emmaSkarstein / Missing-data-and-measurement-error

Supplementary material and reproducible research files for article “A joint Bayesian framework for missing data and measurement error using integrated nested Laplace approximations” by Emma Skarstein, Sara Martino and Stefanie Muff.

Missing-data-and-measurement-error

This repository contains the files both to

1. reproduce all analysis in the article A joint Bayesian framework for missing data and measurement error using integrated nested Laplace approximations,
2. generate the website https://emmaskarstein.github.io/Missing-data-and-measurement-error/.

The website is made using Quarto, and the compiled html-files can be found in the folder called docs. I recommend opening the file at docs/index.html to get started!

If you prefer looking directly at/running R-scripts, you can clone this repository and run the R-scripts in the folder called R. These R-scripts are automatically generated from the Quarto documents using knitr::purl.

How to reproduce figures from article

• Figure 2: Run the file simulation_study.qmd
• Figure 3: Run the file missing_covariate_imputation.qmd
• Figure 4: Run the file missing_and_mismeasured_covariate.qmd

Data sets

See the respective data description files, docs/data_bloodpressure.html, docs/data_nhanes.html, docs/data_simulated.html.

Session info

R-INLA version ..........: 22.05.07
Date ....................: Sat May 7 12:43:31 PM +03 2022 (Version_22.05.07)
Maintainers .............: Havard Rue <[e-mail]>
                         : Finn Lindgren <[e-mail]>
                         : Elias Teixeira Krainski <[e-mail]>
Main web-page ...........: www.r-inla.org
Download-page ...........: inla.r-inla-download.org
Repository ..............: github.com/hrue/r-inla
Email support ...........: [e-mail]
                         : [e-mail]
                         
                         
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23)
 os       macOS Big Sur ... 10.16
 system   x86_64, darwin17.0
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Oslo
 date     2023-09-01
 pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package      * version  date (UTC) lib source
 class          7.3-20   2022-01-16 [1] CRAN (R 4.2.1)
 classInt       0.4-9    2023-02-28 [1] CRAN (R 4.2.0)
 cli            3.6.1    2023-03-23 [1] CRAN (R 4.2.0)
 codetools      0.2-18   2020-11-04 [1] CRAN (R 4.2.1)
 colorspace     2.1-0    2023-01-23 [1] CRAN (R 4.2.0)
 DBI            1.1.3    2022-06-18 [1] CRAN (R 4.2.0)
 e1071          1.7-13   2023-02-01 [1] CRAN (R 4.2.0)
 fansi          1.0.4    2023-01-22 [1] CRAN (R 4.2.0)
 farver         2.1.1    2022-07-06 [1] CRAN (R 4.2.0)
 foreach      * 1.5.2    2022-02-02 [1] CRAN (R 4.2.0)
 ggplot2        3.4.3    2023-08-14 [1] CRAN (R 4.2.0)
 glue           1.6.2    2022-02-24 [1] CRAN (R 4.2.0)
 gtable         0.3.3    2023-03-21 [1] CRAN (R 4.2.0)
 INLA         * 22.05.07 2022-05-07 [1] local
 inlabru        2.7.0    2022-12-02 [1] CRAN (R 4.2.1)
 isoband        0.2.7    2022-12-20 [1] CRAN (R 4.2.0)
 iterators      1.0.14   2022-02-05 [1] CRAN (R 4.2.0)
 KernSmooth     2.23-20  2021-05-03 [1] CRAN (R 4.2.1)
 labeling       0.4.2    2020-10-20 [1] CRAN (R 4.2.0)
 lattice        0.20-45  2021-09-22 [1] CRAN (R 4.2.1)
 lifecycle      1.0.3    2022-10-07 [1] CRAN (R 4.2.0)
 magrittr       2.0.3    2022-03-30 [1] CRAN (R 4.2.0)
 MASS           7.3-57   2022-04-22 [1] CRAN (R 4.2.1)
 Matrix       * 1.4-1    2022-03-23 [1] CRAN (R 4.2.1)
 MatrixModels   0.5-1    2022-09-11 [1] CRAN (R 4.2.0)
 mgcv           1.8-40   2022-03-29 [1] CRAN (R 4.2.1)
 munsell        0.5.0    2018-06-12 [1] CRAN (R 4.2.0)
 nlme           3.1-157  2022-03-25 [1] CRAN (R 4.2.1)
 patchwork      1.1.2    2022-08-19 [1] CRAN (R 4.2.0)
 pillar         1.9.0    2023-03-22 [1] CRAN (R 4.2.0)
 pkgconfig      2.0.3    2019-09-22 [1] CRAN (R 4.2.0)
 plyr           1.8.8    2022-11-11 [1] CRAN (R 4.2.0)
 proxy          0.4-27   2022-06-09 [1] CRAN (R 4.2.0)
 R6             2.5.1    2021-08-19 [1] CRAN (R 4.2.0)
 RColorBrewer   1.1-3    2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp           1.0.11   2023-07-06 [1] CRAN (R 4.2.0)
 rgdal          1.5-32   2022-05-09 [1] CRAN (R 4.2.0)
 rlang          1.1.1    2023-04-28 [1] CRAN (R 4.2.0)
 s2             1.1.4    2023-05-17 [1] CRAN (R 4.2.0)
 scales         1.2.1    2022-08-20 [1] CRAN (R 4.2.0)
 sf             1.0-14   2023-07-11 [1] CRAN (R 4.2.0)
 sp           * 2.0-0    2023-06-22 [1] CRAN (R 4.2.0)
 tibble         3.2.1    2023-03-20 [1] CRAN (R 4.2.0)
 units          0.8-3    2023-08-10 [1] CRAN (R 4.2.0)
 utf8           1.2.3    2023-01-31 [1] CRAN (R 4.2.0)
 vctrs          0.6.3    2023-06-14 [1] CRAN (R 4.2.0)
 viridisLite    0.4.2    2023-05-02 [1] CRAN (R 4.2.0)
 withr          2.5.0    2022-03-03 [1] CRAN (R 4.2.0)
 wk             0.7.3    2023-05-06 [1] CRAN (R 4.2.0)

 [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library

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