This repository is home to the covid.gradient.estimation R package which houses
functions to clean, merge, and analyze data from a variety of sources on county-level
COVID-19 outcomes, sociodemographic measures, and geography using generalized additive
models (GAMs).
This package can be installed by running (in R):
install.packages("devtools")
devtools::install_github("ctesta01/covid.gradient.estimation")Inside the R/ directory are the functions built into the package, which
clean and merge the data stored inside inst/ to create the analytic dataset
that we investigate in the analysis/ code.
R
├── create_analytic_dataset.R # merge datasets together
├── get_absms_from_acs.R # get area-based social metrics from the American Community Survey
├── get_popsizes.R # get the 2020 population estimates from the Census
├── load_covid19_deaths.R # load the NYTimes COVID-19 death counts
└── load_political_lean.R # load the MIT Election Lab votes cast data
There are several datasets installed in the package in the inst/ directory.
Those include a cached copy of the county-level area based social metrics
so that we don't have to query the American Community Survey API every time we
recreate our analytic dataset, the COVID-19 deaths from NYTimes,
and votes cast by county in the 2020 election from the MIT Election Lab.
inst
├── cached_absms.rds
├── mit_election_lab
│ └── countypres_2000-2020.csv
└── nytimes
├── us-counties-2020.csv
├── us-counties-2021.csv
└── us-counties-2022.csv
The analysis work and figure generation is done in the analysis/
directory, where discrete analytic tasks are organized by directories numbered in
the order of analysis steps.
The analyses 01 through 03 can be considered
exploratory data analyses, with 04, 05 main analyses for the non-spatial
modeling results, 06 and 07 supplementary analyses meant to inform the
spatial modeling approach, and 08 exploratory data analysis to illustrate
the importance of taking spatiotemporal autocorrelation into account. 09
includes the code to run the models which assess the association of varying
county-level covariates and COVID-19 mortality after taking into account a
spatiotemporal latent surface. 10 contains the code necessary to generate the
figure illustrating how spline basis functions are used in a GAM.
analysis
├── 01_state_trajectories
├── 02_plot_county_trends
├── 03_county_distributions
├── 04_one_variable_over_time
├── 05_two_variables_at_a_time
├── 06_random_forest
├── 07_xgboost
├── 08_spatiotemporal_autocorrelation
├── 09_spatiotemporal_models
└── 10_supplementary_gam_figures
Finally, the manuscript is produced in the manuscript/ directory.
Effects Associated with Covariates Before and After Adjusting for Spatiotemporal Autocorrelation Figure
This project uses renv to manage dependencies so that the analyses can be
reproduced exactly down to the same release version of each package used.
After cloning this repository and installing renv, you can activate renv and
restore the packages as they were used to conduct these analyses using
renv::restore().
# CRAN ===============================
- DBI [* -> 1.1.3]
- GGally [* -> 2.1.2]
- HDInterval [* -> 0.2.2]
- KernSmooth [* -> 2.23-20]
- MASS [* -> 7.3-56]
- Matrix [* -> 1.4-1]
- R6 [* -> 2.5.1]
- RColorBrewer [* -> 1.1-3]
- Rcpp [* -> 1.0.9]
- RcppEigen [* -> 0.3.3.9.2]
- askpass [* -> 1.1]
- base64enc [* -> 0.1-3]
- bit [* -> 4.0.4]
- bit64 [* -> 4.0.5]
- boot [* -> 1.3-28]
- brew [* -> 1.0-8]
- brio [* -> 1.1.3]
- bslib [* -> 0.4.0]
- cachem [* -> 1.0.6]
- callr [* -> 3.7.2]
- class [* -> 7.3-20]
- classInt [* -> 0.4-8]
- cli [* -> 3.4.1]
- clipr [* -> 0.8.0]
- codetools [* -> 0.2-18]
- colorspace [* -> 2.0-3]
- commonmark [* -> 1.8.0]
- cpp11 [* -> 0.4.2]
- crayon [* -> 1.5.2]
- credentials [* -> 1.3.2]
- crosstalk [* -> 1.2.0]
- curl [* -> 4.3.2]
- data.table [* -> 1.14.2]
- deldir [* -> 1.0-6]
- desc [* -> 1.4.2]
- devtools [* -> 2.4.4]
- diffobj [* -> 0.3.5]
- digest [* -> 0.6.29]
- distributional [* -> 0.3.1]
- doParallel [* -> 1.0.17]
- downlit [* -> 0.4.2]
- dplyr [* -> 1.0.10]
- e1071 [* -> 1.7-11]
- ellipsis [* -> 0.3.2]
- evaluate [* -> 0.16]
- fansi [* -> 1.0.3]
- farver [* -> 2.1.1]
- fastmap [* -> 1.1.0]
- fontawesome [* -> 0.3.0]
- forcats [* -> 0.5.2]
- foreach [* -> 1.5.2]
- foreign [* -> 0.8-82]
- fs [* -> 1.5.2]
- gamm4 [* -> 0.2-6]
- generics [* -> 0.1.3]
- gert [* -> 1.9.0]
- ggcorrplot [* -> 0.1.4]
- ggdist [* -> 3.2.0]
- ggplot2 [* -> 3.3.6]
- ggridges [* -> 0.5.4]
- gh [* -> 1.3.1]
- gitcreds [* -> 0.1.2]
- glue [* -> 1.6.2]
- gridExtra [* -> 2.3]
- gtable [* -> 0.3.1]
- here [* -> 1.0.1]
- highr [* -> 0.9]
- hms [* -> 1.1.2]
- htmltools [* -> 0.5.3]
- htmlwidgets [* -> 1.5.4]
- httpuv [* -> 1.6.6]
- httr [* -> 1.4.4]
- ini [* -> 0.3.1]
- isoband [* -> 0.2.5]
- iterators [* -> 1.0.14]
- janitor [* -> 2.1.0]
- jquerylib [* -> 0.1.4]
- jsonlite [* -> 1.8.2]
- knitr [* -> 1.40]
- labeling [* -> 0.4.2]
- later [* -> 1.3.0]
- lattice [* -> 0.20-45]
- lazyeval [* -> 0.2.2]
- lifecycle [* -> 1.0.2]
- lme4 [* -> 1.1-30]
- lubridate [* -> 1.8.0]
- magrittr [* -> 2.0.3]
- mapproj [* -> 1.2.8]
- maps [* -> 3.4.0]
- maptools [* -> 1.1-4]
- matrixStats [* -> 0.62.0]
- memoise [* -> 2.0.1]
- mgcViz [* -> 0.1.9]
- mgcv [* -> 1.8-40]
- mime [* -> 0.12]
- miniUI [* -> 0.1.1.1]
- minqa [* -> 1.2.4]
- munsell [* -> 0.5.0]
- nlme [* -> 3.1-157]
- nloptr [* -> 2.0.3]
- numDeriv [* -> 2016.8-1.1]
- openssl [* -> 2.0.3]
- pillar [* -> 1.8.1]
- pkgbuild [* -> 1.3.1]
- pkgconfig [* -> 2.0.3]
- pkgdown [* -> 2.0.6]
- pkgload [* -> 1.3.0]
- plotly [* -> 4.10.0]
- plyr [* -> 1.8.7]
- praise [* -> 1.0.0]
- prettyunits [* -> 1.1.1]
- processx [* -> 3.7.0]
- profvis [* -> 0.3.7]
- progress [* -> 1.2.2]
- promises [* -> 1.2.0.1]
- proxy [* -> 0.4-27]
- ps [* -> 1.7.1]
- purrr [* -> 0.3.4]
- qgam [* -> 1.3.4]
- ragg [* -> 1.2.3]
- ranger [* -> 0.14.1]
- rappdirs [* -> 0.3.3]
- rcmdcheck [* -> 1.4.0]
- readr [* -> 2.1.3]
- rematch2 [* -> 2.1.2]
- remotes [* -> 2.4.2]
- reshape [* -> 0.8.9]
- reshape2 [* -> 1.4.4]
- rgdal [* -> 1.5-32]
- rlang [* -> 1.0.6]
- rmarkdown [* -> 2.16]
- roxygen2 [* -> 7.2.1]
- rprojroot [* -> 2.0.3]
- rstudioapi [* -> 0.14]
- rversions [* -> 2.1.2]
- rvest [* -> 1.0.3]
- s2 [* -> 1.1.0]
- sass [* -> 0.4.2]
- scales [* -> 1.2.1]
- selectr [* -> 0.4-2]
- sessioninfo [* -> 1.2.2]
- sf [* -> 1.0-8]
- shiny [* -> 1.7.2]
- snakecase [* -> 0.11.0]
- sourcetools [* -> 0.1.7]
- sp [* -> 1.5-0]
- spData [* -> 2.2.0]
- spdep [* -> 1.2-7]
- stringi [* -> 1.7.8]
- stringr [* -> 1.4.1]
- sys [* -> 3.4]
- systemfonts [* -> 1.0.4]
- testthat [* -> 3.1.4]
- textshaping [* -> 0.3.6]
- tibble [* -> 3.1.8]
- tidycensus [* -> 1.2.3]
- tidyr [* -> 1.2.1]
- tidyselect [* -> 1.1.2]
- tigris [* -> 1.6.1]
- tinytex [* -> 0.42]
- tzdb [* -> 0.3.0]
- units [* -> 0.8-0]
- urlchecker [* -> 1.0.1]
- usethis [* -> 2.1.6]
- utf8 [* -> 1.2.2]
- uuid [* -> 1.1-0]
- vctrs [* -> 0.4.2]
- vip [* -> 0.3.2]
- viridis [* -> 0.6.2]
- viridisLite [* -> 0.4.1]
- vroom [* -> 1.6.0]
- waldo [* -> 0.4.0]
- whisker [* -> 0.4]
- withr [* -> 2.5.0]
- wk [* -> 0.6.0]
- xfun [* -> 0.33]
- xgboost [* -> 1.6.0.1]
- xml2 [* -> 1.3.3]
- xopen [* -> 1.0.0]
- xtable [* -> 1.8-4]
- yaml [* -> 2.3.5]
- zip [* -> 2.2.1]
Read the manuscript in its current form: manuscript.pdf