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$platform setting value
version R version 4.4.1 (2024-06-14)
os macOS 15.1.1
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2024-12-12
pandoc 3.6 @ /opt/homebrew/bin/ (via rmarkdown)
quarto 1.6.1
stan (cmdstanr) 2.36.0Packages
We use the {renv} package to create a stable version-specific library of packages. The official list of packages is included in renv.lock and running this from the root of this project should install everything:
renv::restore()Here’s the full list of packages in a less JSON-y format:
Code
packages_raw <- jsonlite::read_json(here::here("renv.lock"))$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: 230 × 4
package ondiskversion date source
<chr> <chr> <chr> <chr>
1 abind 1.4-5 2016-07-21 RSPM
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 RSPM
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 2.3.2 2024-07-29 RSPM
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 2024-08-05 https://s~
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 RSPM
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 RSPM
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 RSPM
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 foreign 0.8-86 2023-11-28 CRAN (R 4.4.0)
61 fresh 0.2.1 2024-06-26 CRAN (R 4.4.0)
62 fs 1.6.4 2024-04-25 CRAN (R 4.4.0)
63 future 1.33.2 2024-03-26 CRAN (R 4.4.0)
64 future.apply 1.11.2 2024-03-28 CRAN (R 4.4.0)
65 gargle 1.5.2 2023-07-20 CRAN (R 4.4.0)
66 generics 0.1.3 2022-07-05 RSPM
67 getip 0.1-4 2023-12-10 CRAN (R 4.4.0)
68 ggdist 3.3.2 2024-03-05 CRAN (R 4.4.0)
69 ggh4x 0.2.8 2024-01-23 CRAN (R 4.4.0)
70 ggplot2 3.5.1 2024-04-23 CRAN (R 4.4.0)
71 ggridges 0.5.6 2024-01-23 CRAN (R 4.4.0)
72 ggtext 0.1.2 2022-09-16 CRAN (R 4.4.0)
73 globals 0.16.3 2024-03-08 CRAN (R 4.4.0)
74 glue 1.7.0 2024-01-09 RSPM
75 googledrive 2.1.1 2023-06-11 CRAN (R 4.4.0)
76 googlesheets4 1.1.1 2023-06-11 CRAN (R 4.4.0)
77 gridExtra 2.3 2017-09-09 CRAN (R 4.4.0)
78 gridtext 0.1.5 2022-09-16 CRAN (R 4.4.0)
79 gt 0.10.1 2024-01-17 CRAN (R 4.4.0)
80 gtable 0.3.5 2024-04-22 CRAN (R 4.4.0)
81 haven 2.5.4 2023-11-30 CRAN (R 4.4.0)
82 here 1.0.1 2020-12-13 CRAN (R 4.4.0)
83 highr 0.10 2022-12-22 CRAN (R 4.4.0)
84 hms 1.1.3 2023-03-21 CRAN (R 4.4.0)
85 htmltools 0.5.8.1 2024-04-04 CRAN (R 4.4.0)
86 htmlwidgets 1.6.4 2023-12-06 CRAN (R 4.4.0)
87 httpuv 1.6.15 2024-03-26 CRAN (R 4.4.0)
88 httr 1.4.7 2023-08-15 CRAN (R 4.4.0)
89 ids 1.0.1 2017-05-31 CRAN (R 4.4.0)
90 igraph 2.0.3 2024-03-13 CRAN (R 4.4.0)
91 inline 0.3.19 2021-05-31 CRAN (R 4.4.0)
92 insight 0.19.11 2024-05-12 CRAN (R 4.4.0)
93 isoband 0.2.7 2022-12-20 CRAN (R 4.4.0)
94 janitor 2.2.0 2023-02-02 CRAN (R 4.4.0)
95 jpeg 0.1-10 2022-11-29 CRAN (R 4.4.0)
96 jquerylib 0.1.4 2021-04-26 CRAN (R 4.4.0)
97 jsonlite 1.8.8 2023-12-04 RSPM
98 juicyjuice 0.1.0 2022-11-10 CRAN (R 4.4.0)
99 KernSmooth 2.23-22 2023-07-10 CRAN (R 4.4.0)
100 knitr 1.46 2024-04-06 CRAN (R 4.4.0)
101 labeling 0.4.3 2023-08-29 CRAN (R 4.4.0)
102 later 1.3.2 2023-12-06 CRAN (R 4.4.0)
103 lattice 0.22-6 2024-03-20 CRAN (R 4.4.0)
104 lifecycle 1.0.4 2023-11-07 RSPM
105 listenv 0.9.1 2024-01-29 CRAN (R 4.4.0)
106 lmtest 0.9-40 2022-03-21 CRAN (R 4.4.0)
107 loo 2.7.0 2024-02-24 CRAN (R 4.4.0)
108 lubridate 1.9.3 2023-09-27 CRAN (R 4.4.0)
109 magrittr 2.0.3 2022-03-30 RSPM
110 marginaleffects 0.20.1 2024-05-08 CRAN (R 4.4.0)
111 markdown 1.12 2023-12-06 CRAN (R 4.4.0)
112 MASS 7.3-60.2 2024-04-26 CRAN (R 4.4.0)
113 Matrix 1.7-0 2024-03-22 CRAN (R 4.4.0)
114 matrixStats 1.3.0 2024-04-11 RSPM
115 memoise 2.0.1 2021-11-26 CRAN (R 4.4.0)
116 MetBrewer 0.2.0 2022-03-21 CRAN (R 4.4.0)
117 mgcv 1.9-1 2023-12-21 CRAN (R 4.4.0)
118 mime 0.12 2021-09-28 CRAN (R 4.4.0)
119 mirai 1.1.1 2024-07-01 CRAN (R 4.4.0)
120 modelr 0.1.11 2023-03-22 CRAN (R 4.4.0)
121 modelsummary 2.1.0 2024-05-19 CRAN (R 4.4.0)
122 munsell 0.5.1 2024-04-01 CRAN (R 4.4.0)
123 mvtnorm 1.2-5 2024-05-21 CRAN (R 4.4.0)
124 nanonext 1.1.1 2024-06-23 CRAN (R 4.4.0)
125 nleqslv 3.3.5 2023-11-26 CRAN (R 4.4.0)
126 nlme 3.1-164 2023-11-27 CRAN (R 4.4.0)
127 numDeriv 2016.8-1.1 2019-06-06 RSPM
128 openssl 2.2.0 2024-05-16 CRAN (R 4.4.0)
129 openxlsx 4.2.7.1 2024-09-20 RSPM
130 parallelly 1.37.1 2024-02-29 CRAN (R 4.4.0)
131 parameters 0.21.7 2024-05-14 CRAN (R 4.4.0)
132 patchwork 1.2.0 2024-01-08 CRAN (R 4.4.0)
133 performance 0.11.0 2024-03-22 CRAN (R 4.4.0)
134 pillar 1.9.0 2023-03-22 RSPM
135 pingr 2.0.3 2023-12-10 CRAN (R 4.4.0)
136 pkgbuild 1.4.4 2024-03-17 CRAN (R 4.4.0)
137 pkgconfig 2.0.3 2019-09-22 RSPM
138 plyr 1.8.9 2023-10-02 CRAN (R 4.4.0)
139 png 0.1-8 2022-11-29 CRAN (R 4.4.0)
140 posterior 1.5.0 2023-10-31 CRAN (R 4.4.0)
141 prettyunits 1.2.0 2023-09-24 CRAN (R 4.4.0)
142 processx 3.8.4 2024-03-16 RSPM
143 progress 1.2.3 2023-12-06 CRAN (R 4.4.0)
144 promises 1.3.0 2024-04-05 CRAN (R 4.4.0)
145 proxy 0.4-27 2022-06-09 CRAN (R 4.4.0)
146 ps 1.7.6 2024-01-18 CRAN (R 4.4.0)
147 purrr 1.0.2 2023-08-10 CRAN (R 4.4.0)
148 qs 0.26.3 2024-05-16 CRAN (R 4.4.0)
149 quadprog 1.5-8 2019-11-20 CRAN (R 4.4.0)
150 quarto 1.4 2024-03-06 CRAN (R 4.4.0)
151 QuickJSR 1.1.3 2024-01-31 CRAN (R 4.4.0)
152 R.cache 0.16.0 2022-07-21 CRAN (R 4.4.0)
153 R.methodsS3 1.8.2 2022-06-13 CRAN (R 4.4.0)
154 R.oo 1.26.0 2024-01-24 CRAN (R 4.4.0)
155 R.utils 2.12.3 2023-11-18 CRAN (R 4.4.0)
156 R6 2.5.1 2021-08-19 RSPM
157 ragg 1.3.2 2024-05-15 CRAN (R 4.4.0)
158 RApiSerialize 0.1.3 2024-05-14 CRAN (R 4.4.0)
159 rappdirs 0.3.3 2021-01-31 CRAN (R 4.4.0)
160 RColorBrewer 1.1-3 2022-04-03 CRAN (R 4.4.0)
161 Rcpp 1.0.12 2024-01-09 CRAN (R 4.4.0)
162 RcppEigen 0.3.4.0.0 2024-02-28 CRAN (R 4.4.0)
163 RcppParallel 5.1.7 2023-02-27 CRAN (R 4.4.0)
164 reactable 0.4.4 2023-03-12 CRAN (R 4.4.0)
165 reactR 0.5.0 2023-10-11 CRAN (R 4.4.0)
166 readr 2.1.5 2024-01-10 CRAN (R 4.4.0)
167 readxl 1.4.3 2023-07-06 CRAN (R 4.4.0)
168 rematch 2.0.0 2023-08-30 CRAN (R 4.4.0)
169 rematch2 2.1.2 2020-05-01 CRAN (R 4.4.0)
170 renv 1.0.11 2024-10-12 RSPM
171 reprex 2.1.0 2024-01-11 CRAN (R 4.4.0)
172 reshape2 1.4.4 2020-04-09 CRAN (R 4.4.0)
173 rlang 1.1.3 2024-01-10 CRAN (R 4.4.0)
174 rmarkdown 2.27 2024-05-17 CRAN (R 4.4.0)
175 rprojroot 2.0.4 2023-11-05 CRAN (R 4.4.0)
176 rstan 2.32.6 2024-03-05 CRAN (R 4.4.0)
177 rstantools 2.4.0 2024-01-31 CRAN (R 4.4.0)
178 rstudioapi 0.16.0 2024-03-24 CRAN (R 4.4.0)
179 rvest 1.0.4 2024-02-12 CRAN (R 4.4.0)
180 s2 1.1.6 2023-12-19 CRAN (R 4.4.0)
181 sass 0.4.9 2024-03-15 CRAN (R 4.4.0)
182 scales 1.3.0 2023-11-28 CRAN (R 4.4.0)
183 secretbase 0.5.0 2024-04-25 CRAN (R 4.4.0)
184 selectr 0.4-2 2019-11-20 CRAN (R 4.4.0)
185 sessioninfo 1.2.2 2021-12-06 CRAN (R 4.4.0)
186 sf 1.0-16 2024-03-24 CRAN (R 4.4.0)
187 shiny 1.8.1.1 2024-04-02 CRAN (R 4.4.0)
188 shinybusy 0.3.3 2024-03-09 CRAN (R 4.4.0)
189 shinyWidgets 0.8.6 2024-04-24 CRAN (R 4.4.0)
190 snakecase 0.11.1 2023-08-27 CRAN (R 4.4.0)
191 sourcetools 0.1.7-1 2023-02-01 CRAN (R 4.4.0)
192 StanHeaders 2.32.9 2024-05-29 CRAN (R 4.4.0)
193 stringfish 0.16.0 2023-11-28 CRAN (R 4.4.0)
194 stringi 1.8.4 2024-05-06 CRAN (R 4.4.0)
195 stringr 1.5.1 2023-11-14 CRAN (R 4.4.0)
196 styler 1.10.3 2024-04-07 CRAN (R 4.4.0)
197 svUnit 1.0.6 2021-04-19 CRAN (R 4.4.0)
198 sys 3.4.2 2023-05-23 CRAN (R 4.4.0)
199 systemfonts 1.1.0 2024-05-15 CRAN (R 4.4.0)
200 tables 0.9.25 2024-04-13 CRAN (R 4.4.0)
201 tarchetypes 0.9.0 2024-04-17 CRAN (R 4.4.0)
202 targets 1.7.0 2024-04-17 CRAN (R 4.4.0)
203 tensorA 0.36.2.1 2023-12-13 RSPM
204 textshaping 0.3.7 2023-10-09 CRAN (R 4.4.0)
205 tibble 3.2.1 2023-03-20 RSPM
206 tidybayes 3.0.6 2023-08-12 CRAN (R 4.4.0)
207 tidyr 1.3.1 2024-01-24 CRAN (R 4.4.0)
208 tidyselect 1.2.1 2024-03-11 CRAN (R 4.4.0)
209 tidyverse 2.0.0 2023-02-22 CRAN (R 4.4.0)
210 timechange 0.3.0 2024-01-18 CRAN (R 4.4.0)
211 tinytable 0.4.0.1 2024-09-07 Github (vincentarelbundock/tinytab…
212 tinytex 0.51 2024-05-06 CRAN (R 4.4.0)
213 tzdb 0.4.0 2023-05-12 CRAN (R 4.4.0)
214 units 0.8-5 2023-11-28 CRAN (R 4.4.0)
215 utf8 1.2.4 2023-10-22 RSPM
216 uuid 1.2-0 2024-01-14 CRAN (R 4.4.0)
217 V8 4.4.2 2024-02-15 CRAN (R 4.4.0)
218 vctrs 0.6.5 2023-12-01 RSPM
219 viridisLite 0.4.2 2023-05-02 CRAN (R 4.4.0)
220 visNetwork 2.1.2 2022-09-29 CRAN (R 4.4.0)
221 vroom 1.6.5 2023-12-05 CRAN (R 4.4.0)
222 waiter 0.2.5 2022-01-03 CRAN (R 4.4.0)
223 withr 3.0.1 2024-07-31 RSPM
224 wk 0.9.1 2023-11-29 CRAN (R 4.4.0)
225 xfun 0.44 2024-05-15 CRAN (R 4.4.0)
226 xml2 1.3.6 2023-12-04 CRAN (R 4.4.0)
227 xtable 1.8-4 2019-04-21 CRAN (R 4.4.0)
228 yaml 2.3.8 2023-12-11 CRAN (R 4.4.0)
229 zip 2.3.1 2024-01-27 RSPM
230 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
makevars_path <- file.path(Sys.getenv("HOME"), ".R/Makevars")
if (file.exists(makevars_path)) {
writeLines(readLines(makevars_path))
} else {
message("No .R/Makevars on the computer that built this")
}# 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