rstanarm

Package: rstanarm
Type: Package
Title: Bayesian Applied Regression Modeling via Stan
Version: 2.10.1
Date: 2016-06-24
Authors@R: c(person("Jonah", "Gabry", email = "jsg2201@columbia.edu", role = "aut"),
person("Trustees of", "Columbia University", role = "cph"),
person("R Core", "Deveopment Team", role = "cph",
comment = "R/pp_data.R, R/stan_aov.R"),
person("Douglas", "Bates", role = "cph", comment = "R/pp_data.R"),
person("Martin", "Maechler", role = "cph", comment = "R/pp_data.R"),
person("Ben", "Bolker", role = "cph", comment = "R/pp_data.R"),
person("Steve", "Walker", role = "cph", comment = "R/pp_data.R"),
person("Brian", "Ripley", role = "cph",
comment = "R/stan_aov.R, R/stan_polr.R"),
person("William", "Venables", role = "cph", comment = "R/stan_polr.R"),
person("Ben", "Goodrich", email = "benjamin.goodrich@columbia.edu",
role = c("cre", "aut")))
Description: Estimates pre-compiled regression models using the 'rstan' package, which provides
the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the
customary R syntax with a formula and data.frame plus some additional arguments for priors.
License: GPL (>= 3)
Depends: R (>= 3.0.2), Rcpp (>= 0.12.0), methods
Imports: ggplot2 (>= 2.0.0), lme4 (>= 1.1-8), loo (>= 0.1.6), Matrix,
nlme (>= 3.1-124), rstan (>= 2.10.1), shinystan (>= 2.2.0),
stats, utils
Suggests: arm, gamm4, gridExtra, HSAUR3, KernSmooth, knitr, MASS,
rmarkdown, roxygen2, testthat (>= 1.0.2)
LinkingTo: StanHeaders (>= 2.10.0-2), rstan (>= 2.10.1), BH (>=
1.58.0), Rcpp (>= 0.12.0), RcppEigen
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
URL: https://groups.google.com/forum/#!forum/stan-users,
http://mc-stan.org/
BugReports: https://github.com/stan-dev/rstanarm/issues
RoxygenNote: 5.0.1
Packaged: 2016-06-24 17:54:22 UTC; goodrich
Author: Jonah Gabry [aut],
Trustees of Columbia University [cph],
R Core Deveopment Team [cph] (R/pp_data.R, R/stan_aov.R),
Douglas Bates [cph] (R/pp_data.R),
Martin Maechler [cph] (R/pp_data.R),
Ben Bolker [cph] (R/pp_data.R),
Steve Walker [cph] (R/pp_data.R),
Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R),
William Venables [cph] (R/stan_polr.R),
Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Repository: CRAN
Date/Publication: 2016-06-25 19:07:48

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rstanarm' ...
** package 'rstanarm' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I"`"/home/ddbj/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/StanHeaders/include" -I"/home/ddbj/local/lib64/R/library/rstan/include" -I"/home/ddbj/local/lib64/R/library/BH/include" -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"   -fpic  -g -O2  -c Modules.cpp -o Modules.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o rstanarm.so Modules.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/rstanarm/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'rstanarm'
    finding HTML links ... done
    adapt_delta                             html  
    as.matrix.stanreg                       html  
    example_model                           html  
    family.stanreg                          html  
    formula.stanreg                         html  
    get_y                                   html  
    log_lik                                 html  
    loo.stanreg                             html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/loo.stanreg.Rd:80: missing file link 'plot.loo'
    model.frame.stanreg                     html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/model.frame.stanreg.Rd:12: missing file link 'model.frame.merMod'
    model.matrix.stanreg                    html  
    neg_binomial_2                          html  
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    pairs.stanreg                           html  
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    plot.stanreg                            html  
    posterior_interval                      html  
    posterior_linpred                       html  
    posterior_predict                       html  
    posterior_vs_prior                      html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/posterior_vs_prior.Rd:41: missing file link 'scale_color_manual'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/posterior_vs_prior.Rd:42: missing file link 'scale_color_brewer'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/posterior_vs_prior.Rd:53: missing file link 'geom_pointrange'
    pp_check                                html  
    pp_validate                             html  
    predict.stanreg                         html  
    print.kfold                             html  
    print.stanreg                           html  
    priors                                  html  
    rstanarm-datasets                       html  
    rstanarm-package                        html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-package.Rd:41: missing file link 'sampling'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-package.Rd:78: missing file link 'optimizing'
    rstanarm-plots                          html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:22: missing file link 'stan_trace'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:23: missing file link 'stan_hist'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:24: missing file link 'stan_dens'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:25: missing file link 'stan_scat'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:27: missing file link 'stan_diag'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:28: missing file link 'stan_rhat'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:30: missing file link 'stan_ess'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:32: missing file link 'stan_mcse'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/rstanarm-plots.Rd:33: missing file link 'stan_ac'
    se                                      html  
    shinystan                               html  
    stan_gamm4                              html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_gamm4.Rd:23: missing file link 'sampling'
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    stan_glm                                html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_glm.Rd:44: missing file link 'sampling'
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Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_glm.Rd:45: missing file link 'optimizing'
    stan_glmer                              html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_glmer.Rd:39: missing file link 'sampling'
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    stan_lm                                 html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_lm.Rd:38: missing file link 'sampling'
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Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_lm.Rd:39: missing file link 'optimizing'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_lm.Rd:84: missing file link 'lm.wfit'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_lm.Rd:110: missing file link 'lm.fit'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_lm.Rd:111: missing file link 'lm.wfit'
    stan_polr                               html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_polr.Rd:30: missing file link 'sampling'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_polr.Rd:30: missing file link 'vb'
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stan_polr.Rd:31: missing file link 'optimizing'
    stanreg-methods                         html  
Rd warning: /tmp/RtmpZEOxnT/R.INSTALL4793425d47f/rstanarm/man/stanreg-methods.Rd:92: missing file link 'confint.default'
    stanreg-objects                         html  
    summary.stanreg                         html  
    terms.stanreg                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rstanarm)
Making 'packages.html' ... done