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Code for: "The APC-Effect: Stratification in Open Access Publishing"

This repository holds code and data for the preprint "The APC-Effect: Stratification in Open Access Publishing".

Data ingestion pipeline

The main data for this study came from OpenAlex. The basic steps to ingest the data that we took are described in the preprint. Once the data was on our Hadoop/Spark cluster, we started preprocessing to filter down the data to our target set and compute necessary quantities.

The R scripts numbered 00 to 15 were executed in order to achieve this. The resultant file papers_with_concepts.parquet was then used for descriptive analysis. This file is available at https://doi.org/10.5281/zenodo.7014802.

Descriptive analysis

  • The file 21-sample-for-multilevel-model.R was used to create the subsample for the mixture model.

  • The file 20-APC-analysis.Rmd holds the main descriptive analysis. A rendered version is provided in 20-APC-analysis.html which can be viewed in the browser. This also contains interactive figures that allow for further exploration. The dataset that underlies this analysis is available at https://doi.org/10.5281/zenodo.7014802.

  • The file 22-additional-mini-analyses.Rmd includes a few further analyses, one of which is present in the supplement.

Mixture modelling

The mixture model was built iteratively, through the files 11 to 17. The file 17-adapted-mixture.R holds the final R script, which used the Stan model present in 17-adapted-mixture.stan.

Analysis of the model (once sampled) was conducted via the notebook 20-analyse-hurdle.Rmd. Note that rendering this notebook takes a long time (30-60 minutes).

Running the sampler is much more time consuming - the last iteration ran for 10 days on 4 cores with 2.2Ghz. Because of this, we provide the fully sampled models for reanalysis:

  • final_models/hm_final_rerun.rds contains data from the simple hurdle model (from file 13-final-hurdle-model.R).
  • The full file from the full analysis (17-brm-large-sample.rds.bz2) is provided as an attached binary to the release, and needs to be moved to the correct location before the notebook can be rendered.

Version history

To enable full transparency of our steps, this repository includes all steps we took when starting with this particular analysis. To avoid clutter, we deleted many outdated files from the main branch, which now only holds the core files from the analysis. All earlier files are still available on the archive branch.

The paper also contains an analysis of the full set of universities (even those that are not included in the Leiden Ranking). The analysis for this is available in the branch full-country-apc-average.

Given the long version history, the full repository is fairly large (~800Mb). It might therefore be easier to simply download release snapshots which will be available on Zenodo.

Software versions

Software versions on Hadoop Cluster We used Spark2 (v2.3.2) to conduct computations. The full session info is as follows: 
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 3.6.0 (2019-04-26)
 os       CentOS Linux 7 (Core)
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Vienna
 date     2022-10-13
 rstudio  1.1.456 (server)
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────────
 package     * version date (UTC) lib source
 arrow       * 4.0.1   2021-05-28 [1] CRAN (R 3.6.0)
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 3.6.0)
 backports     1.4.1   2021-12-13 [1] CRAN (R 3.6.0)
 base64enc     0.1-3   2015-07-28 [1] CRAN (R 3.6.0)
 bit           4.0.4   2020-08-04 [1] CRAN (R 3.6.0)
 bit64         4.0.5   2020-08-30 [1] CRAN (R 3.6.0)
 brio          1.1.3   2021-11-30 [1] CRAN (R 3.6.0)
 broom         0.7.12  2022-01-28 [1] CRAN (R 3.6.0)
 cachem        1.0.6   2021-08-19 [1] CRAN (R 3.6.0)
 callr         3.7.0   2021-04-20 [1] CRAN (R 3.6.0)
 cellranger    1.1.0   2016-07-27 [1] CRAN (R 3.6.0)
 cli           3.3.0   2022-04-25 [1] CRAN (R 3.6.0)
 colorspace  * 2.0-2   2021-06-24 [1] CRAN (R 3.6.0)
 crayon        1.5.1   2022-03-26 [1] CRAN (R 3.6.0)
 DBI           1.1.2   2021-12-20 [1] CRAN (R 3.6.0)
 dbplyr        2.1.1   2021-04-06 [1] CRAN (R 3.6.0)
 desc          1.4.1   2022-03-06 [1] CRAN (R 3.6.0)
 devtools      2.4.3   2021-11-30 [1] CRAN (R 3.6.0)
 digest        0.6.29  2021-12-01 [1] CRAN (R 3.6.0)
 dplyr       * 1.0.9   2022-04-28 [1] CRAN (R 3.6.0)
 ellipsis      0.3.2   2021-04-29 [1] CRAN (R 3.6.0)
 fansi         1.0.3   2022-03-24 [1] CRAN (R 3.6.0)
 fastmap       1.1.0   2021-01-25 [1] CRAN (R 3.6.0)
 forcats     * 0.5.1   2021-01-27 [1] CRAN (R 3.6.0)
 forge         0.2.0   2019-02-26 [1] CRAN (R 3.6.0)
 fs            1.5.2   2021-12-08 [1] CRAN (R 3.6.0)
 generics      0.1.2   2022-01-31 [1] CRAN (R 3.6.0)
 ggplot2     * 3.3.5   2021-06-25 [1] CRAN (R 3.6.0)
 ggrepel     * 0.9.1   2021-01-15 [1] CRAN (R 3.6.0)
 glue          1.6.2   2022-02-24 [1] CRAN (R 3.6.0)
 gtable        0.3.0   2019-03-25 [1] CRAN (R 3.6.0)
 haven         2.4.3   2021-08-04 [1] CRAN (R 3.6.0)
 hms           1.1.1   2021-09-26 [1] CRAN (R 3.6.0)
 htmltools     0.5.2   2021-08-25 [1] CRAN (R 3.6.0)
 htmlwidgets   1.5.4   2021-09-08 [1] CRAN (R 3.6.0)
 httr          1.4.2   2020-07-20 [1] CRAN (R 3.6.0)
 jsonlite      1.8.0   2022-02-22 [1] CRAN (R 3.6.0)
 knitr         1.37    2021-12-16 [1] CRAN (R 3.6.0)
 lifecycle     1.0.1   2021-09-24 [1] CRAN (R 3.6.0)
 lubridate     1.8.0   2021-10-07 [1] CRAN (R 3.6.0)
 magrittr      2.0.3   2022-03-30 [1] CRAN (R 3.6.0)
 memoise       2.0.1   2021-11-26 [1] CRAN (R 3.6.0)
 modelr        0.1.8   2020-05-19 [1] CRAN (R 3.6.0)
 munsell       0.5.0   2018-06-12 [1] CRAN (R 3.6.0)
 patchwork   * 1.1.1   2020-12-17 [1] CRAN (R 3.6.0)
 pillar        1.7.0   2022-02-01 [1] CRAN (R 3.6.0)
 pkgbuild      1.3.1   2021-12-20 [1] CRAN (R 3.6.0)
 pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 3.6.0)
 pkgload       1.2.4   2021-11-30 [1] CRAN (R 3.6.0)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 3.6.0)
 processx      3.5.3   2022-03-25 [1] CRAN (R 3.6.0)
 ps            1.7.0   2022-04-23 [1] CRAN (R 3.6.0)
 purrr       * 0.3.4   2020-04-17 [1] CRAN (R 3.6.0)
 r2d3          0.2.5   2020-12-18 [1] CRAN (R 3.6.0)
 R6            2.5.1   2021-08-19 [1] CRAN (R 3.6.0)
 Rcpp          1.0.8   2022-01-13 [1] CRAN (R 3.6.0)
 readr       * 2.1.2   2022-01-30 [1] CRAN (R 3.6.0)
 readxl        1.3.1   2019-03-13 [1] CRAN (R 3.6.0)
 remotes       2.4.2   2021-11-30 [1] CRAN (R 3.6.0)
 reprex        2.0.1   2021-08-05 [1] CRAN (R 3.6.0)
 RJSONIO       1.3-1.6 2021-09-16 [1] CRAN (R 3.6.0)
 rlang         1.0.2   2022-03-04 [1] CRAN (R 3.6.0)
 rprojroot     2.0.3   2022-04-02 [1] CRAN (R 3.6.0)
 rstudioapi    0.13    2020-11-12 [1] CRAN (R 3.6.0)
 rvest         1.0.2   2021-10-16 [1] CRAN (R 3.6.0)
 scales      * 1.1.1   2020-05-11 [1] CRAN (R 3.6.0)
 sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 3.6.0)
 sparklyr    * 1.7.5   2022-02-02 [1] CRAN (R 3.6.0)
 stringi       1.7.6   2021-11-29 [1] CRAN (R 3.6.0)
 stringr     * 1.4.0   2019-02-10 [1] CRAN (R 3.6.0)
 testthat      3.1.4   2022-04-26 [1] CRAN (R 3.6.0)
 tibble      * 3.1.6   2021-11-07 [1] CRAN (R 3.6.0)
 tidyr       * 1.2.0   2022-02-01 [1] CRAN (R 3.6.0)
 tidyselect    1.1.2   2022-02-21 [1] CRAN (R 3.6.0)
 tidyverse   * 1.3.1   2021-04-15 [1] CRAN (R 3.6.0)
 tzdb          0.2.0   2021-10-27 [1] CRAN (R 3.6.0)
 usethis       2.1.5   2021-12-09 [1] CRAN (R 3.6.0)
 utf8          1.2.2   2021-07-24 [1] CRAN (R 3.6.0)
 vctrs         0.4.1   2022-04-13 [1] CRAN (R 3.6.0)
 WDI         * 2.7.7   2022-07-16 [1] CRAN (R 3.6.0)
 withr         2.5.0   2022-03-03 [1] CRAN (R 3.6.0)
 xfun          0.29    2021-12-14 [1] CRAN (R 3.6.0)
 xml2          1.3.3   2021-11-30 [1] CRAN (R 3.6.0)
 yaml          2.2.2   2022-01-25 [1] CRAN (R 3.6.0)
Software versions for multilevel modelling 
─ Session info ─────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       Ubuntu 22.04.1 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  de_AT.UTF-8
 ctype    de_AT.UTF-8
 tz       Europe/Vienna
 date     2022-10-13
 rstudio  2022.07.0+548 Spotted Wakerobin (server)
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────────
 package        * version  date (UTC) lib source
 abind            1.4-5    2016-07-21 [1] CRAN (R 4.1.2)
 assertthat       0.2.1    2019-03-21 [1] CRAN (R 4.1.2)
 backports        1.4.1    2021-12-13 [1] CRAN (R 4.1.2)
 base64enc        0.1-3    2015-07-28 [1] CRAN (R 4.1.2)
 bayesplot        1.9.0    2022-03-10 [1] CRAN (R 4.1.2)
 bridgesampling   1.1-2    2021-04-16 [1] CRAN (R 4.1.2)
 brms           * 2.17.0   2022-04-13 [1] CRAN (R 4.1.2)
 Brobdingnag      1.2-7    2022-02-03 [1] CRAN (R 4.1.2)
 broom            1.0.0    2022-07-01 [1] CRAN (R 4.1.2)
 callr            3.7.0    2021-04-20 [1] CRAN (R 4.1.2)
 cellranger       1.1.0    2016-07-27 [1] CRAN (R 4.1.2)
 checkmate        2.1.0    2022-04-21 [1] CRAN (R 4.1.2)
 cli              3.4.1    2022-09-23 [1] CRAN (R 4.1.2)
 cmdstanr       * 0.5.2    2022-07-11 [1] local
 coda             0.19-4   2020-09-30 [1] CRAN (R 4.1.2)
 codetools        0.2-18   2020-11-04 [4] CRAN (R 4.0.3)
 colorspace       2.0-3    2022-02-21 [1] CRAN (R 4.1.2)
 colourpicker     1.1.1    2021-10-04 [1] CRAN (R 4.1.2)
 crayon           1.5.1    2022-03-26 [1] CRAN (R 4.1.2)
 crosstalk        1.2.0    2021-11-04 [1] CRAN (R 4.1.2)
 DBI              1.1.3    2022-06-18 [1] CRAN (R 4.1.2)
 dbplyr           2.2.1    2022-06-27 [1] CRAN (R 4.1.2)
 digest           0.6.29   2021-12-01 [1] CRAN (R 4.1.2)
 distributional   0.3.0    2022-01-05 [1] CRAN (R 4.1.2)
 dplyr          * 1.0.9    2022-04-28 [1] CRAN (R 4.1.2)
 DT               0.23     2022-05-10 [1] CRAN (R 4.1.2)
 dygraphs         1.1.1.6  2018-07-11 [1] CRAN (R 4.1.2)
 ellipsis         0.3.2    2021-04-29 [1] CRAN (R 4.1.2)
 fansi            1.0.3    2022-03-24 [1] CRAN (R 4.1.2)
 farver           2.1.1    2022-07-06 [1] CRAN (R 4.1.2)
 fastmap          1.1.0    2021-01-25 [1] CRAN (R 4.1.2)
 forcats        * 0.5.1    2021-01-27 [1] CRAN (R 4.1.2)
 fs               1.5.2    2021-12-08 [1] CRAN (R 4.1.2)
 generics         0.1.3    2022-07-05 [1] CRAN (R 4.1.2)
 ggplot2        * 3.3.6    2022-05-03 [1] CRAN (R 4.1.2)
 ggridges         0.5.3    2021-01-08 [1] CRAN (R 4.1.2)
 glue             1.6.2    2022-02-24 [1] CRAN (R 4.1.2)
 gridExtra        2.3      2017-09-09 [1] CRAN (R 4.1.2)
 gtable           0.3.0    2019-03-25 [1] CRAN (R 4.1.2)
 gtools           3.9.2.2  2022-06-13 [1] CRAN (R 4.1.2)
 haven            2.5.0    2022-04-15 [1] CRAN (R 4.1.2)
 hms              1.1.1    2021-09-26 [1] CRAN (R 4.1.2)
 htmltools        0.5.2    2021-08-25 [1] CRAN (R 4.1.2)
 htmlwidgets      1.5.4    2021-09-08 [1] CRAN (R 4.1.2)
 httpuv           1.6.5    2022-01-05 [1] CRAN (R 4.1.2)
 httr             1.4.3    2022-05-04 [1] CRAN (R 4.1.2)
 igraph           1.3.2    2022-06-13 [1] CRAN (R 4.1.2)
 inline           0.3.19   2021-05-31 [1] CRAN (R 4.1.2)
 jsonlite         1.8.0    2022-02-22 [1] CRAN (R 4.1.2)
 knitr            1.39     2022-04-26 [1] CRAN (R 4.1.2)
 later            1.3.0    2021-08-18 [1] CRAN (R 4.1.2)
 lattice          0.20-45  2021-09-22 [4] CRAN (R 4.1.1)
 lifecycle        1.0.1    2021-09-24 [1] CRAN (R 4.1.2)
 loo              2.5.1    2022-03-24 [1] CRAN (R 4.1.2)
 lubridate        1.8.0    2021-10-07 [1] CRAN (R 4.1.2)
 magrittr         2.0.3    2022-03-30 [1] CRAN (R 4.1.2)
 markdown         1.1      2019-08-07 [1] CRAN (R 4.1.2)
 Matrix           1.4-0    2021-12-08 [4] CRAN (R 4.1.2)
 matrixStats      0.62.0   2022-04-19 [1] CRAN (R 4.1.2)
 mime             0.12     2021-09-28 [1] CRAN (R 4.1.2)
 miniUI           0.1.1.1  2018-05-18 [1] CRAN (R 4.1.2)
 modelr           0.1.8    2020-05-19 [1] CRAN (R 4.1.2)
 munsell          0.5.0    2018-06-12 [1] CRAN (R 4.1.2)
 mvtnorm          1.1-3    2021-10-08 [1] CRAN (R 4.1.2)
 nlme             3.1-155  2022-01-13 [4] CRAN (R 4.1.2)
 pillar           1.7.0    2022-02-01 [1] CRAN (R 4.1.2)
 pkgbuild         1.3.1    2021-12-20 [1] CRAN (R 4.1.2)
 pkgconfig        2.0.3    2019-09-22 [1] CRAN (R 4.1.2)
 plyr             1.8.7    2022-03-24 [1] CRAN (R 4.1.2)
 posterior        1.2.2    2022-06-09 [1] CRAN (R 4.1.2)
 prettyunits      1.1.1    2020-01-24 [1] CRAN (R 4.1.2)
 processx         3.7.0    2022-07-07 [1] CRAN (R 4.1.2)
 promises         1.2.0.1  2021-02-11 [1] CRAN (R 4.1.2)
 ps               1.7.1    2022-06-18 [1] CRAN (R 4.1.2)
 purrr          * 0.3.4    2020-04-17 [1] CRAN (R 4.1.2)
 R6               2.5.1    2021-08-19 [1] CRAN (R 4.1.2)
 Rcpp           * 1.0.9    2022-07-08 [1] CRAN (R 4.1.2)
 RcppParallel     5.1.5    2022-01-05 [1] CRAN (R 4.1.2)
 readr          * 2.1.2    2022-01-30 [1] CRAN (R 4.1.2)
 readxl           1.4.0    2022-03-28 [1] CRAN (R 4.1.2)
 reprex           2.0.1    2021-08-05 [1] CRAN (R 4.1.2)
 reshape2         1.4.4    2020-04-09 [1] CRAN (R 4.1.2)
 rlang            1.0.6    2022-09-24 [1] CRAN (R 4.1.2)
 rstan            2.21.5   2022-04-11 [1] CRAN (R 4.1.2)
 rstantools       2.2.0    2022-04-08 [1] CRAN (R 4.1.2)
 rstudioapi       0.13     2020-11-12 [1] CRAN (R 4.1.2)
 rvest            1.0.2    2021-10-16 [1] CRAN (R 4.1.2)
 scales           1.2.0    2022-04-13 [1] CRAN (R 4.1.2)
 sessioninfo      1.2.2    2021-12-06 [1] CRAN (R 4.1.2)
 shiny            1.7.1    2021-10-02 [1] CRAN (R 4.1.2)
 shinyjs          2.1.0    2021-12-23 [1] CRAN (R 4.1.2)
 shinystan        2.6.0    2022-03-03 [1] CRAN (R 4.1.2)
 shinythemes      1.2.0    2021-01-25 [1] CRAN (R 4.1.2)
 StanHeaders      2.21.0-7 2020-12-17 [1] CRAN (R 4.1.2)
 stringi          1.7.8    2022-07-11 [1] CRAN (R 4.1.2)
 stringr        * 1.4.0    2019-02-10 [1] CRAN (R 4.1.2)
 tensorA          0.36.2   2020-11-19 [1] CRAN (R 4.1.2)
 threejs          0.3.3    2020-01-21 [1] CRAN (R 4.1.2)
 tibble         * 3.1.7    2022-05-03 [1] CRAN (R 4.1.2)
 tidyr          * 1.2.0    2022-02-01 [1] CRAN (R 4.1.2)
 tidyselect       1.1.2    2022-02-21 [1] CRAN (R 4.1.2)
 tidyverse      * 1.3.1    2021-04-15 [1] CRAN (R 4.1.2)
 tzdb             0.3.0    2022-03-28 [1] CRAN (R 4.1.2)
 utf8             1.2.2    2021-07-24 [1] CRAN (R 4.1.2)
 vctrs            0.4.1    2022-04-13 [1] CRAN (R 4.1.2)
 withr            2.5.0    2022-03-03 [1] CRAN (R 4.1.2)
 xfun             0.31     2022-05-10 [1] CRAN (R 4.1.2)
 xml2             1.3.3    2021-11-30 [1] CRAN (R 4.1.2)
 xtable           1.8-4    2019-04-21 [1] CRAN (R 4.1.2)
 xts              0.12.1   2020-09-09 [1] CRAN (R 4.1.2)
 zoo              1.8-10   2022-04-15 [1] CRAN (R 4.1.2)
Software versions for analysing mixture model The analysis of the mixture model was last rendered with the following versions 
─ Session info ─────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23 ucrt)
 os       Windows 10 x64 (build 19044)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  German_Austria.utf8
 ctype    German_Austria.utf8
 tz       Europe/Berlin
 date     2022-10-13
 rstudio  2022.07.1+554 Spotted Wakerobin (desktop)
 pandoc   2.11.0.2 @ C:\\Users\\tklebel\\AppData\\Local\\Pandoc\\pandoc.exe

─ Packages ─────────────────────────────────────────────────────────────────────
 ! package         * version  date (UTC) lib source
   abind             1.4-5    2016-07-21 [1] CRAN (R 4.2.0)
   arrayhelpers      1.1-0    2020-02-04 [1] CRAN (R 4.2.1)
   assertthat        0.2.1    2019-03-21 [1] CRAN (R 4.2.1)
   backports         1.4.1    2021-12-13 [1] CRAN (R 4.2.0)
   base64enc         0.1-3    2015-07-28 [1] CRAN (R 4.2.0)
   bayesplot       * 1.9.0    2022-03-10 [1] CRAN (R 4.2.1)
   bridgesampling    1.1-2    2021-04-16 [1] CRAN (R 4.2.1)
   brms            * 2.18.0   2022-09-19 [1] CRAN (R 4.2.1)
   Brobdingnag       1.2-7    2022-02-03 [1] CRAN (R 4.2.1)
   broom             1.0.1    2022-08-29 [1] CRAN (R 4.2.1)
   callr             3.7.2    2022-08-22 [1] CRAN (R 4.2.1)
   cellranger        1.1.0    2016-07-27 [1] CRAN (R 4.2.1)
   checkmate         2.1.0    2022-04-21 [1] CRAN (R 4.2.1)
   cli               3.4.0    2022-09-08 [1] CRAN (R 4.2.1)
   coda              0.19-4   2020-09-30 [1] CRAN (R 4.2.1)
   codetools         0.2-18   2020-11-04 [2] CRAN (R 4.2.1)
   colorspace      * 2.0-3    2022-02-21 [1] CRAN (R 4.2.1)
   colourpicker      1.1.1    2021-10-04 [1] CRAN (R 4.2.1)
   crayon            1.5.1    2022-03-26 [1] CRAN (R 4.2.1)
   crosstalk         1.2.0    2021-11-04 [1] CRAN (R 4.2.1)
   data.table        1.14.2   2021-09-27 [1] CRAN (R 4.2.1)
   DBI               1.1.3    2022-06-18 [1] CRAN (R 4.2.1)
   dbplyr            2.2.1    2022-06-27 [1] CRAN (R 4.2.1)
   digest            0.6.29   2021-12-01 [1] CRAN (R 4.2.1)
   distributional    0.3.1    2022-09-02 [1] CRAN (R 4.2.1)
   dplyr           * 1.0.10   2022-09-01 [1] CRAN (R 4.2.1)
   DT                0.25     2022-09-12 [1] CRAN (R 4.2.1)
   dygraphs          1.1.1.6  2018-07-11 [1] CRAN (R 4.2.1)
   ellipsis          0.3.2    2021-04-29 [1] CRAN (R 4.2.1)
   extrafont         0.18     2022-04-12 [1] CRAN (R 4.2.0)
   extrafontdb       1.0      2012-06-11 [1] CRAN (R 4.2.0)
   fansi             1.0.3    2022-03-24 [1] CRAN (R 4.2.1)
   farver            2.1.1    2022-07-06 [1] CRAN (R 4.2.1)
   fastmap           1.1.0    2021-01-25 [1] CRAN (R 4.2.1)
   forcats         * 0.5.2    2022-08-19 [1] CRAN (R 4.2.1)
   fs                1.5.2    2021-12-08 [1] CRAN (R 4.2.1)
   gargle            1.2.1    2022-09-08 [1] CRAN (R 4.2.1)
   generics          0.1.3    2022-07-05 [1] CRAN (R 4.2.1)
   ggdist            3.2.0    2022-07-19 [1] CRAN (R 4.2.1)
   ggplot2         * 3.3.6    2022-05-03 [1] CRAN (R 4.2.1)
   ggrepel           0.9.1    2021-01-15 [1] CRAN (R 4.2.1)
   ggridges          0.5.4    2022-09-26 [1] CRAN (R 4.2.1)
   glue              1.6.2    2022-02-24 [1] CRAN (R 4.2.1)
   googledrive       2.0.0    2021-07-08 [1] CRAN (R 4.2.1)
   googlesheets4     1.0.1    2022-08-13 [1] CRAN (R 4.2.1)
   gridExtra         2.3      2017-09-09 [1] CRAN (R 4.2.1)
   gtable            0.3.1    2022-09-01 [1] CRAN (R 4.2.1)
   gtools            3.9.3    2022-07-11 [1] CRAN (R 4.2.1)
   haven             2.5.1    2022-08-22 [1] CRAN (R 4.2.1)
   here              1.0.1    2020-12-13 [1] CRAN (R 4.2.1)
   hms               1.1.2    2022-08-19 [1] CRAN (R 4.2.1)
   htmltools         0.5.3    2022-07-18 [1] CRAN (R 4.2.1)
   htmlwidgets       1.5.4    2021-09-08 [1] CRAN (R 4.2.1)
   httpuv            1.6.6    2022-09-08 [1] CRAN (R 4.2.1)
   httr              1.4.4    2022-08-17 [1] CRAN (R 4.2.1)
   igraph            1.3.4    2022-07-19 [1] CRAN (R 4.2.1)
   inline            0.3.19   2021-05-31 [1] CRAN (R 4.2.1)
   jsonlite          1.8.0    2022-02-22 [1] CRAN (R 4.2.1)
   knitr             1.40     2022-08-24 [1] CRAN (R 4.2.1)
   later             1.3.0    2021-08-18 [1] CRAN (R 4.2.1)
   lattice           0.20-45  2021-09-22 [2] CRAN (R 4.2.1)
   lazyeval          0.2.2    2019-03-15 [1] CRAN (R 4.2.1)
   lifecycle         1.0.2    2022-09-09 [1] CRAN (R 4.2.1)
   loo               2.5.1    2022-03-24 [1] CRAN (R 4.2.1)
   lubridate         1.8.0    2021-10-07 [1] CRAN (R 4.2.1)
   magrittr          2.0.3    2022-03-30 [1] CRAN (R 4.2.1)
   marginaleffects * 0.7.1    2022-09-25 [1] CRAN (R 4.2.1)
   markdown          1.1      2019-08-07 [1] CRAN (R 4.2.1)
   Matrix            1.4-1    2022-03-23 [2] CRAN (R 4.2.1)
   matrixStats       0.62.0   2022-04-19 [1] CRAN (R 4.2.1)
   MetBrewer       * 0.2.0    2022-03-21 [1] CRAN (R 4.2.1)
   mime              0.12     2021-09-28 [1] CRAN (R 4.2.0)
   miniUI            0.1.1.1  2018-05-18 [1] CRAN (R 4.2.1)
   modelr          * 0.1.9    2022-08-19 [1] CRAN (R 4.2.1)
   munsell           0.5.0    2018-06-12 [1] CRAN (R 4.2.1)
   mvtnorm           1.1-3    2021-10-08 [1] CRAN (R 4.2.0)
   nlme              3.1-157  2022-03-25 [2] CRAN (R 4.2.1)
   pillar            1.8.1    2022-08-19 [1] CRAN (R 4.2.1)
   pkgbuild          1.3.1    2021-12-20 [1] CRAN (R 4.2.1)
   pkgconfig         2.0.3    2019-09-22 [1] CRAN (R 4.2.1)
   plotly            4.10.0   2021-10-09 [1] CRAN (R 4.2.1)
   plyr              1.8.7    2022-03-24 [1] CRAN (R 4.2.1)
   posterior         1.3.1    2022-09-06 [1] CRAN (R 4.2.1)
   prettyunits       1.1.1    2020-01-24 [1] CRAN (R 4.2.1)
   processx          3.7.0    2022-07-07 [1] CRAN (R 4.2.1)
   promises          1.2.0.1  2021-02-11 [1] CRAN (R 4.2.1)
   prompt            1.0.1    2021-03-12 [1] CRAN (R 4.2.1)
   ps                1.7.1    2022-06-18 [1] CRAN (R 4.2.1)
   purrr           * 0.3.4    2020-04-17 [1] CRAN (R 4.2.1)
   R6                2.5.1    2021-08-19 [1] CRAN (R 4.2.1)
   Rcpp            * 1.0.9    2022-07-08 [1] CRAN (R 4.2.1)
 D RcppParallel      5.1.5    2022-01-05 [1] CRAN (R 4.2.1)
   readr           * 2.1.2    2022-01-30 [1] CRAN (R 4.2.1)
   readxl            1.4.1    2022-08-17 [1] CRAN (R 4.2.1)
   reprex            2.0.2    2022-08-17 [1] CRAN (R 4.2.1)
   reshape2          1.4.4    2020-04-09 [1] CRAN (R 4.2.1)
   rlang             1.0.5    2022-08-31 [1] CRAN (R 4.2.1)
   rprojroot         2.0.3    2022-04-02 [1] CRAN (R 4.2.1)
   rstan             2.21.7   2022-09-08 [1] CRAN (R 4.2.1)
   rstantools        2.2.0    2022-04-08 [1] CRAN (R 4.2.1)
   rstudioapi        0.14     2022-08-22 [1] CRAN (R 4.2.1)
   Rttf2pt1          1.3.8    2020-01-10 [1] CRAN (R 4.2.1)
   rvest             1.0.3    2022-08-19 [1] CRAN (R 4.2.1)
   scales          * 1.2.1    2022-08-20 [1] CRAN (R 4.2.1)
   sessioninfo       1.2.2    2021-12-06 [1] CRAN (R 4.2.1)
   shiny             1.7.2    2022-07-19 [1] CRAN (R 4.2.1)
   shinyjs           2.1.0    2021-12-23 [1] CRAN (R 4.2.1)
   shinystan         2.6.0    2022-03-03 [1] CRAN (R 4.2.1)
   shinythemes       1.2.0    2021-01-25 [1] CRAN (R 4.2.1)
   StanHeaders       2.21.0-7 2020-12-17 [1] CRAN (R 4.2.1)
   stringi           1.7.8    2022-07-11 [1] CRAN (R 4.2.1)
   stringr         * 1.4.1    2022-08-20 [1] CRAN (R 4.2.1)
   svUnit            1.0.6    2021-04-19 [1] CRAN (R 4.2.1)
   tensorA           0.36.2   2020-11-19 [1] CRAN (R 4.2.0)
   threejs           0.3.3    2020-01-21 [1] CRAN (R 4.2.1)
   tibble          * 3.1.8    2022-07-22 [1] CRAN (R 4.2.1)
   tidybayes       * 3.0.2    2022-01-05 [1] CRAN (R 4.2.1)
   tidyr           * 1.2.1    2022-09-08 [1] CRAN (R 4.2.1)
   tidyselect        1.1.2    2022-02-21 [1] CRAN (R 4.2.1)
   tidyverse       * 1.3.2    2022-07-18 [1] CRAN (R 4.2.1)
   tzdb              0.3.0    2022-03-28 [1] CRAN (R 4.2.1)
   utf8              1.2.2    2021-07-24 [1] CRAN (R 4.2.1)
   vctrs             0.4.1    2022-04-13 [1] CRAN (R 4.2.1)
   viridisLite       0.4.1    2022-08-22 [1] CRAN (R 4.2.1)
   WDI             * 2.7.8    2022-09-25 [1] CRAN (R 4.2.1)
   withr             2.5.0    2022-03-03 [1] CRAN (R 4.2.1)
   xfun              0.33     2022-09-12 [1] CRAN (R 4.2.1)
   xml2              1.3.3    2021-11-30 [1] CRAN (R 4.2.1)
   xtable            1.8-4    2019-04-21 [1] CRAN (R 4.2.1)
   xts               0.12.1   2020-09-09 [1] CRAN (R 4.2.1)
   zoo               1.8-11   2022-09-17 [1] CRAN (R 4.2.1)

 D ── DLL MD5 mismatch, broken installation.

Licenses

All code and data in this repository is made available under the CC-BY-SA 4.0 license.

The initial data sources had the following licenses: