Meaningfully reducing consumption of meat and animal products is an unsolved problem: results from a meta-analysis

Main code files:

• MAP-reduction-meta.Rmd is the paper
• supplement-MAP-reduction.Rmd is the Supplement
• ./scripts/*.R is where most of the R code lives, e.g. for tables and figures. ¹
• ./functions/*.R are mostly adapted/lifted from a previous project, along with some new things for making tables.

Data

• ./data/vegan-meta.csv is our dataset of studies
• ./data/RPMC-data.csv is a supplementary dataset of studies aimed at reducing consumption of red and processed meat
• ./data/excluded-studies.csv is our list of studies we looked at but didn't include & why
• ./data/review-of-reviews.csv is a list of prior reviews we looked at to find studies

Everything else

• project setup, license, .bib, .gitignore, etc.
• supplementary-analyses/* are some scripts we used to to analyze original datasets where that was helpful for calculating an effect size.

To reproduce the paper locally

(Assuming you use Rstudio)

1. Download this repo (git clone https://github.com/hsflabstanford/vegan-meta.git)
2. Open vegan-meta.Rproj (all paths are set relative to its directory)
3. Make sure everything in ./scripts/libraries.R is installed
4. Either run run.sh or knit the .Rmd files

SessionInfo

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       macOS 15.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2024-11-15
 rstudio  2024.09.1+394 Cranberry Hibiscus (desktop)
 pandoc   3.5 @ /opt/homebrew/bin/ (via rmarkdown)

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package         * version    date (UTC) lib source
 cli               3.6.3      2024-06-21 [1] CRAN (R 4.4.0)
 colorspace        2.1-1      2024-07-26 [1] CRAN (R 4.4.0)
 digest            0.6.37     2024-08-19 [1] CRAN (R 4.4.1)
 dplyr           * 1.1.4      2023-11-17 [1] CRAN (R 4.4.0)
 evaluate          1.0.1      2024-10-10 [1] CRAN (R 4.4.1)
 fansi             1.0.6      2023-12-08 [1] CRAN (R 4.4.0)
 fastmap           1.2.0      2024-05-15 [1] CRAN (R 4.4.0)
 forcats         * 1.0.0      2023-01-29 [1] CRAN (R 4.4.0)
 generics          0.1.3      2022-07-05 [1] CRAN (R 4.4.0)
 ggplot2         * 3.5.1      2024-04-23 [1] CRAN (R 4.4.0)
 ggtext          * 0.1.2      2022-09-16 [1] CRAN (R 4.4.0)
 glue              1.8.0      2024-09-30 [1] CRAN (R 4.4.1)
 gridtext          0.1.5      2022-09-16 [1] CRAN (R 4.4.0)
 gtable            0.3.5      2024-04-22 [1] CRAN (R 4.4.0)
 htmltools         0.5.8.1    2024-04-04 [1] CRAN (R 4.4.0)
 kableExtra      * 1.4.0      2024-01-24 [1] CRAN (R 4.4.0)
 knitr             1.48       2024-07-07 [1] CRAN (R 4.4.0)
 lattice           0.22-6     2024-03-20 [1] CRAN (R 4.4.1)
 lifecycle         1.0.4      2023-11-07 [1] CRAN (R 4.4.0)
 magrittr          2.0.3      2022-03-30 [1] CRAN (R 4.4.0)
 mathjaxr          1.6-0      2022-02-28 [1] CRAN (R 4.4.0)
 Matrix          * 1.7-0      2024-04-26 [1] CRAN (R 4.4.1)
 metadat         * 1.2-0      2022-04-06 [1] CRAN (R 4.4.0)
 metafor         * 4.6-0      2024-03-28 [1] CRAN (R 4.4.0)
 MetaUtility     * 2.1.2      2021-10-30 [1] CRAN (R 4.4.0)
 munsell           0.5.1      2024-04-01 [1] CRAN (R 4.4.0)
 nlme              3.1-164    2023-11-27 [1] CRAN (R 4.4.1)
 numDeriv        * 2016.8-1.1 2019-06-06 [1] CRAN (R 4.4.0)
 pillar            1.9.0      2023-03-22 [1] CRAN (R 4.4.0)
 pkgconfig         2.0.3      2019-09-22 [1] CRAN (R 4.4.0)
 PublicationBias * 2.4.0      2024-10-22 [1] Github (mathurlabstanford/PublicationBias@748b33e)
 purrr           * 1.0.2      2023-08-10 [1] CRAN (R 4.4.0)
 R6                2.5.1      2021-08-19 [1] CRAN (R 4.4.0)
 rbibutils         2.3        2024-10-04 [1] CRAN (R 4.4.1)
 Rcpp              1.0.13     2024-07-17 [1] CRAN (R 4.4.0)
 Rdpack            2.6.1      2024-08-06 [1] CRAN (R 4.4.0)
 rlang             1.1.4      2024-06-04 [1] CRAN (R 4.4.0)
 rmarkdown         2.28       2024-08-17 [1] CRAN (R 4.4.0)
 robumeta        * 2.1        2023-03-28 [1] CRAN (R 4.4.0)
 rstudioapi        0.17.1     2024-10-22 [1] CRAN (R 4.4.1)
 rticles         * 0.27       2024-04-06 [1] CRAN (R 4.4.0)
 scales          * 1.3.0      2023-11-28 [1] CRAN (R 4.4.0)
 sessioninfo       1.2.2      2021-12-06 [1] CRAN (R 4.4.0)
 stringi           1.8.4      2024-05-06 [1] CRAN (R 4.4.0)
 stringr         * 1.5.1      2023-11-14 [1] CRAN (R 4.4.0)
 svglite           2.1.3      2023-12-08 [1] CRAN (R 4.4.0)
 systemfonts       1.1.0      2024-05-15 [1] CRAN (R 4.4.0)
 tibble            3.2.1      2023-03-20 [1] CRAN (R 4.4.0)
 tidyr           * 1.3.1      2024-01-24 [1] CRAN (R 4.4.0)
 tidyselect        1.2.1      2024-03-11 [1] CRAN (R 4.4.0)
 utf8              1.2.4      2023-10-22 [1] CRAN (R 4.4.0)
 vctrs             0.6.5      2023-12-01 [1] CRAN (R 4.4.0)
 viridisLite       0.4.2      2023-05-02 [1] CRAN (R 4.4.0)
 withr             3.0.1      2024-07-31 [1] CRAN (R 4.4.0)
 xfun              0.48       2024-10-03 [1] CRAN (R 4.4.1)
 xml2              1.3.6      2023-12-04 [1] CRAN (R 4.4.0)

Footnotes

1. The scripts are intended to be self-contained, loading all necessary libraries, functions, and data. This causes some repetitiveness when knitting the document, but it ensures that future replicators can create specific tables or figures without needing to sift through the .Rmd files to determine dependencies loaded earlier. ↩