brms | brms R package for Bayesian generalized multivariate non | Data Visualization library
kandi X-RAY | brms Summary
kandi X-RAY | brms Summary
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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QUESTION
I am using the Howell1 dataset from rethinking package.
...ANSWER
Answered 2021-Jan-21 at 11:38It 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:
QUESTION
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 (brmsfit
s) 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?
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 18:53I 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)
QUESTION
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 18:15After 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.
QUESTION
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 02:52Two points for consideration:
- Ungroup the result from
spread_draws
, otherwise you won't be able to reorder the levels ofsubject
; - Use
fct_reorder
from theforcats
package in tidyverse. It's designed for this exact purpose.
QUESTION
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 02:53Your 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.
QUESTION
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 20:11I 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!
QUESTION
(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 16:04I 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.
QUESTION
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 04:37This 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
QUESTION
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 14:48I have found a simple yet elegant solution to this problem by converting the list produced by conditional_effects into a dataframe
QUESTION
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 16:39The 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:
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