Open harryprince opened 6 years ago
Fail to run example at https://github.com/rmcelreath/glmer2stan#2-binomial-with-varying-intercepts
library(lme4) devtools::install_github("rmcelreath/glmer2stan") library(glmer2stan)
Input:
data(cbpp) # built into lme4 m2_lme4 <- glmer( cbind(incidence,size-incidence) ~ period + (1|herd) , data=cbpp , family=binomial ) cbpp$herd_index <- as.integer(cbpp$herd) m2_g2s <- glmer2stan( cbind(incidence,size-incidence) ~ period + (1|herd_index) , data=cbpp , family="binomial" )
Error:
Error in UseMethod("extract_") : no applicable method for 'extract_' applied to an object of class "stanfit"
According to this issue: https://github.com/stan-dev/rstan/issues/118, it seems rstan/tidyr extract() namespace conflict.
SessionInfo:
R version 3.4.3 (2017-11-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] glmer2stan_0.995 lme4_1.1-17 bindrcpp_0.2 MDPtoolbox_4.0.3 linprog_0.9-2 lpSolve_5.6.13 [7] Matrix_1.2-12 promises_1.0.1 sparklyr_0.7.0-9026 forcats_0.2.0 stringr_1.3.0 dplyr_0.7.4 [13] purrr_0.2.4 readr_1.1.1 tidyr_0.8.0 tibble_1.4.2 tidyverse_1.2.1 rethinking_1.59 [19] rstan_2.17.3 StanHeaders_2.17.2 ggplot2_2.2.1 RMySQL_0.10.13 DBI_0.8 loaded via a namespace (and not attached): [1] minqa_1.2.4 colorspace_1.3-2 smoof_1.5.1 rsconnect_0.8.7 [5] rprojroot_1.3-2 base64enc_0.1-3 rstudioapi_0.7 listenv_0.7.0 [9] ParamHelpers_1.10 hash_2.2.6 mvtnorm_1.0-7 lubridate_1.7.1 [13] xml2_1.2.0 splines_3.4.3 codetools_0.2-15 mnormt_1.5-5 [17] knitr_1.20 mco_1.0-15.1 zeallot_0.1.0 jsonlite_1.5 [21] nloptr_1.0.4 broom_0.4.4 dbplyr_1.2.1 mlrMBO_1.1.1 [25] tfruns_1.3 shiny_1.0.5 compiler_3.4.3 httr_1.3.1 [29] backports_1.1.2 assertthat_0.2.0 lazyeval_0.2.1 cli_1.0.0 [33] later_0.7.1 addinpromises_0.1.0 htmltools_0.3.6 tools_3.4.3 [37] misc3d_0.8-4 igraph_1.2.1 coda_0.19-1 gtable_0.2.0 [41] glue_1.2.0 reshape2_1.4.3 parallelMap_1.3 Rcpp_0.12.17 [45] cellranger_1.1.0 RJSONIO_1.3-0 nlme_3.1-131 psych_1.8.3.3 [49] mlr_2.12 globals_0.11.0 rvest_0.3.2 mime_0.5 [53] devtools_1.13.4 future_1.8.1 MASS_7.3-47 scales_0.5.0 [57] hms_0.4.0 plot3D_1.1.1 inline_0.3.15 RColorBrewer_1.1-2 [61] BBmisc_1.11 geohash_0.3.0 yaml_2.1.19 curl_3.1 [65] memoise_1.1.0 reticulate_1.7.1 gridExtra_2.3 loo_2.0.0 [69] keras_2.1.6.9001 stringi_1.1.6 highr_0.6 tensorflow_1.5.0.9001 [73] checkmate_1.8.5 lhs_0.16 rlang_0.2.0 pkgconfig_2.0.1 [77] matrixStats_0.53.1 evaluate_0.10.1 lattice_0.20-35 bindr_0.1 [81] htmlwidgets_1.0 tidyselect_0.2.4 plyr_1.8.4 magrittr_1.5 [85] R6_2.2.2 pillar_1.1.0 haven_1.1.0 whisker_0.3-2 [89] foreign_0.8-69 withr_2.1.2 survival_2.41-3 tibbletime_0.1.0.9001 [93] modelr_0.1.1 crayon_1.3.4 utf8_1.1.3 plotly_4.7.1 [97] rmarkdown_1.9 grid_3.4.3 readxl_1.0.0 data.table_1.10.4-3 [101] git2r_0.20.0 ReinforcementLearning_1.0.2 digest_0.6.15 xtable_1.8-2 [105] httpuv_1.3.5 openssl_1.0.1 pool_0.1.4 stats4_3.4.3 [109] munsell_0.4.3 viridisLite_0.3.0
Fail to run example at https://github.com/rmcelreath/glmer2stan#2-binomial-with-varying-intercepts
Input:
Error:
According to this issue: https://github.com/stan-dev/rstan/issues/118, it seems rstan/tidyr extract() namespace conflict.
SessionInfo: