brms | brms R package for Bayesian generalized multivariate non | Data Visualization library

 by   paul-buerkner R Version: v2.19.0 License: GPL-2.0

kandi X-RAY | brms Summary

kandi X-RAY | brms Summary

brms is a R library typically used in Analytics, Data Visualization applications. brms has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has medium support. You can download it from GitHub.

The brms package provides an interface to fit Bayesian generalized (non-)linear multivariate multilevel models using Stan, which is a C++ package for performing full Bayesian inference (see The formula syntax is very similar to that of the package lme4 to provide a familiar and simple interface for performing regression analyses. A wide range of response distributions are supported, allowing users to fit – among others – linear, robust linear, count data, survival, response times, ordinal, zero-inflated, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, missing value imputation, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Multivariate models (i.e., models with multiple response variables) can be fit, as well. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks, cross-validation, and Bayes factors.
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              brms has a medium active ecosystem.
              It has 1120 star(s) with 169 fork(s). There are 49 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 126 open issues and 1193 have been closed. On average issues are closed in 41 days. There are 5 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of brms is v2.19.0

            kandi-Quality Quality

              brms has no bugs reported.

            kandi-Security Security

              brms has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              brms is licensed under the GPL-2.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              brms releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

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            brms Key Features

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            brms Examples and Code Snippets

            No Code Snippets are available at this moment for brms.

            Community Discussions

            QUESTION

            Request to help understand an apparent discrepancy between tidybayes::add_predicted_draws and brms::posterior_predict
            Asked 2021-Jan-21 at 11:38

            I am using the Howell1 dataset from rethinking package.

            ...

            ANSWER

            Answered 2021-Jan-21 at 11:38

            It turned out that the discrepancy was arising due to seed setting not being honored by brms::posterior_predict

            Upon discussing with developer of brms package in github, he root caused the issue to be the following:

            If you have set options(mc.cores = ), posterior_predict will evaluate in parallel by default, unless you change the core argument. On windows, parallel execution is done via parallel::parLapply and I don't know how that function respects seeds, if at all. When executing the code in serial (with 1 core) the results are reproducible.

            Once I set the mc.cores to 1, I no longer see the discrepancy between posterior_predict and add_predicted_draws.

            Hence I am marking the issue as resolved.

            The relevant github links are:

            1. https://github.com/mjskay/tidybayes/issues/280
            2. https://github.com/paul-buerkner/brms/issues/1073

            Source https://stackoverflow.com/questions/65756978

            QUESTION

            How to save numerous brms fit as distinct R objects or Rds/Rda file?
            Asked 2020-Oct-30 at 03:20

            I'm trying to fit a Bayesian model using brms::brm() replacing the prior of one parameter in the model one after another by purrr::map2() (I have 63 priors for that parameter). I can 'theoretically' save the each fitted model as a distinct object in the global environment (i.e. my workspace) by list2env(), thanks to the answer of my previous question. By list2env(), the objects (brmsfits) would be saved after the all 63 iterations are done. However, when I run the whole code, always I get an error message saying Error in scan(con, nlines = 1, sep = ",", quiet = TRUE) : could not allocate memory (0 Mb) in C function 'R_AllocStringBuffer' and no brmsfit object is stored in the global environment, although the model fitting seems to be done 63 times, as much as my prior exist.

            Therefore, I would like to save each brmsfit object as an R object and as an .Rds or .Rda file immediately after its iteration done as to avoid such a memory problem. But, what should I do to realise that?

            MWE

            Note that the following command is just a "schematic" example, with publicly available data, of what I'm trying to do. It will work without the problem I mentioned above, since the data and the model in brm() in this example are way simpler and the number of priors is much fewer than what I'm tackling.

            ...

            ANSWER

            Answered 2020-Oct-29 at 18:53

            I think you could use something like the following (which is a simpler version that avoids where your data comes from, variable names, model specification, and all that)

            Source https://stackoverflow.com/questions/64589572

            QUESTION

            BRM model compiling but returning model object
            Asked 2020-Oct-05 at 16:03

            I am building a hierarchical model using the BRMS package in R, and having trouble fitting a model successfully. When running the code it outputs "Compiling Stan program...", runs for about five minutes, and then stops. There are no other messages or errors, but there is no model object.

            Some reproducible code from an example online, though I imagine this is not code related since the same issue occurs in my model and this one downloaded from a tutorial. When running the following code the only console output is:

            ...

            ANSWER

            Answered 2020-Jul-23 at 18:15

            After more digging, it turns out this is a bug introduced in the latest release of rstan (v 2.21.1), reverting back to the last version (2.19.3) has solved the issue for me.

            Source https://stackoverflow.com/questions/63025052

            QUESTION

            Caterpillar plot of posterior brms samples: Order factors in a ggdist plot (stat_slab)
            Asked 2020-Sep-10 at 02:52

            I ran a bayesian linear mixed model with brms and can plot the estimates nicely but I can't figure out how to order the single-subject estimates based on the mean of the posterior samples (so as to get a caterpillar plot). This is what I've done.

            Toy data:

            ...

            ANSWER

            Answered 2020-Sep-10 at 02:52

            Two points for consideration:

            1. Ungroup the result from spread_draws, otherwise you won't be able to reorder the levels of subject;
            2. Use fct_reorder from the forcats package in tidyverse. It's designed for this exact purpose.

            Source https://stackoverflow.com/questions/63813576

            QUESTION

            Area within ROPE region does not have homogeneous color fill when using stat_slab
            Asked 2020-Aug-30 at 05:42

            I ran some multilevel models using brms and am following the examples here to plot draws from the posterior for each parameter.

            Here's a toy dataset to reproduce the problem

            ...

            ANSWER

            Answered 2020-Aug-28 at 02:53

            Your plot looks fine and gives me the following output. I am running R 4.0.2 and RStudio version 1.2.5 on windows. However, my output looks like yours if I expand it horizontally.

            Source https://stackoverflow.com/questions/63622108

            QUESTION

            Combine ggplot's facet_grid with bmrs conditional_effects
            Asked 2020-Aug-27 at 20:11

            I have a (toy) dataset where each subject did 10 repetitions of a task, where they had to guess the distance between two points shown. In this dataset I have the ratings given by external judges (not the participants themselves) on the performance of each of those subjects.

            ...

            ANSWER

            Answered 2020-Aug-27 at 20:11

            I ended up doing this by creating all plots separately in a loop, making sure the xlim and ylim are all the same, saving them into a list, then plotting them with ggarrange and annotate_figure (both from ggpubr). It doesn't look as pretty without the facet labels, but it's good enough!

            Source https://stackoverflow.com/questions/63199197

            QUESTION

            Brms: plotting three-way interaction in ordinal regression
            Asked 2020-Aug-25 at 16:04

            (crossposting from mcstan)

            Operating system: Ubuntu 18.04.5 LTS

            brms version: 2.13.5

            I have run a Bayesian ordinal regression using Buerkner's brms package (which provides a user-friendly interface to stan) and now am trying to plot the effect of three categorical predictors (Morphology, Cluster2, CountryExperiment) on the response variable (a Likert scale with 7 points). Following closely the information written by Paul Buerkner on conditional_effects for his package, I used the following code:

            ...

            ANSWER

            Answered 2020-Aug-25 at 16:04

            I managed to get what I want using the ordinal regression's posterior samples to reconstruct the response's probabilities for all cells in the factorial design. I used Equation (5) p 79 in Buerkner & Vuorre's paper to find the probability of each of my 7 responses (along a 7-point Likert scale) for each of the 12 conditions (all combinations of my three variables). Equation (5) defines the probability P(Response=k) of each response category k as a function of (i) the 6 thresholds that split the underlying continuous scale, (ii) the predictor variables, and (iii) the corresponding regression coefficients. It was tedious but it works... It would be nice to develop a function that does that automatically.

            Source https://stackoverflow.com/questions/63574471

            QUESTION

            Negative binomial regression in R using brm causing error when using multiple cores
            Asked 2020-May-27 at 09:32

            I am calculating a negative binomial regression using the brm function from the brms package. As this takes quite some time, I would like to use multiple cores as suggested in the documentation.

            ...

            ANSWER

            Answered 2020-May-27 at 04:37

            This is a known issue that has to do with RStudio. Check out these related posts on the Stan forums and Github.

            Github: https://github.com/rstudio/rstudio/issues/6692

            Stan forums: https://discourse.mc-stan.org/t/r-4-0-0-and-cran-macos-binaries/13989/13

            Source https://stackoverflow.com/questions/61987580

            QUESTION

            Change linetype aestetics conditional effects
            Asked 2020-May-08 at 14:48

            I ran a brms model with two continuous predictors and am trying to plot the effect. Specifically, I want to customize the linetype of the predictor to make it photocopy safe.

            I took a look at the following topic already: https://discourse.mc-stan.org/t/change-aesthetics-conditional-effects/13500 but there it is only explained how to change the color of the line and the color of the ribbon, but I want to change the linetype of the lines using for example scale_linetype_manual.

            I use the reproducible example also used in that topic:

            ...

            ANSWER

            Answered 2020-May-08 at 14:48

            I have found a simple yet elegant solution to this problem by converting the list produced by conditional_effects into a dataframe

            Source https://stackoverflow.com/questions/61677785

            QUESTION

            Maven update version of specific dependency
            Asked 2020-Mar-03 at 11:59

            I am trying to update the version of particular dependency in my Spring Boot project using the below command. However the dependency version is not getting updated. This is the command I am using:

            ...

            ANSWER

            Answered 2018-Feb-06 at 16:39

            The goal versions:use-latest-snapshots updates only release versions, see Advancing dependency versions :

            versions:use-latest-snapshots searches the pom for all non-SNAPSHOT versions which have been a newer -SNAPSHOT version and replaces them with the latest -SNAPSHOT version.

            but in your POM is a snapshot version:

            Spring Boot project's dependency:

            Source https://stackoverflow.com/questions/48605114

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

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            You can download it from GitHub.

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