (R 4.1.3)
P lattice 0.20-45 2021-09-22 [?] CRAN (R 4.1.3)
P lifecycle 1.0.4 2023-11-07 [?] CRAN (R 4.1.3)
P lubridate * 1.9.3 2023-09-27 [?] CRAN (R 4.1.3)
P magrittr 2.0.3 2022-03-30 [?] CRAN (R 4.1.3)
P Matrix * 1.5-4 2023-04-04 [?] CRAN (R 4.1.3)
P munsell 0.5.0 2018-06-12 [?] CRAN (R 4.1.3)
P openxlsx * 4.2.5.2 2023-02-06 [?] CRAN (R 4.1.3)
P pdftools * 3.4.0 2023-09-25 [?] CRAN (R 4.1.3)
P pillar 1.9.0 2023-03-22 [?] CRAN (R 4.1.3)
P pkgconfig 2.0.3 2019-09-22 [?] CRAN (R 4.1.3)
P pracma * 2.4.4 2023-11-10 [?] CRAN (R 4.1.3)
P purrr * 1.0.2 2023-08-10 [?] CRAN (R 4.1.3)
P qpdf 1.3.2 2023-03-17 [?] CRAN (R 4.1.3)
P R6 2.5.1 2021-08-19 [?] CRAN (R 4.1.3)
P Rcpp 1.0.11 2023-07-06 [?] CRAN (R 4.1.3)
P readr * 2.1.4 2023-02-10 [?] CRAN (R 4.1.3)
P readxl * 1.4.3 2023-07-06 [?] CRAN (R 4.1.3)
renv * 1.0.3 2023-09-19 [1] CRAN (R 4.1.3)
P rlang 1.1.2 2023-11-04 [?] CRAN (R 4.1.3)
P rmarkdown 2.25 2023-09-18 [?] CRAN (R 4.1.3)
P rprojroot 2.0.4 2023-11-05 [?] CRAN (R 4.1.3)
P rstudioapi 0.15.0 2023-07-07 [?] CRAN (R 4.1.3)
P rvest * 1.0.3 2022-08-19 [?] CRAN (R 4.1.3)
P scales 1.2.1 2022-08-20 [?] CRAN (R 4.1.3)
P sessioninfo * 1.2.2 2021-12-06 [?] CRAN (R 4.1.3)
P stringi 1.8.2 2023-11-23 [?] CRAN (R 4.1.3)
P stringr * 1.5.1 2023-11-14 [?] CRAN (R 4.1.3)
P tibble * 3.2.1 2023-03-20 [?] CRAN (R 4.1.3)
P tidyr * 1.3.0 2023-01-24 [?] CRAN (R 4.1.3)
P tidyselect 1.2.0 2022-10-10 [?] CRAN (R 4.1.3)
P tidyverse * 2.0.0 2023-02-22 [?] CRAN (R 4.1.3)
P timechange 0.2.0 2023-01-11 [?] CRAN (R 4.1.3)
P tzdb 0.4.0 2023-05-12 [?] CRAN (R 4.1.3)
P utf8 1.2.4 2023-10-22 [?] CRAN (R 4.1.3)
P vctrs 0.6.4 2023-10-12 [?] CRAN (R 4.1.3)
P withr 2.5.2 2023-10-30 [?] CRAN (R 4.1.3)
P xfun 0.41 2023-11-01 [?] CRAN (R 4.1.3)
P xml2 1.3.5 2023-07-06 [?] CRAN (R 4.1.3)
P yaml 2.3.7 2023-01-23 [?] CRAN (R 4.1.3)
P zip 2.3.0 2023-04-17 [?] CRAN (R 4.1.3)
[1] C:/Users/bschluter/Desktop/Postdoc/Projects/parental_death_drugs_firearms/renv/library/R-4.1/x86_64-w64-mingw32
[2] C:/Users/bschluter/AppData/Local/R/cache/R/renv/sandbox/R-4.1/x86_64-w64-mingw32/5d681d51
P -- Loaded and on-disk path mismatch.
----------------------------------------------------------------------> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods
[7] base
other attached packages:
[1] sessioninfo_1.2.2 renv_1.0.3 Matrix_1.5-4
[4] pracma_2.4.4 rvest_1.0.3 pdftools_3.4.0
[7] readxl_1.4.3 openxlsx_4.2.5.2 here_1.0.1
[10] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[13] dplyr_1.1.4 purrr_1.0.2 readr_2.1.4
[16] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.4
[19] tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] qpdf_1.3.2 tidyselect_1.2.0 xfun_0.41
[4] lattice_0.20-45 colorspace_2.1-0 vctrs_0.6.4
[7] generics_0.1.3 htmltools_0.5.7 yaml_2.3.7
[10] utf8_1.2.4 rlang_1.1.2 pillar_1.9.0
[13] glue_1.6.2 withr_2.5.2 lifecycle_1.0.4
[16] munsell_0.5.0 gtable_0.3.4 cellranger_1.1.0
[19] zip_2.3.0 evaluate_0.23 knitr_1.45
[22] tzdb_0.4.0 fastmap_1.1.1 fansi_1.0.5
[25] Rcpp_1.0.11 scales_1.2.1 hms_1.1.3
[28] askpass_1.2.0 digest_0.6.33 stringi_1.8.2
[31] grid_4.1.3 rprojroot_2.0.4 cli_3.6.1
[34] tools_4.1.3 magrittr_2.0.3 pkgconfig_2.0.3
[37] xml2_1.3.5 timechange_0.2.0 rmarkdown_2.25
[40] httr_1.4.7 rstudioapi_0.15.0 R6_2.5.1
[43] compiler_4.1.3