Hi all,
I have recently tried changing the distribution family of my brm model from the default to hurdle_gamma(), see model below:
mentalStHurdle <- brm(formula = Inaccuracy ~ lg10JerksZ*mentalState*lg10OwnStimDiff_jerkZ +
(1 + lg10JerksZ*lg10OwnStimDiff_jerkZ*mentalState || allVidIDs) +
(1 + lg10JerksZ*lg10OwnStimDiff_jerkZ*mentalState || allSubs),
data = db, family = hurdle_gamma(),
warmup = 1000, iter = 4000,
cores = options(mc.cores = parallel::detectCores()),
chains = 4, control = list(adapt_delta = .99),
prior = prior1, sample_prior = TRUE,
save_all_pars = TRUE)
Previously, when I ran the model with the default (gaussian) family it ran without any problems. Now with hurdle_gamma specified it doesn’t run at all.
First I see this error come up:
Error in withCallingHandlers(expr, warning = function(w) if (inherits(w, :
'list' object cannot be coerced to type 'double'
When I try running again for good luck (without changing anything), I see the stan starting message for what seems like ages:
Compiling Stan program...
until I eventually get this (error?) message:
make cmd is
make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' -f '/Users/bianca/.R/Makevars' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file28b5f49a0a6.so' OBJECTS='file28b5f49a0a6.o'
make would use
/usr/local/opt/llvm/bin/clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include/" -I"/Users/bianca/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -isystem "/usr/local/opt/llvm/include" -isysroot "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" -fPIC -Wall -g -O2 -c file28b5f49a0a6.cpp -o file28b5f49a0a6.o
if test "zfile28b5f49a0a6.o" != "z"; then \
echo /usr/local/opt/llvm/bin/clang++ -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L"/usr/local/opt/llvm/lib" -L"/usr/local/Cellar/gettext/0.21/lib" --sysroot="/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" -o file28b5f49a0a6.so file28b5f49a0a6.o '/Users/bianca/Library/R/4.0/library/rstan/lib//libStanServices.a' -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/lib/' -ltbb -ltbbmalloc -ltbbmalloc_proxy -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
/usr/local/opt/llvm/bin/clang++ -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L"/Library/Frameworks/R.framework/Resources/lib" -L"/usr/local/opt/llvm/lib" -L"/usr/local/Cellar/gettext/0.21/lib" --sysroot="/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" -o file28b5f49a0a6.so file28b5f49a0a6.o '/Users/bianca/Library/R/4.0/library/rstan/lib//libStanServices.a' -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/StanHeaders/lib/' -lStanHeaders -L'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/lib/' -ltbb -ltbbmalloc -ltbbmalloc_proxy -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
fi
I have no idea what this all means, so would really appreciate any help!
In case it is of any help, here is my session info:
> session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS Catalina 10.15.6
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2020-10-03
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [2] CRAN (R 4.0.2)
afex * 0.28-0 2020-09-20 [2] CRAN (R 4.0.2)
arrayhelpers 1.1-0 2020-02-04 [2] CRAN (R 4.0.2)
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.0.2)
backports 1.1.10 2020-09-15 [2] CRAN (R 4.0.2)
base64enc 0.1-3 2015-07-28 [2] CRAN (R 4.0.2)
bayesplot 1.7.2 2020-05-28 [2] CRAN (R 4.0.2)
blob 1.2.1 2020-01-20 [2] CRAN (R 4.0.2)
boot 1.3-25 2020-04-26 [2] CRAN (R 4.0.2)
bridgesampling 1.0-0 2020-02-26 [2] CRAN (R 4.0.2)
brms * 2.13.5 2020-07-31 [2] CRAN (R 4.0.2)
Brobdingnag 1.2-6 2018-08-13 [2] CRAN (R 4.0.2)
broom * 0.7.0 2020-07-09 [2] CRAN (R 4.0.2)
callr 3.4.4 2020-09-07 [2] CRAN (R 4.0.2)
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lmerTest * 3.1-2 2020-04-08 [2] CRAN (R 4.0.2)
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magrittr 1.5 2014-11-22 [2] CRAN (R 4.0.2)
markdown 1.1 2019-08-07 [2] CRAN (R 4.0.2)
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Rcpp * 1.0.5 2020-07-06 [2] CRAN (R 4.0.2)
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readr * 1.3.1 2018-12-21 [2] CRAN (R 4.0.2)
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reshape 0.8.8 2018-10-23 [2] CRAN (R 4.0.2)
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rio 0.5.16 2018-11-26 [2] CRAN (R 4.0.2)
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rstan * 2.21.2 2020-07-27 [1] CRAN (R 4.0.2)
rstantools 2.1.1 2020-07-06 [2] CRAN (R 4.0.2)
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Select * 1.4 2018-05-11 [2] CRAN (R 4.0.2)
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stringi 1.5.3 2020-09-09 [2] CRAN (R 4.0.2)
stringr * 1.4.0 2019-02-10 [2] CRAN (R 4.0.2)
svUnit 1.0.3 2020-04-20 [2] CRAN (R 4.0.2)
testthat 2.3.2 2020-03-02 [2] CRAN (R 4.0.2)
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tibble * 3.0.3 2020-07-10 [2] CRAN (R 4.0.2)
tidybayes * 2.1.1 2020-06-19 [2] CRAN (R 4.0.2)
tidyr * 1.1.2 2020-08-27 [2] CRAN (R 4.0.2)
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tidyverse * 1.3.0 2019-11-21 [2] CRAN (R 4.0.2)
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wesanderson * 0.3.6 2018-04-20 [2] CRAN (R 4.0.2)
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[1] /Users/bianca/Library/R/4.0/library
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library