Reproducible code for our manuscript Estimated childhood lead exposure from drinking water in Chicago.
Almost all data files are publicly available and are described in the manuscript. After downloading necessary data files, run the code in numerical order. The data from the Healthy Chicago Surveys are not publicly available, but the code can be easily modified to run without it.
Please direct any corrections or inquiries to [email protected].
Our session info is below.
> sessioninfo::session_info(pkgs = "attached")
─ Session info ───────────────────────────────────────────────────────────────────────────
setting value
version R version 3.6.3 (2020-02-29)
os macOS 10.16
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-10-10
rstudio 1.2.1335 (desktop)
pandoc NA
─ Packages ───────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
bonsai * 0.2.1 2022-11-29 [1] CRAN (R 3.6.3)
broom * 1.0.4 2023-03-11 [1] CRAN (R 3.6.3)
censusxy * 1.1.1 2022-12-06 [1] CRAN (R 3.6.3)
cowplot * 1.1.1 2020-12-30 [1] CRAN (R 3.6.2)
dials * 1.2.0 2023-04-03 [1] CRAN (R 3.6.3)
dplyr * 1.1.1 2023-03-22 [1] CRAN (R 3.6.3)
egg * 0.4.5 2019-07-13 [1] CRAN (R 3.6.3)
EnvStats * 2.8.1 2023-08-22 [1] CRAN (R 3.6.3)
forcats * 0.5.1 2021-01-27 [1] CRAN (R 3.6.2)
ggallin * 0.1.1 2017-10-02 [1] CRAN (R 3.6.3)
ggdensity * 1.0.0 2023-02-09 [1] CRAN (R 3.6.3)
ggeasy * 0.1.4 2023-03-12 [1] CRAN (R 3.6.3)
ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 3.6.3)
ggthemes * 4.2.4 2021-01-20 [1] CRAN (R 3.6.2)
glmnet * 4.1-3 2021-11-02 [1] CRAN (R 3.6.2)
gridExtra * 2.3 2017-09-09 [1] CRAN (R 3.6.0)
infer * 1.0.4 2022-12-02 [1] CRAN (R 3.6.3)
janitor * 2.1.0 2021-01-05 [1] CRAN (R 3.6.2)
lightgbm * 3.3.5 2023-01-16 [1] CRAN (R 3.6.3)
lubridate * 1.8.0 2021-10-07 [1] CRAN (R 3.6.2)
Matrix * 1.2-18 2019-11-27 [1] CRAN (R 3.6.3)
mice * 3.15.0 2022-11-19 [1] CRAN (R 3.6.3)
modeldata * 1.1.0 2023-01-25 [1] CRAN (R 3.6.3)
naniar * 1.0.0 2023-02-02 [1] CRAN (R 3.6.3)
parsnip * 1.1.0 2023-04-12 [1] CRAN (R 3.6.3)
patchwork * 1.1.2 2022-08-19 [1] CRAN (R 3.6.3)
probably * 1.0.2 2023-06-29 [1] CRAN (R 3.6.3)
purrr * 1.0.1 2023-01-10 [1] CRAN (R 3.6.3)
R6 * 2.5.1 2021-08-19 [1] CRAN (R 3.6.2)
ranger * 0.14.1 2022-06-18 [1] CRAN (R 3.6.3)
RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 3.6.3)
readr * 1.4.0 2020-10-05 [1] CRAN (R 3.6.2)
readxl * 1.3.1 2019-03-13 [1] CRAN (R 3.6.0)
recipes * 1.0.7 2023-08-10 [1] CRAN (R 3.6.3)
rsample * 1.1.1 2022-12-07 [1] CRAN (R 3.6.3)
rusps * 0.1.0 2022-12-28 [1] Github (hansthompson/rusps@36090a4)
scales * 1.2.1 2022-08-20 [1] CRAN (R 3.6.3)
sf * 1.0-1 2021-06-29 [1] CRAN (R 3.6.2)
shapviz * 0.9.0 2023-06-09 [1] CRAN (R 3.6.3)
stringr * 1.5.0 2022-12-02 [1] CRAN (R 3.6.3)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 3.6.3)
tidycensus * 1.3.1 2023-01-09 [1] CRAN (R 3.6.3)
tidymodels * 1.0.0 2022-07-13 [1] CRAN (R 3.6.3)
tidyr * 1.3.0 2023-01-24 [1] CRAN (R 3.6.3)
tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 3.6.2)
tmaptools * 3.1-1 2021-01-19 [1] CRAN (R 3.6.3)
tune * 1.1.1 2023-04-11 [1] CRAN (R 3.6.3)
workflows * 1.1.3 2023-02-22 [1] CRAN (R 3.6.3)
workflowsets * 1.0.1 2023-04-06 [1] CRAN (R 3.6.3)
XML * 3.99-0.3 2020-01-20 [1] CRAN (R 3.6.0)
yardstick * 1.2.0 2023-04-21 [1] CRAN (R 3.6.3)