brms: An R Package for Bayesian Multilevel Models Using Stan
Citations
4,497 citations
Cites background or methods from "brms: An R Package for Bayesian Mul..."
...…with predictors of zero-inflation, but they are relatively slow (as we will show) because they rely on Markov chain Monte Carlo (MCMC) sampling (Bürkner, 2017; Hadfield, 2010). gamlss is a flexible package that fits generalized additive models with predictors on all parameters of a…...
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...Several R packages are available for fitting zero-inflated models: pscl, INLA, MCMCglmm, glmmADMB, mgcv, brms, and gamlss (Table 1; Zeileis et al., 2008; Rue et al., 2009; Hadfield, 2010; Skaug et al., 2012; Wood et al., 2016; Bürkner, 2017; Stasinopoulos et al., 2017)....
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...We compared the estimates of fixed effects and the amount of time required for fitting the same model in INLA, MCMCglmm, glmmADMB, mgcv, and brms (Rue et al., 2009; Hadfield, 2010; Skaug et al., 2012; Wood et al., 2016; Bürkner, 2017)....
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...The MCMCglmm and brms packages can fit zero-inflated GLMMs with predictors of zero-inflation, but they are relatively slow (as we will show) because they rely on Markov chain Monte Carlo (MCMC) sampling (Bürkner, 2017; Hadfield, 2010)....
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...For Bayesian methods, the important aspect of timing is sampling efficiency (minimum effective samples per unit time, Bürkner, 2017), but this is not compatible with the MLE methods, so we limit our presentation of the timings of the Bayesian methods....
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1,463 citations
Cites background or methods from "brms: An R Package for Bayesian Mul..."
...In the control argument we increase adapt_delta to get rid of a few divergent transitions (cf. Stan Development Team, 2017b; Bürkner, 2017)....
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...The brms package (Bürkner, 2017) presented in this paper aims to remove these hurdles for a wide range of regression models by allowing the user to benefit from the merits of Stan by using extended lme4-like formula syntax (Bates et al., 2015), with which many R users are familiar....
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...The first is explained in Bürkner (2017), while the latter three are documented in help(brmsformula)....
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...A general overview of the package is given in Bürkner (2017)....
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...The models described in Bürkner (2017) are a sub-class of the models described here....
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547 citations
505 citations
Cites methods from "brms: An R Package for Bayesian Mul..."
...…generated by a variety of models objects, including popular modeling packages such as rstanarm (Goodrich, Gabry, Ali, & Brilleman, 2018), brms (Bürkner, 2017), BayesFactor (Morey & Rouder, 2018), and emmeans (Lenth, 2019), thus making it a useful tool supporting the usage and development of…...
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434 citations
References
272,030 citations
50,607 citations
"brms: An R Package for Bayesian Mul..." refers methods in this paper
...These are lme4 (Bates et al. 2015) and MCMCglmm (HadĄeld 2010), which are possibly the most general and widely applied R packages for MLMs, as well as rstanarm (Gabry and Goodrich 2016) and rethinking (McElreath 2016), which are both based on Stan....
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35,161 citations
18,761 citations
"brms: An R Package for Bayesian Mul..." refers methods in this paper
...Furthermore, Gibbs-sampling requires priors to be conjugate to the likelihood of parameters in order to work efficiently (Gelman et al. 2014), thus reducing the freedom of the researcher in choosing a prior that reĆects his or her beliefs....
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...…primarily using combinations of Metropolis-Hastings updates (Metropolis, Rosenbluth, Rosenbluth, Teller, and Teller 1953; Hastings 1970) and Gibbs-sampling (Geman and Geman 1984; Gelfand and Smith 1990), sometimes also coupled with slice-sampling (Damien, WakeĄeld, and Walker 1999; Neal 2003)....
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...With the exception of the latter, all of these programs are primarily using combinations of Metropolis-Hastings updates (Metropolis, Rosenbluth, Rosenbluth, Teller, and Teller 1953; Hastings 1970) and Gibbs-sampling (Geman and Geman 1984; Gelfand and Smith 1990), sometimes also coupled with slice-sampling (Damien, WakeĄeld, and Walker 1999; Neal 2003)....
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...With the exception of the latter, all of these programs are primarily using combinations of Metropolis-Hastings updates (Metropolis, Rosenbluth, Rosenbluth, Teller, and Teller 1953; Hastings 1970) and Gibbs-sampling (Geman and Geman 1984; Gelfand and Smith 1990), sometimes also coupled with slice-sampling (Damien, Wakefield, and Walker 1999; Neal 2003)....
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14,965 citations
"brms: An R Package for Bayesian Mul..." refers methods in this paper
...…all of these programs are primarily using combinations of Metropolis-Hastings updates (Metropolis, Rosenbluth, Rosenbluth, Teller, and Teller 1953; Hastings 1970) and Gibbs-sampling (Geman and Geman 1984; Gelfand and Smith 1990), sometimes also coupled with slice-sampling (Damien, WakeĄeld, and…...
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