Code
library(tidyverse)Computing environment
Platform
Here are the details of the R environment we used when running this analysis:
Code
# Injecting Stan info into the platform info adapted from TJ Mahr:
# https://github.com/tjmahr/tjmahr.github.io/commit/b8be089
session_info <- sessioninfo::session_info()
session_info$platform$`quarto` <- as.character(quarto::quarto_version())
session_info$platform$`stan (cmdstanr)` <- cmdstanr::cmdstan_version()
session_info$platform setting value
version R version 4.4.0 (2024-04-24)
os macOS Sonoma 14.5
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2024-07-16
pandoc 3.1.12.3 @ /Applications/Positron.app/Contents/Resources/app/bin/pandoc/ (via rmarkdown)
quarto 1.6.1
stan (cmdstanr) 2.34.1Packages
We use the {renv} package to create a stable version-specific library of packages. The official list of packages is included in renv.lock and running this from the root of this project should install everything:
renv::restore()Here’s the full list of packages in a less JSON-y format:
Code
packages_raw <- jsonlite::read_json(here::here("renv.lock"))$Packages |>
enframe()
packages_in_project <- sessioninfo::package_info(packages_raw$name) |>
as_tibble()
packages_in_project |>
select(package, ondiskversion, date, source) |>
print(n = Inf)# A tibble: 227 × 4
package ondiskversion date source
<chr> <chr> <chr> <chr>
1 abind 1.4-5 2016-07-21 CRAN (R 4.4.0)
2 anytime 0.3.9 2020-08-27 CRAN (R 4.4.0)
3 arrayhelpers 1.1-0 2020-02-04 CRAN (R 4.4.0)
4 askpass 1.2.0 2023-09-03 CRAN (R 4.4.0)
5 backports 1.5.0 2024-05-23 CRAN (R 4.4.0)
6 base64enc 0.1-3 2015-07-28 CRAN (R 4.4.0)
7 base64url 1.4 2018-05-14 CRAN (R 4.4.0)
8 bayesplot 1.11.1 2024-02-15 CRAN (R 4.4.0)
9 bayestestR 0.13.2 2024-02-12 CRAN (R 4.4.0)
10 BH 1.84.0-0 2024-01-10 CRAN (R 4.4.0)
11 bigD 0.2.0 2022-09-05 CRAN (R 4.4.0)
12 bit 4.0.5 2022-11-15 CRAN (R 4.4.0)
13 bit64 4.0.5 2020-08-30 CRAN (R 4.4.0)
14 bitops 1.0-7 2021-04-24 CRAN (R 4.4.0)
15 blob 1.2.4 2023-03-17 CRAN (R 4.4.0)
16 bridgesampling 1.1-2 2021-04-16 CRAN (R 4.4.0)
17 brms 2.21.0 2024-03-20 CRAN (R 4.4.0)
18 Brobdingnag 1.2-9 2022-10-19 CRAN (R 4.4.0)
19 broom 1.0.6 2024-05-17 CRAN (R 4.4.0)
20 bs4Dash 2.3.3 2024-01-23 CRAN (R 4.4.0)
21 bslib 0.7.0 2024-03-29 CRAN (R 4.4.0)
22 cachem 1.1.0 2024-05-16 CRAN (R 4.4.0)
23 callr 3.7.6 2024-03-25 CRAN (R 4.4.0)
24 cellranger 1.1.0 2016-07-27 CRAN (R 4.4.0)
25 checkmate 2.3.1 2023-12-04 CRAN (R 4.4.0)
26 class 7.3-22 2023-05-03 CRAN (R 4.4.0)
27 classInt 0.4-10 2023-09-05 CRAN (R 4.4.0)
28 cli 3.6.2 2023-12-11 CRAN (R 4.4.0)
29 clipr 0.8.0 2022-02-22 CRAN (R 4.4.0)
30 cmdstanr 0.8.1 2024-07-06 https://stan-dev.r-universe.dev (R…
31 coda 0.19-4.1 2024-01-31 CRAN (R 4.4.0)
32 codetools 0.2-20 2024-03-31 CRAN (R 4.4.0)
33 collapse 2.0.15 2024-07-08 CRAN (R 4.4.0)
34 colorspace 2.1-0 2023-01-23 CRAN (R 4.4.0)
35 commonmark 1.9.1 2024-01-30 CRAN (R 4.4.0)
36 conflicted 1.2.0 2023-02-01 CRAN (R 4.4.0)
37 countrycode 1.6.0 2024-03-22 CRAN (R 4.4.0)
38 cpp11 0.4.7 2023-12-02 CRAN (R 4.4.0)
39 crayon 1.5.2 2022-09-29 CRAN (R 4.4.0)
40 crew 0.9.5 2024-06-24 CRAN (R 4.4.0)
41 curl 5.2.1 2024-03-01 CRAN (R 4.4.0)
42 data.table 1.15.4 2024-03-30 CRAN (R 4.4.0)
43 datawizard 0.10.0 2024-03-26 CRAN (R 4.4.0)
44 DBI 1.2.2 2024-02-16 CRAN (R 4.4.0)
45 dbplyr 2.5.0 2024-03-19 CRAN (R 4.4.0)
46 desc 1.4.3 2023-12-10 CRAN (R 4.4.0)
47 digest 0.6.35 2024-03-11 CRAN (R 4.4.0)
48 distributional 0.4.0 2024-02-07 CRAN (R 4.4.0)
49 dplyr 1.1.4 2023-11-17 CRAN (R 4.4.0)
50 dtplyr 1.3.1 2023-03-22 CRAN (R 4.4.0)
51 e1071 1.7-14 2023-12-06 CRAN (R 4.4.0)
52 emoji 15.0 2022-11-03 CRAN (R 4.4.0)
53 evaluate 0.23 2023-11-01 CRAN (R 4.4.0)
54 extraDistr 1.10.0 2023-11-30 CRAN (R 4.4.0)
55 fansi 1.0.6 2023-12-08 CRAN (R 4.4.0)
56 farver 2.1.2 2024-05-13 CRAN (R 4.4.0)
57 fastmap 1.2.0 2024-05-15 CRAN (R 4.4.0)
58 fontawesome 0.5.2 2023-08-19 CRAN (R 4.4.0)
59 forcats 1.0.0 2023-01-29 CRAN (R 4.4.0)
60 fresh 0.2.1 2024-06-26 CRAN (R 4.4.0)
61 fs 1.6.4 2024-04-25 CRAN (R 4.4.0)
62 future 1.33.2 2024-03-26 CRAN (R 4.4.0)
63 future.apply 1.11.2 2024-03-28 CRAN (R 4.4.0)
64 gargle 1.5.2 2023-07-20 CRAN (R 4.4.0)
65 generics 0.1.3 2022-07-05 CRAN (R 4.4.0)
66 getip 0.1-4 2023-12-10 CRAN (R 4.4.0)
67 ggdist 3.3.2 2024-03-05 CRAN (R 4.4.0)
68 ggh4x 0.2.8 2024-01-23 CRAN (R 4.4.0)
69 ggplot2 3.5.1 2024-04-23 CRAN (R 4.4.0)
70 ggridges 0.5.6 2024-01-23 CRAN (R 4.4.0)
71 ggtext 0.1.2 2022-09-16 CRAN (R 4.4.0)
72 globals 0.16.3 2024-03-08 CRAN (R 4.4.0)
73 glue 1.7.0 2024-01-09 CRAN (R 4.4.0)
74 googledrive 2.1.1 2023-06-11 CRAN (R 4.4.0)
75 googlesheets4 1.1.1 2023-06-11 CRAN (R 4.4.0)
76 gridExtra 2.3 2017-09-09 CRAN (R 4.4.0)
77 gridtext 0.1.5 2022-09-16 CRAN (R 4.4.0)
78 gt 0.10.1 2024-01-17 CRAN (R 4.4.0)
79 gtable 0.3.5 2024-04-22 CRAN (R 4.4.0)
80 haven 2.5.4 2023-11-30 CRAN (R 4.4.0)
81 here 1.0.1 2020-12-13 CRAN (R 4.4.0)
82 highr 0.10 2022-12-22 CRAN (R 4.4.0)
83 hms 1.1.3 2023-03-21 CRAN (R 4.4.0)
84 htmltools 0.5.8.1 2024-04-04 CRAN (R 4.4.0)
85 htmlwidgets 1.6.4 2023-12-06 CRAN (R 4.4.0)
86 httpuv 1.6.15 2024-03-26 CRAN (R 4.4.0)
87 httr 1.4.7 2023-08-15 CRAN (R 4.4.0)
88 ids 1.0.1 2017-05-31 CRAN (R 4.4.0)
89 igraph 2.0.3 2024-03-13 CRAN (R 4.4.0)
90 inline 0.3.19 2021-05-31 CRAN (R 4.4.0)
91 insight 0.19.11 2024-05-12 CRAN (R 4.4.0)
92 isoband 0.2.7 2022-12-20 CRAN (R 4.4.0)
93 janitor 2.2.0 2023-02-02 CRAN (R 4.4.0)
94 jpeg 0.1-10 2022-11-29 CRAN (R 4.4.0)
95 jquerylib 0.1.4 2021-04-26 CRAN (R 4.4.0)
96 jsonlite 1.8.8 2023-12-04 CRAN (R 4.4.0)
97 juicyjuice 0.1.0 2022-11-10 CRAN (R 4.4.0)
98 KernSmooth 2.23-22 2023-07-10 CRAN (R 4.4.0)
99 knitr 1.46 2024-04-06 CRAN (R 4.4.0)
100 labeling 0.4.3 2023-08-29 CRAN (R 4.4.0)
101 later 1.3.2 2023-12-06 CRAN (R 4.4.0)
102 lattice 0.22-6 2024-03-20 CRAN (R 4.4.0)
103 lifecycle 1.0.4 2023-11-07 CRAN (R 4.4.0)
104 listenv 0.9.1 2024-01-29 CRAN (R 4.4.0)
105 lmtest 0.9-40 2022-03-21 CRAN (R 4.4.0)
106 loo 2.7.0 2024-02-24 CRAN (R 4.4.0)
107 lubridate 1.9.3 2023-09-27 CRAN (R 4.4.0)
108 magrittr 2.0.3 2022-03-30 CRAN (R 4.4.0)
109 marginaleffects 0.20.1 2024-05-08 CRAN (R 4.4.0)
110 markdown 1.12 2023-12-06 CRAN (R 4.4.0)
111 MASS 7.3-60.2 2024-04-26 CRAN (R 4.4.0)
112 Matrix 1.7-0 2024-03-22 CRAN (R 4.4.0)
113 matrixStats 1.3.0 2024-04-11 CRAN (R 4.4.0)
114 memoise 2.0.1 2021-11-26 CRAN (R 4.4.0)
115 MetBrewer 0.2.0 2022-03-21 CRAN (R 4.4.0)
116 mgcv 1.9-1 2023-12-21 CRAN (R 4.4.0)
117 mime 0.12 2021-09-28 CRAN (R 4.4.0)
118 mirai 1.1.1 2024-07-01 CRAN (R 4.4.0)
119 modelr 0.1.11 2023-03-22 CRAN (R 4.4.0)
120 modelsummary 2.1.0 2024-05-19 CRAN (R 4.4.0)
121 munsell 0.5.1 2024-04-01 CRAN (R 4.4.0)
122 mvtnorm 1.2-5 2024-05-21 CRAN (R 4.4.0)
123 nanonext 1.1.1 2024-06-23 CRAN (R 4.4.0)
124 nleqslv 3.3.5 2023-11-26 CRAN (R 4.4.0)
125 nlme 3.1-164 2023-11-27 CRAN (R 4.4.0)
126 numDeriv 2016.8-1.1 2019-06-06 CRAN (R 4.4.0)
127 openssl 2.2.0 2024-05-16 CRAN (R 4.4.0)
128 parallelly 1.37.1 2024-02-29 CRAN (R 4.4.0)
129 parameters 0.21.7 2024-05-14 CRAN (R 4.4.0)
130 patchwork 1.2.0 2024-01-08 CRAN (R 4.4.0)
131 performance 0.11.0 2024-03-22 CRAN (R 4.4.0)
132 pillar 1.9.0 2023-03-22 CRAN (R 4.4.0)
133 pingr 2.0.3 2023-12-10 CRAN (R 4.4.0)
134 pkgbuild 1.4.4 2024-03-17 CRAN (R 4.4.0)
135 pkgconfig 2.0.3 2019-09-22 CRAN (R 4.4.0)
136 plyr 1.8.9 2023-10-02 CRAN (R 4.4.0)
137 png 0.1-8 2022-11-29 CRAN (R 4.4.0)
138 posterior 1.5.0 2023-10-31 CRAN (R 4.4.0)
139 prettyunits 1.2.0 2023-09-24 CRAN (R 4.4.0)
140 processx 3.8.4 2024-03-16 CRAN (R 4.4.0)
141 progress 1.2.3 2023-12-06 CRAN (R 4.4.0)
142 promises 1.3.0 2024-04-05 CRAN (R 4.4.0)
143 proxy 0.4-27 2022-06-09 CRAN (R 4.4.0)
144 ps 1.7.6 2024-01-18 CRAN (R 4.4.0)
145 purrr 1.0.2 2023-08-10 CRAN (R 4.4.0)
146 qs 0.26.3 2024-05-16 CRAN (R 4.4.0)
147 quadprog 1.5-8 2019-11-20 CRAN (R 4.4.0)
148 quarto 1.4 2024-03-06 CRAN (R 4.4.0)
149 QuickJSR 1.1.3 2024-01-31 CRAN (R 4.4.0)
150 R.cache 0.16.0 2022-07-21 CRAN (R 4.4.0)
151 R.methodsS3 1.8.2 2022-06-13 CRAN (R 4.4.0)
152 R.oo 1.26.0 2024-01-24 CRAN (R 4.4.0)
153 R.utils 2.12.3 2023-11-18 CRAN (R 4.4.0)
154 R6 2.5.1 2021-08-19 CRAN (R 4.4.0)
155 ragg 1.3.2 2024-05-15 CRAN (R 4.4.0)
156 RApiSerialize 0.1.3 2024-05-14 CRAN (R 4.4.0)
157 rappdirs 0.3.3 2021-01-31 CRAN (R 4.4.0)
158 RColorBrewer 1.1-3 2022-04-03 CRAN (R 4.4.0)
159 Rcpp 1.0.12 2024-01-09 CRAN (R 4.4.0)
160 RcppEigen 0.3.4.0.0 2024-02-28 CRAN (R 4.4.0)
161 RcppParallel 5.1.7 2023-02-27 CRAN (R 4.4.0)
162 reactable 0.4.4 2023-03-12 CRAN (R 4.4.0)
163 reactR 0.5.0 2023-10-11 CRAN (R 4.4.0)
164 readr 2.1.5 2024-01-10 CRAN (R 4.4.0)
165 readxl 1.4.3 2023-07-06 CRAN (R 4.4.0)
166 rematch 2.0.0 2023-08-30 CRAN (R 4.4.0)
167 rematch2 2.1.2 2020-05-01 CRAN (R 4.4.0)
168 renv 1.0.7 2024-04-11 CRAN (R 4.4.0)
169 reprex 2.1.0 2024-01-11 CRAN (R 4.4.0)
170 reshape2 1.4.4 2020-04-09 CRAN (R 4.4.0)
171 rlang 1.1.3 2024-01-10 CRAN (R 4.4.0)
172 rmarkdown 2.27 2024-05-17 CRAN (R 4.4.0)
173 rprojroot 2.0.4 2023-11-05 CRAN (R 4.4.0)
174 rstan 2.32.6 2024-03-05 CRAN (R 4.4.0)
175 rstantools 2.4.0 2024-01-31 CRAN (R 4.4.0)
176 rstudioapi 0.16.0 2024-03-24 CRAN (R 4.4.0)
177 rvest 1.0.4 2024-02-12 CRAN (R 4.4.0)
178 s2 1.1.6 2023-12-19 CRAN (R 4.4.0)
179 sass 0.4.9 2024-03-15 CRAN (R 4.4.0)
180 scales 1.3.0 2023-11-28 CRAN (R 4.4.0)
181 secretbase 0.5.0 2024-04-25 CRAN (R 4.4.0)
182 selectr 0.4-2 2019-11-20 CRAN (R 4.4.0)
183 sessioninfo 1.2.2 2021-12-06 CRAN (R 4.4.0)
184 sf 1.0-16 2024-03-24 CRAN (R 4.4.0)
185 shiny 1.8.1.1 2024-04-02 CRAN (R 4.4.0)
186 shinybusy 0.3.3 2024-03-09 CRAN (R 4.4.0)
187 shinyWidgets 0.8.6 2024-04-24 CRAN (R 4.4.0)
188 snakecase 0.11.1 2023-08-27 CRAN (R 4.4.0)
189 sourcetools 0.1.7-1 2023-02-01 CRAN (R 4.4.0)
190 StanHeaders 2.32.9 2024-05-29 CRAN (R 4.4.0)
191 stringfish 0.16.0 2023-11-28 CRAN (R 4.4.0)
192 stringi 1.8.4 2024-05-06 CRAN (R 4.4.0)
193 stringr 1.5.1 2023-11-14 CRAN (R 4.4.0)
194 styler 1.10.3 2024-04-07 CRAN (R 4.4.0)
195 svUnit 1.0.6 2021-04-19 CRAN (R 4.4.0)
196 sys 3.4.2 2023-05-23 CRAN (R 4.4.0)
197 systemfonts 1.1.0 2024-05-15 CRAN (R 4.4.0)
198 tables 0.9.25 2024-04-13 CRAN (R 4.4.0)
199 tarchetypes 0.9.0 2024-04-17 CRAN (R 4.4.0)
200 targets 1.7.0 2024-04-17 CRAN (R 4.4.0)
201 tensorA 0.36.2.1 2023-12-13 CRAN (R 4.4.0)
202 textshaping 0.3.7 2023-10-09 CRAN (R 4.4.0)
203 tibble 3.2.1 2023-03-20 CRAN (R 4.4.0)
204 tidybayes 3.0.6 2023-08-12 CRAN (R 4.4.0)
205 tidyr 1.3.1 2024-01-24 CRAN (R 4.4.0)
206 tidyselect 1.2.1 2024-03-11 CRAN (R 4.4.0)
207 tidyverse 2.0.0 2023-02-22 CRAN (R 4.4.0)
208 timechange 0.3.0 2024-01-18 CRAN (R 4.4.0)
209 tinytable 0.3.0.30 2024-07-17 Github (vincentarelbundock/tinytab…
210 tinytex 0.51 2024-05-06 CRAN (R 4.4.0)
211 tzdb 0.4.0 2023-05-12 CRAN (R 4.4.0)
212 units 0.8-5 2023-11-28 CRAN (R 4.4.0)
213 utf8 1.2.4 2023-10-22 CRAN (R 4.4.0)
214 uuid 1.2-0 2024-01-14 CRAN (R 4.4.0)
215 V8 4.4.2 2024-02-15 CRAN (R 4.4.0)
216 vctrs 0.6.5 2023-12-01 CRAN (R 4.4.0)
217 viridisLite 0.4.2 2023-05-02 CRAN (R 4.4.0)
218 visNetwork 2.1.2 2022-09-29 CRAN (R 4.4.0)
219 vroom 1.6.5 2023-12-05 CRAN (R 4.4.0)
220 waiter 0.2.5 2022-01-03 CRAN (R 4.4.0)
221 withr 3.0.0 2024-01-16 CRAN (R 4.4.0)
222 wk 0.9.1 2023-11-29 CRAN (R 4.4.0)
223 xfun 0.44 2024-05-15 CRAN (R 4.4.0)
224 xml2 1.3.6 2023-12-04 CRAN (R 4.4.0)
225 xtable 1.8-4 2019-04-21 CRAN (R 4.4.0)
226 yaml 2.3.8 2023-12-11 CRAN (R 4.4.0)
227 zoo 1.8-12 2023-04-13 CRAN (R 4.4.0) Makevars
Because {brms} generates Stan code that is then compiled and run as binary executable programs, knowing about the compilation environment is helpful. Here are all the things that influence compiling (different paths, flags, external libraries, etc.) that are included in ~/.R/Makevars:
Code
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))# Adapted from Luis Puerto's Makevars here:
# https://gist.github.com/luispuerto/9b5fc37a117c94ebb07f1a1d93e6665e
#
# And Dirk Eddelbuettel's Makevars here:
# http://dirk.eddelbuettel.com/blog/2017/11/27/#011_faster_package_installation_one
#
# And this from Patrick Schratz:
# https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/
#
# ------------------------------------------------------------------------------
# MAKE SURE YOU SYMLINK THE M1 BLAS TO GET LIGHTNING FAST COMPUTATIONS!!!
# https://www.mail-archive.com/r-sig-mac@r-project.org/msg06199.html
# ------------------------------------------------------------------------------
#
# Homebrew bin / opt / lib locations
HB=/opt/homebrew/bin
HO=/opt/homebrew/opt
HL=/opt/homebrew/lib
HI=/opt/homebrew/include
# ## Figure out the Homebrew path
# BP=`brew --prefix`
# HB=$(BP)/bin
# HO=$(BP)/opt
# HL=$(BP)/lib
# HI=$(BP)/include
# xcode headers
XH=$(shell xcrun -show-sdk-path)
# ccache
CCACHE=$(HB)/ccache
CCACHE=
# Make using all cores (set # to # of cores on your machine)
# Check https://stackoverflow.com/q/2499070 for more info.
# Run `sysctl -n hw.logicalcpu` to check the number of threads https://stackoverflow.com/a/56607839
# As a rule of thumb the number should be between cores and threads.
MAKE=make -j4
# Version
VER=13
# LLVM (Clang) compiler options
CC=$(CCACHE) $(HO)/llvm/bin/clang
CXX=$(CC)++
CXX11=$(CC)++
CXX14=$(CC)++
CXX17=$(CC)++
# Homebrew Fortran
FC=$(CCACHE) $(HB)/gfortran
F77=$(FC)
#FLIBS=-L$(HL)/gcc/$(VER) -lgfortran -lquadmath -lm
FLIBS=-L$(HL)/gcc/$(VER) -lgfortran -lm
# STD libraries
CXX1XSTD=-std=c++0x
CXX11STD=-std=c++11
CXX14STD=-std=c++14
CXX17STD=-std=c++17
# FLAGS
STD_FLAGS=-I$(HI) -g -O3 -Wall -pedantic -mtune=native -pipe -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -Wno-unneeded-internal-declaration -Wno-unknown-pragmas -Wno-deprecated-declarations
CFLAGS=$(STD_FLAGS)
CXXFLAGS=$(STD_FLAGS)
# Preprocessor FLAGS
# NB: -isysroot refigures the include path to the Xcode SDK we set above
CPPFLAGS=-isysroot $(XH) -I$(HI) \
-I$(HO)/llvm/include -I$(HO)/openssl/include \
-I$(HO)/gettext/include -I$(HO)/tcl-tk/include
# Linker flags (suggested by homebrew)
# LDFLAGS+=-L$(HO)/llvm/lib -Wl,-rpath,$(HO)/llvm/lib
LDFLAGS+=-L$(HO)/llvm/lib/c++ -Wl,-rpath,$(HO)/llvm/lib/c++
LDFLAGS+=-L$(HO)/jpeg/lib
# Flags for OpenMP support that should allow packages that want to use
# OpenMP to do so (data.table), and other packages that bork with
# -fopenmp flag (stringi) to be left alone
SHLIB_OPENMP_CFLAGS=-fopenmp
SHLIB_OPENMP_CXXFLAGS=-fopenmp
SHLIB_OPENMP_CXX11FLAGS=-fopenmp
SHLIB_OPENMP_CXX14FLAGS=-fopenmp
SHLIB_OPENMP_FCFLAGS=-fopenmp
SHLIB_OPENMP_FFLAGS=-fopenmp