Brms model doesn't run after custom family (hurdle_gamma()) specified

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)
 car              3.0-9      2020-08-11 [2] CRAN (R 4.0.2)
 carData          3.0-4      2020-05-22 [2] CRAN (R 4.0.2)
 cellranger       1.1.0      2016-07-27 [2] CRAN (R 4.0.2)
 cli              2.0.2      2020-02-28 [2] CRAN (R 4.0.2)
 coda             0.19-3     2019-07-05 [2] CRAN (R 4.0.2)
 codetools        0.2-16     2018-12-24 [2] CRAN (R 4.0.2)
 colorspace       1.4-1      2019-03-18 [2] CRAN (R 4.0.2)
 colourpicker     1.1.0      2020-09-14 [2] CRAN (R 4.0.2)
 crayon           1.3.4      2017-09-16 [2] CRAN (R 4.0.2)
 crosstalk        1.1.0.1    2020-03-13 [2] CRAN (R 4.0.2)
 curl             4.3        2019-12-02 [2] CRAN (R 4.0.1)
 data.table     * 1.13.0     2020-07-24 [2] CRAN (R 4.0.2)
 DBI              1.1.0      2019-12-15 [2] CRAN (R 4.0.2)
 dbplyr           1.4.4      2020-05-27 [2] CRAN (R 4.0.2)
 desc             1.2.0      2018-05-01 [2] CRAN (R 4.0.2)
 devtools       * 2.3.2      2020-09-18 [2] CRAN (R 4.0.2)
 digest           0.6.25     2020-02-23 [2] CRAN (R 4.0.2)
 distributional   0.2.0      2020-08-03 [2] CRAN (R 4.0.2)
 dplyr          * 1.0.2      2020-08-18 [2] CRAN (R 4.0.2)
 DT               0.15       2020-08-05 [2] CRAN (R 4.0.2)
 dygraphs         1.1.1.6    2018-07-11 [2] CRAN (R 4.0.2)
 ellipsis         0.3.1      2020-05-15 [2] CRAN (R 4.0.2)
 fansi            0.4.1      2020-01-08 [2] CRAN (R 4.0.2)
 farver           2.0.3      2020-01-16 [2] CRAN (R 4.0.2)
 fastmap          1.0.1      2019-10-08 [2] CRAN (R 4.0.2)
 forcats        * 0.5.0      2020-03-01 [2] CRAN (R 4.0.2)
 foreign          0.8-80     2020-05-24 [2] CRAN (R 4.0.2)
 fs               1.5.0      2020-07-31 [2] CRAN (R 4.0.2)
 generics         0.0.2      2018-11-29 [2] CRAN (R 4.0.2)
 GGally           2.0.0      2020-06-06 [2] CRAN (R 4.0.2)
 ggdist           2.2.0      2020-07-12 [2] CRAN (R 4.0.2)
 ggmcmc         * 1.5.0      2020-08-29 [2] CRAN (R 4.0.2)
 ggplot2        * 3.3.2      2020-06-19 [2] CRAN (R 4.0.2)
 ggridges       * 0.5.2      2020-01-12 [2] CRAN (R 4.0.2)
 ggthemes       * 4.2.0      2019-05-13 [2] CRAN (R 4.0.2)
 glue             1.4.2      2020-08-27 [2] CRAN (R 4.0.2)
 gridExtra        2.3        2017-09-09 [2] CRAN (R 4.0.2)
 gtable           0.3.0      2019-03-25 [2] CRAN (R 4.0.2)
 gtools           3.8.2      2020-03-31 [2] CRAN (R 4.0.2)
 haven            2.3.1      2020-06-01 [2] CRAN (R 4.0.2)
 HDInterval     * 0.2.2      2020-05-23 [2] CRAN (R 4.0.2)
 hms              0.5.3      2020-01-08 [2] CRAN (R 4.0.2)
 htmltools        0.5.0      2020-06-16 [2] CRAN (R 4.0.2)
 htmlwidgets      1.5.1      2019-10-08 [2] CRAN (R 4.0.2)
 httpuv           1.5.4      2020-06-06 [2] CRAN (R 4.0.2)
 httr             1.4.2      2020-07-20 [2] CRAN (R 4.0.2)
 igraph           1.2.5      2020-03-19 [2] CRAN (R 4.0.2)
 inline           0.3.16     2020-09-06 [2] CRAN (R 4.0.2)
 jsonlite         1.7.1      2020-09-07 [2] CRAN (R 4.0.2)
 later            1.1.0.1    2020-06-05 [2] CRAN (R 4.0.2)
 lattice          0.20-41    2020-04-02 [2] CRAN (R 4.0.2)
 lifecycle        0.2.0      2020-03-06 [2] CRAN (R 4.0.2)
 lme4           * 1.1-23     2020-04-07 [2] CRAN (R 4.0.1)
 lmerTest       * 3.1-2      2020-04-08 [2] CRAN (R 4.0.2)
 loo              2.3.1      2020-07-14 [2] CRAN (R 4.0.2)
 lubridate        1.7.9      2020-06-08 [2] CRAN (R 4.0.2)
 magrittr         1.5        2014-11-22 [2] CRAN (R 4.0.2)
 markdown         1.1        2019-08-07 [2] CRAN (R 4.0.2)
 MASS             7.3-51.6   2020-04-26 [2] CRAN (R 4.0.2)
 Matrix         * 1.2-18     2019-11-27 [2] CRAN (R 4.0.2)
 matrixStats      0.57.0     2020-09-25 [2] CRAN (R 4.0.2)
 memoise          1.1.0      2017-04-21 [2] CRAN (R 4.0.2)
 mime             0.9        2020-02-04 [2] CRAN (R 4.0.2)
 miniUI           0.1.1.1    2018-05-18 [2] CRAN (R 4.0.2)
 minqa            1.2.4      2014-10-09 [2] CRAN (R 4.0.2)
 modelr           0.1.8      2020-05-19 [2] CRAN (R 4.0.2)
 munsell          0.5.0      2018-06-12 [2] CRAN (R 4.0.2)
 mvtnorm          1.1-1      2020-06-09 [2] CRAN (R 4.0.2)
 nlme             3.1-148    2020-05-24 [2] CRAN (R 4.0.2)
 nloptr           1.2.2.2    2020-07-02 [2] CRAN (R 4.0.2)
 numDeriv         2016.8-1.1 2019-06-06 [2] CRAN (R 4.0.2)
 openxlsx         4.2.2      2020-09-17 [2] CRAN (R 4.0.2)
 pillar           1.4.6      2020-07-10 [2] CRAN (R 4.0.2)
 pkgbuild         1.1.0      2020-07-13 [2] CRAN (R 4.0.2)
 pkgconfig        2.0.3      2019-09-22 [2] CRAN (R 4.0.2)
 pkgload          1.1.0      2020-05-29 [2] CRAN (R 4.0.2)
 plyr           * 1.8.6      2020-03-03 [2] CRAN (R 4.0.2)
 prettyunits      1.1.1      2020-01-24 [2] CRAN (R 4.0.2)
 processx         3.4.4      2020-09-03 [2] CRAN (R 4.0.2)
 promises         1.1.1      2020-06-09 [2] CRAN (R 4.0.2)
 ps               1.3.4      2020-08-11 [2] CRAN (R 4.0.2)
 purrr          * 0.3.4      2020-04-17 [2] CRAN (R 4.0.2)
 R6               2.4.1      2019-11-12 [2] CRAN (R 4.0.2)
 RColorBrewer   * 1.1-2      2014-12-07 [2] CRAN (R 4.0.2)
 Rcpp           * 1.0.5      2020-07-06 [2] CRAN (R 4.0.2)
 RcppParallel     5.0.2      2020-06-24 [2] CRAN (R 4.0.2)
 readr          * 1.3.1      2018-12-21 [2] CRAN (R 4.0.2)
 readxl           1.3.1      2019-03-13 [2] CRAN (R 4.0.2)
 remotes          2.2.0      2020-07-21 [2] CRAN (R 4.0.2)
 reprex           0.3.0      2019-05-16 [2] CRAN (R 4.0.2)
 reshape          0.8.8      2018-10-23 [2] CRAN (R 4.0.2)
 reshape2         1.4.4      2020-04-09 [2] CRAN (R 4.0.2)
 rio              0.5.16     2018-11-26 [2] CRAN (R 4.0.2)
 rlang            0.4.7      2020-07-09 [2] CRAN (R 4.0.2)
 rprojroot        1.3-2      2018-01-03 [2] CRAN (R 4.0.2)
 rsconnect        0.8.16     2019-12-13 [2] CRAN (R 4.0.2)
 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)
 rstudioapi       0.11       2020-02-07 [2] CRAN (R 4.0.2)
 rvest            0.3.6      2020-07-25 [2] CRAN (R 4.0.2)
 scales           1.1.1      2020-05-11 [2] CRAN (R 4.0.2)
 Select         * 1.4        2018-05-11 [2] CRAN (R 4.0.2)
 sessioninfo      1.1.1      2018-11-05 [2] CRAN (R 4.0.2)
 shiny            1.5.0      2020-06-23 [2] CRAN (R 4.0.2)
 shinyjs          2.0.0      2020-09-09 [2] CRAN (R 4.0.2)
 shinystan        2.5.0      2018-05-01 [2] CRAN (R 4.0.2)
 shinythemes      1.1.2      2018-11-06 [2] CRAN (R 4.0.2)
 StanHeaders    * 2.21.0-6   2020-08-16 [2] CRAN (R 4.0.2)
 statmod          1.4.34     2020-02-17 [2] CRAN (R 4.0.2)
 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)
 threejs          0.3.3      2020-01-21 [2] CRAN (R 4.0.2)
 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)
 tidyselect       1.1.0      2020-05-11 [2] CRAN (R 4.0.2)
 tidyverse      * 1.3.0      2019-11-21 [2] CRAN (R 4.0.2)
 usethis        * 1.6.3      2020-09-17 [2] CRAN (R 4.0.2)
 V8               3.2.0      2020-06-19 [2] CRAN (R 4.0.2)
 vctrs            0.3.4      2020-08-29 [2] CRAN (R 4.0.2)
 viridis        * 0.5.1      2018-03-29 [2] CRAN (R 4.0.2)
 viridisLite    * 0.3.0      2018-02-01 [2] CRAN (R 4.0.1)
 wesanderson    * 0.3.6      2018-04-20 [2] CRAN (R 4.0.2)
 withr            2.3.0      2020-09-22 [2] CRAN (R 4.0.2)
 xml2             1.3.2      2020-04-23 [2] CRAN (R 4.0.2)
 xtable           1.8-4      2019-04-21 [2] CRAN (R 4.0.2)
 xts              0.12.1     2020-09-09 [2] CRAN (R 4.0.2)
 zip            * 2.1.1      2020-08-27 [2] CRAN (R 4.0.2)
 zoo              1.8-8      2020-05-02 [2] CRAN (R 4.0.2)

[1] /Users/bianca/Library/R/4.0/library
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
1 Like

Hi

you use RStudio 4.0.2, but then you don’t use Xcode’s compiler?