Source for "Bayesian aggregation of average data: An application in drug development"

Date: 13th May 2020

This repository includes updated R and Stan source files used to generate the main outputs in our paper on Bayesian aggregation of average data. The updated codes ensure that the source runs with the RStan 2.19 release.

The code is distributed under the BSD-3 license, see LICENSE.

Please cite our work when you use these codes or apply our approach:

S. Weber, A. Gelman, D. Lee, M. Betancourt, A. Vehtari, A. Racine (2018), "Bayesian aggregation of average data: An application in drug development", Ann. Appl. Stat., Volume 12, Number 3 (2018), 1583-1604.

URL: https://projecteuclid.org/euclid.aoas/1536652966
doi: 10.1214/17-AOAS1122
arXiv: 1602.02055

These sources are also available in their original form as supplemental material to the original article under the DOI

doi: 10.1214/17-AOAS1122SUPP

To use the code, we recommend to start with one of the examples below as template and modify it to your needs.

The repository includes a Docker image defintion which is configured to use R 4.0.0 and R packages as dated from the 20th April of 2020. To run the scripts with this environment please first build locally the Docker image with the build-rimage.sh script. Once the Docker image is created you can run the analysis in the source directory via

• Analytical linear example: ./run-docker-cmd.sh ./linear_baad.R
• Non-linear example: ./run-docker-cmd.sh ./pkpd_baad.R

Outputs from these scripts will be saved in the current source directory directly. Note that the scripts assume a bash shell as commonly used on Linux or Mac.

Updates will be posted to https://github.com/wds15/baad

Contents

• build-rimage.sh Build Docker image
• run-docker-cmd.sh Run analysis with Docker image as container
• Dockerfile Docker image R 4.0.0 with R packages from 20th April 2020
• linear_baad.R Linear example
• pkpd_badd.R Non-linear example
• utils_baad.R Various utility functions

Software used

R session info:

R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] plyr_1.8.6         mvtnorm_1.1-0      abind_1.4-5        rstan_2.19.3
[5] ggplot2_3.3.0      StanHeaders_2.19.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6        RColorBrewer_1.1-2  pillar_1.4.3
 [4] compiler_4.0.0      prettyunits_1.1.1   tools_4.0.0
 [7] digest_0.6.25       pkgbuild_1.0.6      lifecycle_0.2.0
[10] tibble_3.0.0        gtable_0.3.0        lattice_0.20-41
[13] pkgconfig_2.0.3     rlang_0.4.5         Matrix_1.2-18
[16] cli_2.0.2           parallel_4.0.0      loo_2.2.0
[19] gridExtra_2.3       withr_2.1.2         vctrs_0.2.4
[22] stats4_4.0.0        grid_4.0.0          glue_1.4.0
[25] inline_0.3.15       R6_2.4.1            BH_1.72.0-3
[28] processx_3.4.2      fansi_0.4.1         farver_2.0.3
[31] callr_3.4.3         magrittr_1.5        codetools_0.2-16
[34] scales_1.1.0        ps_1.3.2            ellipsis_0.3.0
[37] matrixStats_0.56.0  assertthat_0.2.1    colorspace_1.4-1
[40] labeling_0.3        munsell_0.5.0       crayon_1.3.4
[43] RcppEigen_0.3.3.7.0