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$platform setting value
version R version 4.3.0 (2023-04-21)
os macOS Ventura 13.3.1
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-05-05
pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
quarto 1.3.333
stan (cmdstanr) 2.32.1Packages
We use the {renv} package to create a stable version-specific library of packages. The official list of packages is included in renv.lock and running this from the root of this project should install everything:
renv::restore()Here’s the full list of packages in a less JSON-y format:
Code
packages_raw <- jsonlite::read_json(here::here("renv.lock"))$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: 232 × 4
package ondiskversion date source
<chr> <chr> <chr> <chr>
1 abind 1.4-5 2016-07-21 CRAN (R 4.3.0)
2 anytime 0.3.9 2020-08-27 CRAN (R 4.3.0)
3 arrayhelpers 1.1-0 2020-02-04 CRAN (R 4.3.0)
4 askpass 1.1 2019-01-13 CRAN (R 4.3.0)
5 backports 1.4.1 2021-12-13 CRAN (R 4.3.0)
6 base64enc 0.1-3 2015-07-28 CRAN (R 4.3.0)
7 base64url 1.4 2018-05-14 CRAN (R 4.3.0)
8 bayesplot 1.10.0 2022-11-16 CRAN (R 4.3.0)
9 bayestestR 0.13.1 2023-04-07 CRAN (R 4.3.0)
10 BH 1.81.0-1 2023-01-22 CRAN (R 4.3.0)
11 bigD 0.2.0 2022-09-05 CRAN (R 4.3.0)
12 bit 4.0.5 2022-11-15 CRAN (R 4.3.0)
13 bit64 4.0.5 2020-08-30 CRAN (R 4.3.0)
14 bitops 1.0-7 2021-04-24 CRAN (R 4.3.0)
15 blob 1.2.4 2023-03-17 CRAN (R 4.3.0)
16 bridgesampling 1.1-2 2021-04-16 CRAN (R 4.3.0)
17 brms 2.19.0 2023-03-14 CRAN (R 4.3.0)
18 Brobdingnag 1.2-9 2022-10-19 CRAN (R 4.3.0)
19 broom 1.0.4 2023-03-11 CRAN (R 4.3.0)
20 bs4Dash 2.2.1 2022-12-20 CRAN (R 4.3.0)
21 bslib 0.4.2 2022-12-16 CRAN (R 4.3.0)
22 cachem 1.0.8 2023-05-01 CRAN (R 4.3.0)
23 callr 3.7.3 2022-11-02 CRAN (R 4.3.0)
24 cellranger 1.1.0 2016-07-27 CRAN (R 4.3.0)
25 checkmate 2.2.0 2023-04-27 CRAN (R 4.3.0)
26 class 7.3-21 2023-01-23 CRAN (R 4.3.0)
27 classInt 0.4-9 2023-02-28 CRAN (R 4.3.0)
28 cli 3.6.1 2023-03-23 CRAN (R 4.3.0)
29 clipr 0.8.0 2022-02-22 CRAN (R 4.3.0)
30 clock 0.6.1 2022-07-18 CRAN (R 4.3.0)
31 clustermq 0.8.95.5 2023-02-19 CRAN (R 4.3.0)
32 cmdstanr 0.5.3 2023-05-04 local
33 coda 0.19-4 2020-09-30 CRAN (R 4.3.0)
34 codetools 0.2-19 2023-02-01 CRAN (R 4.3.0)
35 collapse 1.9.5 2023-04-07 CRAN (R 4.3.0)
36 colorspace 2.1-0 2023-01-23 CRAN (R 4.3.0)
37 colourpicker 1.2.0 2022-10-28 CRAN (R 4.3.0)
38 commonmark 1.9.0 2023-03-17 CRAN (R 4.3.0)
39 conflicted 1.2.0 2023-02-01 CRAN (R 4.3.0)
40 countrycode 1.4.0 2022-05-04 CRAN (R 4.3.0)
41 cpp11 0.4.3 2022-10-12 CRAN (R 4.3.0)
42 crayon 1.5.2 2022-09-29 CRAN (R 4.3.0)
43 crosstalk 1.2.0 2021-11-04 CRAN (R 4.3.0)
44 curl 5.0.0 2023-01-12 CRAN (R 4.3.0)
45 data.table 1.14.8 2023-02-17 CRAN (R 4.3.0)
46 datawizard 0.7.1 2023-04-03 CRAN (R 4.3.0)
47 DBI 1.1.3 2022-06-18 CRAN (R 4.3.0)
48 dbplyr 2.3.2 2023-03-21 CRAN (R 4.3.0)
49 desc 1.4.2 2022-09-08 CRAN (R 4.3.0)
50 digest 0.6.31 2022-12-11 CRAN (R 4.3.0)
51 distributional 0.3.2 2023-03-22 CRAN (R 4.3.0)
52 dplyr 1.1.2 2023-04-20 CRAN (R 4.3.0)
53 DT 0.27 2023-01-17 CRAN (R 4.3.0)
54 dtplyr 1.3.1 2023-03-22 CRAN (R 4.3.0)
55 dygraphs 1.1.1.6 2018-07-11 CRAN (R 4.3.0)
56 e1071 1.7-13 2023-02-01 CRAN (R 4.3.0)
57 ellipsis 0.3.2 2021-04-29 CRAN (R 4.3.0)
58 emoji 15.0 2022-11-03 CRAN (R 4.3.0)
59 evaluate 0.20 2023-01-17 CRAN (R 4.3.0)
60 extraDistr 1.9.1 2020-09-07 CRAN (R 4.3.0)
61 fansi 1.0.4 2023-01-22 CRAN (R 4.3.0)
62 farver 2.1.1 2022-07-06 CRAN (R 4.3.0)
63 fastmap 1.1.1 2023-02-24 CRAN (R 4.3.0)
64 fontawesome 0.5.1 2023-04-18 CRAN (R 4.3.0)
65 forcats 1.0.0 2023-01-29 CRAN (R 4.3.0)
66 fresh 0.2.0 2020-05-29 CRAN (R 4.3.0)
67 fs 1.6.2 2023-04-25 CRAN (R 4.3.0)
68 furrr 0.3.1 2022-08-15 CRAN (R 4.3.0)
69 future 1.32.0 2023-03-07 CRAN (R 4.3.0)
70 future.callr 0.8.1 2022-12-14 CRAN (R 4.3.0)
71 gargle 1.4.0 2023-04-15 CRAN (R 4.3.0)
72 generics 0.1.3 2022-07-05 CRAN (R 4.3.0)
73 ggdist 3.2.1 2023-01-18 CRAN (R 4.3.0)
74 ggplot2 3.4.2 2023-04-03 CRAN (R 4.3.0)
75 ggridges 0.5.4 2022-09-26 CRAN (R 4.3.0)
76 globals 0.16.2 2022-11-21 CRAN (R 4.3.0)
77 glue 1.6.2 2022-02-24 CRAN (R 4.3.0)
78 googledrive 2.1.0 2023-03-22 CRAN (R 4.3.0)
79 googlesheets4 1.1.0 2023-03-23 CRAN (R 4.3.0)
80 gridExtra 2.3 2017-09-09 CRAN (R 4.3.0)
81 gt 0.9.0 2023-03-31 CRAN (R 4.3.0)
82 gtable 0.3.3 2023-03-21 CRAN (R 4.3.0)
83 gtools 3.9.4 2022-11-27 CRAN (R 4.3.0)
84 haven 2.5.2 2023-02-28 CRAN (R 4.3.0)
85 HDInterval 0.2.4 2022-11-17 CRAN (R 4.3.0)
86 here 1.0.1 2020-12-13 CRAN (R 4.3.0)
87 highr 0.10 2022-12-22 CRAN (R 4.3.0)
88 hms 1.1.3 2023-03-21 CRAN (R 4.3.0)
89 htmltools 0.5.5 2023-03-23 CRAN (R 4.3.0)
90 htmlwidgets 1.6.2 2023-03-17 CRAN (R 4.3.0)
91 httpuv 1.6.9 2023-02-14 CRAN (R 4.3.0)
92 httr 1.4.5 2023-02-24 CRAN (R 4.3.0)
93 ids 1.0.1 2017-05-31 CRAN (R 4.3.0)
94 igraph 1.4.2 2023-04-07 CRAN (R 4.3.0)
95 inline 0.3.19 2021-05-31 CRAN (R 4.3.0)
96 insight 0.19.1 2023-03-18 CRAN (R 4.3.0)
97 isoband 0.2.7 2022-12-20 CRAN (R 4.3.0)
98 janitor 2.2.0 2023-02-02 CRAN (R 4.3.0)
99 jquerylib 0.1.4 2021-04-26 CRAN (R 4.3.0)
100 jsonlite 1.8.4 2022-12-06 CRAN (R 4.3.0)
101 juicyjuice 0.1.0 2022-11-10 CRAN (R 4.3.0)
102 kableExtra 1.3.4.9000 2023-05-05 Github (haozhu233/kableExtra@292f6…
103 KernSmooth 2.23-20 2021-05-03 CRAN (R 4.3.0)
104 knitr 1.42 2023-01-25 CRAN (R 4.3.0)
105 labeling 0.4.2 2020-10-20 CRAN (R 4.3.0)
106 later 1.3.1 2023-05-02 CRAN (R 4.3.0)
107 lattice 0.21-8 2023-04-05 CRAN (R 4.3.0)
108 lazyeval 0.2.2 2019-03-15 CRAN (R 4.3.0)
109 lifecycle 1.0.3 2022-10-07 CRAN (R 4.3.0)
110 listenv 0.9.0 2022-12-16 CRAN (R 4.3.0)
111 loo 2.6.0 2023-03-31 CRAN (R 4.3.0)
112 lubridate 1.9.2 2023-02-10 CRAN (R 4.3.0)
113 magrittr 2.0.3 2022-03-30 CRAN (R 4.3.0)
114 marginaleffects 0.11.1 2023-03-31 CRAN (R 4.3.0)
115 markdown 1.6 2023-04-07 CRAN (R 4.3.0)
116 MASS 7.3-58.4 2023-03-07 CRAN (R 4.3.0)
117 Matrix 1.5-4 2023-04-04 CRAN (R 4.3.0)
118 matrixStats 0.63.0 2022-11-18 CRAN (R 4.3.0)
119 memoise 2.0.1 2021-11-26 CRAN (R 4.3.0)
120 MetBrewer 0.2.0 2022-03-21 CRAN (R 4.3.0)
121 mgcv 1.8-42 2023-03-02 CRAN (R 4.3.0)
122 mime 0.12 2021-09-28 CRAN (R 4.3.0)
123 miniUI 0.1.1.1 2018-05-18 CRAN (R 4.3.0)
124 modelr 0.1.11 2023-03-22 CRAN (R 4.3.0)
125 modelsummary 1.4.0 2023-04-26 CRAN (R 4.3.0)
126 munsell 0.5.0 2018-06-12 CRAN (R 4.3.0)
127 mvtnorm 1.1-3 2021-10-08 CRAN (R 4.3.0)
128 narray 0.5.1 2022-10-02 CRAN (R 4.3.0)
129 nleqslv 3.3.4 2023-01-14 CRAN (R 4.3.0)
130 nlme 3.1-162 2023-01-31 CRAN (R 4.3.0)
131 numDeriv 2016.8-1.1 2019-06-06 CRAN (R 4.3.0)
132 openssl 2.0.6 2023-03-09 CRAN (R 4.3.0)
133 packrat 0.9.1 2023-02-27 CRAN (R 4.3.0)
134 parallelly 1.35.0 2023-03-23 CRAN (R 4.3.0)
135 parameters 0.21.0 2023-04-19 CRAN (R 4.3.0)
136 patchwork 1.1.2 2022-08-19 CRAN (R 4.3.0)
137 performance 0.10.3 2023-04-07 CRAN (R 4.3.0)
138 pillar 1.9.0 2023-03-22 CRAN (R 4.3.0)
139 pingr 2.0.2 2022-10-26 CRAN (R 4.3.0)
140 pkgbuild 1.4.0 2022-11-27 CRAN (R 4.3.0)
141 pkgconfig 2.0.3 2019-09-22 CRAN (R 4.3.0)
142 plyr 1.8.8 2022-11-11 CRAN (R 4.3.0)
143 posterior 1.4.1 2023-03-14 CRAN (R 4.3.0)
144 prettyunits 1.1.1 2020-01-24 CRAN (R 4.3.0)
145 processx 3.8.1 2023-04-18 CRAN (R 4.3.0)
146 progress 1.2.2 2019-05-16 CRAN (R 4.3.0)
147 promises 1.2.0.1 2021-02-11 CRAN (R 4.3.0)
148 proxy 0.4-27 2022-06-09 CRAN (R 4.3.0)
149 ps 1.7.5 2023-04-18 CRAN (R 4.3.0)
150 purrr 1.0.1 2023-01-10 CRAN (R 4.3.0)
151 qs 0.25.5 2023-02-22 CRAN (R 4.3.0)
152 quadprog 1.5-8 2019-11-20 CRAN (R 4.3.0)
153 quarto 1.2 2022-07-06 CRAN (R 4.3.0)
154 R6 2.5.1 2021-08-19 CRAN (R 4.3.0)
155 ragg 1.2.5 2023-01-12 CRAN (R 4.3.0)
156 RApiSerialize 0.1.2 2022-08-25 CRAN (R 4.3.0)
157 rappdirs 0.3.3 2021-01-31 CRAN (R 4.3.0)
158 RColorBrewer 1.1-3 2022-04-03 CRAN (R 4.3.0)
159 Rcpp 1.0.10 2023-01-22 CRAN (R 4.3.0)
160 RcppEigen 0.3.3.9.3 2022-11-05 CRAN (R 4.3.0)
161 RcppParallel 5.1.7 2023-02-27 CRAN (R 4.3.0)
162 reactable 0.4.4 2023-03-12 CRAN (R 4.3.0)
163 reactR 0.4.4 2021-02-22 CRAN (R 4.3.0)
164 readr 2.1.4 2023-02-10 CRAN (R 4.3.0)
165 readxl 1.4.2 2023-02-09 CRAN (R 4.3.0)
166 rematch 1.0.1 2016-04-21 CRAN (R 4.3.0)
167 rematch2 2.1.2 2020-05-01 CRAN (R 4.3.0)
168 renv 0.17.3 2023-04-06 CRAN (R 4.3.0)
169 reprex 2.0.2 2022-08-17 CRAN (R 4.3.0)
170 reshape2 1.4.4 2020-04-09 CRAN (R 4.3.0)
171 rlang 1.1.1 2023-04-28 CRAN (R 4.3.0)
172 rmarkdown 2.21 2023-03-26 CRAN (R 4.3.0)
173 rprojroot 2.0.3 2022-04-02 CRAN (R 4.3.0)
174 rsconnect 0.8.29 2023-01-09 CRAN (R 4.3.0)
175 rstan 2.21.8 2023-01-17 CRAN (R 4.3.0)
176 rstantools 2.3.1 2023-03-30 CRAN (R 4.3.0)
177 rstudioapi 0.14 2022-08-22 CRAN (R 4.3.0)
178 rvest 1.0.3 2022-08-19 CRAN (R 4.3.0)
179 s2 1.1.3 2023-04-27 CRAN (R 4.3.0)
180 sass 0.4.6 2023-05-03 CRAN (R 4.3.0)
181 scales 1.2.1 2022-08-20 CRAN (R 4.3.0)
182 selectr 0.4-2 2019-11-20 CRAN (R 4.3.0)
183 sessioninfo 1.2.2 2021-12-06 CRAN (R 4.3.0)
184 sf 1.0-12 2023-03-19 CRAN (R 4.3.0)
185 shiny 1.7.4 2022-12-15 CRAN (R 4.3.0)
186 shinybusy 0.3.1 2022-05-10 CRAN (R 4.3.0)
187 shinyjs 2.1.0 2021-12-23 CRAN (R 4.3.0)
188 shinystan 2.6.0 2022-03-03 CRAN (R 4.3.0)
189 shinythemes 1.2.0 2021-01-25 CRAN (R 4.3.0)
190 shinyWidgets 0.7.6 2023-01-08 CRAN (R 4.3.0)
191 snakecase 0.11.0 2019-05-25 CRAN (R 4.3.0)
192 sourcetools 0.1.7-1 2023-02-01 CRAN (R 4.3.0)
193 StanHeaders 2.21.0-7 2020-12-17 CRAN (R 4.3.0)
194 stringfish 0.15.7 2022-04-13 CRAN (R 4.3.0)
195 stringi 1.7.12 2023-01-11 CRAN (R 4.3.0)
196 stringr 1.5.0 2022-12-02 CRAN (R 4.3.0)
197 svglite 2.1.1 2023-01-10 CRAN (R 4.3.0)
198 svUnit 1.0.6 2021-04-19 CRAN (R 4.3.0)
199 sys 3.4.1 2022-10-18 CRAN (R 4.3.0)
200 systemfonts 1.0.4 2022-02-11 CRAN (R 4.3.0)
201 tables 0.9.17 2023-05-02 CRAN (R 4.3.0)
202 tarchetypes 0.7.6 2023-05-02 CRAN (R 4.3.0)
203 targets 1.0.0 2023-04-24 CRAN (R 4.3.0)
204 tensorA 0.36.2 2020-11-19 CRAN (R 4.3.0)
205 textshaping 0.3.6 2021-10-13 CRAN (R 4.3.0)
206 threejs 0.3.3 2020-01-21 CRAN (R 4.3.0)
207 tibble 3.2.1 2023-03-20 CRAN (R 4.3.0)
208 tidybayes 3.0.4 2023-03-14 CRAN (R 4.3.0)
209 tidyr 1.3.0 2023-01-24 CRAN (R 4.3.0)
210 tidyselect 1.2.0 2022-10-10 CRAN (R 4.3.0)
211 tidyverse 2.0.0 2023-02-22 CRAN (R 4.3.0)
212 timechange 0.2.0 2023-01-11 CRAN (R 4.3.0)
213 tinytex 0.45 2023-04-18 CRAN (R 4.3.0)
214 tzdb 0.3.0 2022-03-28 CRAN (R 4.3.0)
215 units 0.8-2 2023-04-27 CRAN (R 4.3.0)
216 utf8 1.2.3 2023-01-31 CRAN (R 4.3.0)
217 uuid 1.1-0 2022-04-19 CRAN (R 4.3.0)
218 V8 4.3.0 2023-04-08 CRAN (R 4.3.0)
219 vctrs 0.6.2 2023-04-19 CRAN (R 4.3.0)
220 viridisLite 0.4.2 2023-05-02 CRAN (R 4.3.0)
221 visNetwork 2.1.2 2022-09-29 CRAN (R 4.3.0)
222 vroom 1.6.3 2023-04-28 CRAN (R 4.3.0)
223 waiter 0.2.5 2022-01-03 CRAN (R 4.3.0)
224 webshot 0.5.4 2022-09-26 CRAN (R 4.3.0)
225 withr 2.5.0 2022-03-03 CRAN (R 4.3.0)
226 wk 0.7.2 2023-03-17 CRAN (R 4.3.0)
227 xfun 0.39 2023-04-20 CRAN (R 4.3.0)
228 xml2 1.3.4 2023-04-27 CRAN (R 4.3.0)
229 xtable 1.8-4 2019-04-21 CRAN (R 4.3.0)
230 xts 0.13.1 2023-04-16 CRAN (R 4.3.0)
231 yaml 2.3.7 2023-01-23 CRAN (R 4.3.0)
232 zoo 1.8-12 2023-04-13 CRAN (R 4.3.0) 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
# xcode headers
XH=$(shell xcrun -show-sdk-path)
# ccache
CCACHE=$(HB)/ccache
CCACHE=
# Make using all cores (set # to # of cores on your machine)
# Check https://stackoverflow.com/q/2499070 for more info.
# Run `sysctl -n hw.logicalcpu` to check the number of threads https://stackoverflow.com/a/56607839
# As a rule of thumb the number should be between cores and threads.
MAKE=make -j4
# Version
VER=12
# LLVM (Clang) compiler options
CC=$(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)/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