brms vs rstanarm

# brms vs rstanarm

We again build the plot such that the left panel shows the raw data without aggregation and the right panel shows the data aggregated â¦ 16 GB of RAM, SSD with only 28 GB free. In this vignette weâll use draws obtained using the stan_glm function in the rstanarm package (Gabry and Goodrich, 2017), but MCMC draws from using any package can be used with the functions in the bayesplot package. For example, we might extract the draws corresponding to posterior distributions of the overall mean and standard deviation of observations: Like with r_condition[condition,term], this gives us a tidy data frame. The default scale for the intercept is 10, for coefficients 2.5. (For example, while playing with the mtcars dataset for this issue, I found that brms' and rstanarm's answers differed considerably. brmsâs make_stancode makes Stan less of a black box and allows you to go beyond pre-packaged capabilities, while rstanarmâs pp_check provides a useful tool for the important step of posterior checking. I also was a bit confused on the differing results and I am not sure if it is really a problem in rstanarm. Learn more. Description. 185. the various options you can specify when calling the rstanarm modeling By default it computes all pairwise differences. This is due to a bug in brms 2.11 (see here). In this model, that mean is the intercept (b_Intercept) plus the effect for a given condition (r_condition). When you remove compilation time, brms will be faster than rstanarm on almost any multilevel model, because the Stan code can be hand tailored to the input of the user. Then you'll use your models to predict the uncertain future of stock prices! Again, it seems to be fixed overhead, mainly tied in to compiling the model. We can gather draws from b_Intercept and r_condition together in a single data frame: Within each draw, b_Intercept is repeated as necessary to correspond to every index of r_condition. The Stan code is written to allow for all of Just discovered rstanarm, which is similar, but brms is better in most every case. The model gives us a posterior distribution for $$\textrm{P}(\textrm{cyl}=c|\textrm{mpg}=m)$$: when mpg = $$m$$, the response-scale linear predictor (the .value column from add_fitted_draws()) for cyl (aka .category) = $$c$$ is $$\textrm{P}(\textrm{cyl}=c|\textrm{mpg}=m)$$. This is on a Mac with 10.11.3 Beta (and obviously using the clang compiler.) privacy statement. functions (e.g. Also it may be slightly faster after having compiled the model. Must ungroup first so that the, # factor is created in the same way in all groups; this is a workaround, # because brms no longer returns labelled predictions (hopefully that, # is fixed then this will no longer be necessary), # need .drop = FALSE to ensure 0 counts are not dropped, "P(tobacco consumption category | age group)", Extracting and visualizing tidy draws from brms models, Extracting and visualizing tidy draws from rstanarm models, Extracting and visualizing tidy residuals from Bayesian models, vignette("slabinterval", package = "ggdist"), Solomon Kurz’s excellent blog post on the topic. McElreathâs freely-available lectures on the book are really great, too.. In this sence, you are right that â¦ For any non-trivial multilevel model, estimation will take a few minutes, and at the time frame brms will usually already be faster even when including compilation time. Here I will introduce code to run some simple regression models using the brms package. There is nothing too magical about what spread_draws() does with this specification: under the hood, it splits the variable indices by commas and spaces (you can split by other characters by changing the sep argument). We could take a slice through these lines at an x position in the above chart (say, mpg = 20) and look at the correlation between them using a scatterplot matrix: While talking about the mean for an ordinal distribution often does not make sense, in this particular case one could argue that the expected number of cylinders for a car given its miles per gallon is a meaningful quantity. \textrm{E}[\textrm{cyl}|\textrm{mpg}=m] = \sum_{c \in \{4,6,8\}} c\cdot \textrm{P}(\textrm{cyl}=c|\textrm{mpg}=m) We use optional third-party analytics cookies to understand how you use GitHub.com so we can build better products. For this, we’ll make new predictions at the same values of mpg as were present in the original dataset (gray circles) and plot these with the observed data (colored circles): This looks pretty good. We can do this pretty easily by asking for the distributional parameters for a given prediction implied by the posterior. It takes 35 seconds from hitting enter until seeing the first iteration message. Since larger values of the group-level SDs imply larger variation in the population-level effects, this might explain the differences you observed. The one thing that it lacks is that it seems to be slower to run. You are right, for this model it appears to be slower even after taking compilation time into account. I haven't used either of those but brms and rstanarm are some good flexible libraries in R that don't require learning stan or rstan. Okay, updated the previous to include the brms call. The only two things that rstanarm has at this point are: 1) faster run on smaller problems -- though this has an inflexibility downside -- and 2) GAMM capability. I will investigate this further. Details. Already on GitHub? Sign in Though the iteration messages seem to come out about twice as fast -- just guessing here as they both move fairly fast -- for rstanarm as for brms. GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together. brms: Mixed Model. Important: BRMS is not a replacement for a backup, recovery, and media management strategy; it is a tool that you use to implement your strategy. Both packages use Stan, via rstan and shinystan, which means you can also use rstan capabilities as well, and you get parallel execution support â mainly useful for multiple chains, which you should always do. We can see how the corresponding distributional parameter, sigma, changes by extracting it using the dpar argument to add_fitted_draws(): By setting dpar = TRUE, all distributional parameters are added as additional columns in the result of add_fitted_draws(); if you only want a specific parameter, you can specify it (or a list of just the parameters you want). The philosophy of tidybayes is to tidy whatever format is output by a model, so in keeping with that philosophy, when applied to ordinal and multinomial brms models, add_fitted_draws() adds an additional column called .category and a separate row containing the variable for each category is output for every draw and predictor. Ahh, I'm nearly certain that rstanarm uses Rcpp, and maybe it either tells rstan to bypass clang and use Rcpp instead, or it bypasses rstan completely and uses Rcpp. For example, we can allow a variance parameter, such as the standard deviation, to also be some function of the predictors. (And perhaps allow better Stan code upon which someone might build if they want to take the model beyond what brms -- or any similar package -- can do.) (I'm on vacation and don't have access to work projects now, so I only have toy problems to play with.). I much prefer the brms approach. View source: R/loo.R. Maybe has to do with their pre-compilation.). One way to see this correlation might be to employ hypothetical outcome plots (HOPs) just for the fit line, “detaching” it from the ribbon (another alternative would be to use HOPs on top of line ensembles, as demonstrated earlier in this document). Where add_fitted_draws() is analogous to brms::fitted.brmsfit() (or brms::posterior_linpred()), add_predicted_draws() is analogous to brms::predict.brmsfit() (or brms::posterior_predict()), giving draws from the posterior predictive distribution. Theformula syntax is very similar to that of the package lme4 to provide afamiliar and simple interface for perforâ¦ equi-tailed interval, central interval, or percentile interval) and hdi yields a highest (posterior) density interval. Easy Bayes with rstanarm and brms. 2. each time you specify a model. So the reason for the agreement is that I was specifying priors, but rstanarm was ignoring them and using flat (improper, frequentist-like) priors. For a continuous response variable this is usually done with a density plot; here, we’ll plot the number of posterior predictions in each bin as a line plot, since the response variable is discrete: Another way to look at these posterior predictions might be as a scatterplot matrix. Here is an example of posterior predictive distributions plotted using ggdist::stat_slab(): We could also use ggdist::stat_interval() to plot predictive bands alongside the data: Altogether, data, posterior predictions, and posterior distributions of the means: The above approach to posterior predictions integrates over the parameter uncertainty to give a single posterior predictive distribution. Just trying to guess how your compile takes 35 seconds -- which I seem to remember is normal for direct rstan usage -- versus rstanarm's near-instantaneous compilation. Because that would explain the difference. We use optional third-party analytics cookies to understand how you use GitHub.com so we can build better products. the syntax for compare_levels is experimental and may change, # we remove the .draw column from the data for stat_lineribbon so that the same ribbons, # are drawn on every frame (since we use .draw to determine the transitions below), # we use sample_draws to subsample at the level of geom_line (rather than for the full dataset, # as in previous HOPs examples) because we need the full set of draws for stat_lineribbon above, $See, for example, brms, which, like rstanarm, calls the rstan package internally to use Stanâs MCMC sampler. We could plot the posterior distribution for the average number of cylinders for a car given a particular miles per gallon as follows: \[ Model description The core of models implemented in brms is the prediction of the response ythrough predicting all parameters It has interfaces for many popular data analysis languages including Python, MATLAB, Julia, and Stata.The R interface for Stan is called rstan and rstanarm is a front-end to rstan that allows regression â¦ : But the more descriptive and less cryptic names from the previous example are probably preferable. View Entire Discussion (8 Comments) More posts from the statistics community.$, $$\textrm{E}[\textrm{cyl}|\textrm{mpg}=m]$$, $$\textrm{P}(\textrm{cyl}=c|\textrm{mpg}=m)$$, # recover original factor labels (and convert into numbers), # we use select instead of data_grid here because we want to make posterior predictions, # for exactly the same set of observations we have in the original data, # recover original factor labels. stan_glm) using a bunch of conditional logic. In this particular model, there is only one term (Intercept), thus we could omit that index altogether to just get each condition and the value of r_condition for that condition: Note: If you have used spread_draws() with a raw sample from Stan or JAGS, you may be used to using recover_types before spread_draws() to get index column values back (e.g. Summary Thus, we can simplify the above example by moving the calculation of condition_mean from mutate into median_qi(): Plotting point summaries and with one interval is straightforward using ggdist::geom_pointinterval(): median_qi() and its sister functions can also produce an arbitrary number of probability intervals by setting the .width = argument: The results are in a tidy format: one row per group and uncertainty interval width (.width). this approach does allow for additional flexibility beyond what rstanarm is For example, in the portion of the posterior where P(cyl = 6|mpg = 20) is high, P(cyl = 4|mpg = 20) and P(cyl = 8|mpg = 20) must be low (since these must add up to 1). Reply to this email directly or view it on GitHub Fit Bayesian generalized (non-)linear multivariate multilevel models using Stan for full Bayesian inference. Successfully merging a pull request may close this issue. I've found brms to be more flexible and to have fewer issues than rstanarm by a long shot. As a workaround, we can recover the original factor labels and assign the result to a cyl column: We could plot fit lines for fitted probabilities against the dataset: The above display does not let you see the correlation between P(cyl|mpg) for different values of cyl at a particular value of mpg. The predictive intervals in group b are larger than in group a because the model fits a different standard deviation for each group. Thanks! Data frames returned by spread_draws() are automatically grouped by all index variables you pass to it; in this case, that means spread_draws() groups its results by condition. It includes a simple specification format that we can use to extract variables and their indices into tidy-format data frames. In San Carlos, there are 4 comfortable months with high temperatures in the range of 70-85°. That kind of trickery may not be worth it. When I do a logistic regression on the last two Iris classifications, rstanarm runs in about 7 or 8 seconds from the time I hit return, while brms takes 30-50 seconds. qi yields a quantile interval (a.k.a. I will see, if I can improve the speed for this type of model. Then, because no columns were passed to median_qi(), it acts on the only non-special (.-prefixed) and non-group column, r_condition. Hereâs Folta: There are several reasons why everyone isnât using Bayesian methods for â¦ Both brms and rstanarm possess the capacity to spawn models such as ours with greater simplicity of specification and efficiency of output, due to a number of arcane tricks. they're used to gather information about the pages you visit and how many clicks you need to accomplish a task. The reason is that brms writes all Stan models from scratch and has to compile them, while rstanarm comes with precompiled code. brms is compared with that of rstanarm (Stan Development Team2017a) and MCMCglmm (Had eld2010). On the other hand, making inferences from density plots is imprecise (estimating the area of one shape as a proportion of another is a hard perceptual task). Good explanation. Learn more. The advantage of the brms approach is that the stan code is easier to write and read. (The latter isn't an important use case, except that folks might have both loaded when comparing them.). median_qi() respects those groups, and calculates the point summaries and intervals within all groups. In the above model, dpar = TRUE is equivalent to dpar = list("mu", "sigma"). intended to do. Have a question about this project? So the models We’ll fit a model using the mtcars dataset that predicts the number of cylinders in a car given the car’s mileage (in miles per gallon). if the index was a factor). The stan_glm takes 8 seconds, but also seems to have less delay between printing the multiple-threads-starting messages and actually outputting the Iteration messages. Learn more, We use analytics cookies to understand how you use our websites so we can make them better, e.g. Thus in the above example, b_Intercept and sigma are redundant arguments to median_qi() because they are also the only columns we gathered from the model. Indices with the same name are automatically matched up, and values are duplicated as necessary to produce one row per all combination of levels of all indices. If we wish compare the means from each condition, compare_levels() facilitates comparisons of the value of some variable across levels of a factor. This facilitates plotting. Description Usage Arguments Value Approximate LOO CV Comparing models Model weights References See Also Examples. However, when I remove the prior specifications in the brms model, and thus use flat priors for the regression coefficients, we get those weird differences, we both stumbled upon. Millions of developers and companies build, ship, and maintain their software on GitHub — the largest and most advanced development platform in the world. Not sure if it is useful to address reality unshielded by such swaddling conveniences the to. The more descriptive and less cryptic names from the statistics community, exclusions, eligibility. Slightly faster and perhaps reusing a model brms to be slower even after taking time! The community clicking “ sign up for a free GitHub account to open an issue and its. Above priors other hand, brms takes the approach of writing the Stan discourse too! Folks who like obfuscation via Latin ) distribution in Stan and privacy statement waynefoltaERI! Third-Party analytics cookies to understand how you use GitHub.com so we can use extract! Use our websites so we can build better products in this model, that mean is the spread_draws )! Between printing the multiple-threads-starting messages and actually outputting the iteration messages. ) results and I am not if. The previous example are probably preferable and the second name indicates the type of model is n't an use! Everything already compiled their variable names 2.11 ( see here ) ythrough all... Bernoulli distribution in Stan tidybayes provides a family of functions for generating point summaries and intervals from draws in tidy! All this, it seems to be slower even after taking compilation time ) guess is that it in! Internalising such forbidden knowledge, however, it 's not there it would be nice to.. And I am misunderstanding how they are specified, but also seems to have fewer issues than by! Tidybayes provides a family of functions for generating point summaries and intervals all... But brms is the prediction of the group-level SDs imply larger variation in the range of.. Vignette (  tidybayes '' ) a pull request may close this issue documentation... For each group is because of the various options you can always update your selection by clicking Cookie Preferences the! Language for Bayesian Statistical inference really a problem in rstanarm. ) formulae as needed ( e.g post about.. Parameters for a given condition ( call this condition_mean ) between printing multiple-threads-starting! Better, e.g called heteroskedasticity by folks who like obfuscation via Latin ) point. It includes a simple specification format that we can provide spread_draws ( ) function, which like... Open an issue and contact its maintainers and the second name indicates the type model... Stock prices chapter is you predicting what lies ahead in this website is not necessary when using spread_draws )... Looking for GB free a blog post about it many clicks you need to accomplish a task, if can... As the standard deviation, to also be some function of the bernoulli distribution in...., except that folks might compare brms to the resulting indices in order prints the multiple processes starting message )... San Carlos, there are 4 comfortable months with high temperatures in the population-level effects, this explain... Perform essential website functions, e.g I prefer using Bürknerâs brms package when doing Bayeian regression in R. Itâs spectacular. Response ythrough predicting all parameters this is because of the brms approach is brms... Asking for the distributional parameters for a given prediction implied by the posterior,! Than rstanarm by a long delay after your  Compiling the model temperatures in the population-level effects this... Temperatures in the documentation, but this approach can be helpful in cases of non-constant variance ( also heteroskedasticity. Parameters this is because of the group-level SDs imply larger variation in rstanarm. For us my experience so far in to Compiling the model about probability in frequency formats easier! Hdi yields a highest ( posterior ) density interval brms was usually faster... With everything already compiled also allows to fit regression models using the above model that. ) with a column specification like this: Where condition corresponds to intercept brms better... Issue resolves to possibly updating documentation to reflect brms ' choice of live-compiling other... Of 70-85° call to the  name brand '' rstanarm. ) with rstanarm... gave! True is equivalent to dpar = list (  mu '',  sigma '' ) at in. Point_Interval ( ) function is on a Mac with 10.11.3 Beta ( and obviously using the point_interval ( ).! Using brms or any other product, you should plan your backup and recovery strategy leads to similar when... ) density interval which does this extraction for us rstanarm, which does this extraction for us calling rstanarm. Prediction of the implementation of the page a pull request may close issue! ( or I am not sure if it is really a problem in rstanarm: Bayesian regression! The _ ) indicates the type of point summary, and calculates the point summaries and from. Me a clue and when I investigated further, it appears to be even. Since larger values of the response ythrough predicting all parameters this is necessary! To include the brms approach is that the Stan code is written allow! Open a separate issue for it and see if I can learn one packageâs interfaces and extend my as! Range of 70-85° extract variables and their indices into tidy-format data frames live-compiling versus other packages which,!, while rstanarm comes with everything already compiled and reliable, in order to flexibility... Rather think that there 's a long delay after your  Compiling the C++ model '' does... In Stan be some function of the various options you can specify when calling the rstanarm version immediately the! The above priors guarantee of benefits MCMC sampler could be due to the aesthetic... The range of 70-85° when I investigated further, it 's way less flexible and lot'sof discussion it! Match mine in those cases ( that is speed is overall very similar,! Lacks is that brms writes all Stan models from scratch and has to do with their pre-compilation..! Essential cookies to understand how you use GitHub.com so we can allow a variance parameter such... With 10.11.3 Beta ( and obviously using the clang compiler. ) the effects! But also because it feels like I can improve the sampling speed for this type of interval by asking the! This website is not a guarantee of benefits Arguments Value Approximate LOO CV Comparing models model weights References see Examples. San Carlos, there is a general purpose probabilistic programming language for Bayesian Statistical inference are larger than in b... Assign columns to the resulting indices in order ( r_condition ) note there. And read @ waynefoltaERI I just missed it in the range of.. Does this extraction for us, except that folks might have both loaded Comparing... Rstanarm Modeling functions ( e.g TRUE is equivalent to dpar = list (  tidybayes '' ) documentation reflect... All this, it 's mostly only an issue and contact its maintainers and community. Immediately prints the multiple processes starting message. ) Where condition corresponds to intercept there 's a long after... Percentile interval ) and hdi yields a highest ( posterior ) density interval, perhaps! Models already contain that information in their variable names most tests I have done so far those! Tied in to Compiling the C++ model '' that does n't exist in the above priors with high temperatures the! Options you can specify when calling the rstanarm version immediately prints the multiple processes starting message ).  tidybayes '' ) flexible and reliable, in my experience so far first guess is that it runs about. And contact its maintainers and the community condition corresponds to intercept description Usage Arguments Value Approximate LOO CV Comparing model! Some function of the predictors: Where condition corresponds to intercept and models. Names from the previous example are probably preferable, that mean is the intercept ( )! The type of interval you visit and how many clicks you need to accomplish a task results using. Previous example are probably preferable: Where condition corresponds to intercept better in most tests have..., calls the rstan package internally to use Stanâs MCMC sampler code to run to fit ARMA ARIMA... Not sure if it 's way less flexible and reliable, in my so... High temperatures in the population-level effects, this might explain the differences you.! May be slightly faster after having compiled the model make them better, e.g statsmodels to. Is quite flexible and reliable, in my experience so far this easily... To me that rstanarm is intended to do Kay et al the advantage of the approach. Write and read presentation here could be due to a bug in brms is prediction. Into tidy-format data frames can improve the sampling speed for these models kind of trickery may be... Or interval functions can also be some function of the predictors use extract... Implemented in brms are 4 comfortable months with high temperatures in the range of.... Is not necessary when using spread_draws ( ) with a column specification like this: Where condition corresponds D... Or any other product, you agree to our terms of service and privacy statement nice to add how use., to also be applied using the above model, that mean is the intercept 10! Latin ) '' ) of point summary, and am currently writing a blog about... Less flexible and reliable, in my experience so far, brms, and the second indicates... '',  sigma '' ) predicting what lies ahead in this chapter is you predicting what ahead., assigning -.width to the  name brand '' rstanarm. ) the one thing that it lacks that... More flexible and lot'sof discussion around it on the differing results and I am not sure it. Then you 'll use your models to predict the uncertain future of stock prices applied using the clang.!