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                <text>Bayesian Item Response Modeling in R with brms and Stan</text>
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                <text>: item response theory, Bayesian statistics, R, Stan, brms.&#13;
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                <text>Item response theory (IRT) is widely applied in the human sciences to model persons’&#13;
responses on a set of items measuring one or more latent constructs. While several&#13;
R packages have been developed that implement IRT models, they tend to be restricted to&#13;
respective pre-specified classes of models. Further, most implementations are frequentist&#13;
while the availability of Bayesian methods remains comparably limited. I demonstrate&#13;
how to use the R package brms together with the probabilistic programming language&#13;
Stan to specify and fit a wide range of Bayesian IRT models using flexible and intuitive&#13;
multilevel formula syntax. Further, item and person parameters can be related in both a&#13;
linear or non-linear manner. Various distributions for categorical, ordinal, and continuous&#13;
responses are supported. Users may even define their own custom response distribution&#13;
for use in the presented framework. Common IRT model classes that can be specified&#13;
natively in the presented framework include 1PL and 2PL logistic models optionally also&#13;
containing guessing parameters, graded response and partial credit ordinal models, as&#13;
well as drift diffusion models of response times coupled with binary decisions. Posterior&#13;
distributions of item and person parameters can be conveniently extracted and postprocessed. Model fit can be evaluated and compared using Bayes factors and efficient&#13;
cross-validation procedures.</text>
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                <text>University of Stuttgart</text>
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                <text>Fajar bagus W</text>
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                  <text>VOLUME 100 Tahun 2021</text>
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                <text>Efficient Bayesian Structural Equation Modeling in Stan</text>
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                <text> Bayesian SEM, blavaan, JAGS, MCMC, structural equation model, Stan.</text>
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                <text>Structural equation models comprise a large class of popular statistical models, including factor analysis models, certain mixed models, and extensions thereof. Model&#13;
estimation is complicated by the fact that we typically have multiple interdependent response variables and multiple latent variables (which may also be called random effects&#13;
or hidden variables), often leading to slow and inefficient posterior sampling. In this paper, we describe and illustrate a general, efficient approach to Bayesian SEM estimation&#13;
in Stan, contrasting it with previous implementations in R package blavaan (Merkle and&#13;
Rosseel 2018). After describing the approaches in detail, we conduct a practical comparison under multiple scenarios. The comparisons show that the new approach is clearly&#13;
better. We also discuss ways that the approach may be extended to other models that&#13;
are of interest to psychometricians.</text>
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                <text>Edgar C. Merkle</text>
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            <description>A related resource from which the described resource is derived</description>
            <elementTextContainer>
              <elementText elementTextId="88035">
                <text>https://www.jstatsoft.org/article/view/v100i06</text>
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            <name>Publisher</name>
            <description>An entity responsible for making the resource available</description>
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              <elementText elementTextId="88036">
                <text>University of Missouri</text>
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            <name>Date</name>
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                <text>November 2021</text>
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                <text>Fajar Bagus</text>
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                  <text>VOLUME 100 Tahun 2021</text>
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                  <text>Fajar bagus W</text>
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                <text>ABCpy: A High-Performance Computing Perspective to Approximate Bayesian Computation</text>
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            <description>The topic of the resource</description>
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                <text>ABC, HPC, Spark, MPI, parallel, imbalance, Python library.&#13;
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                <text>ABCpy is a highly modular scientific library for approximate Bayesian computation&#13;
(ABC) written in Python. The main contribution of this paper is to document a software&#13;
engineering effort that enables domain scientists to easily apply ABC to their research&#13;
without being ABC experts; using ABCpy they can easily run large parallel simulations&#13;
without much knowledge about parallelization. Further, ABCpy enables ABC experts to&#13;
easily develop new inference schemes and evaluate them in a standardized environment&#13;
and to extend the library with new algorithms. These benefits come mainly from the&#13;
modularity of ABCpy. We give an overview of the design of ABCpy and provide a performance evaluation concentrating on parallelization. This points us towards the inherent&#13;
imbalance in some of the ABC algorithms. We develop a dynamic scheduling MPI implementation to mitigate this issue and evaluate the various ABC algorithms according to&#13;
their adaptability towards high-performance computing</text>
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                <text>Ritabrata Dutta</text>
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              <elementText elementTextId="88046">
                <text>https://www.jstatsoft.org/article/view/v100i07</text>
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            <description>An entity responsible for making the resource available</description>
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                <text>University of Warwick</text>
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            <name>Date</name>
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                <text>November 2021</text>
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                <text>Fajar bagus W</text>
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                <text>English</text>
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                  <text>VOLUME 100 Tahun 2021</text>
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                <elementText elementTextId="87970">
                  <text>https://www.jstatsoft.org/issue/view/v100</text>
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                  <text>Fajar bagus W</text>
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                <text>pexm: A JAGS Module for Applications Involving the Piecewise Exponential Distribution</text>
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                <text>: MCMC, Bayesian inference, semiparametric, survival analysis</text>
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                <text>In this study, we present a new module built for users interested in a programming&#13;
language similar to BUGS to fit a Bayesian model based on the piecewise exponential (PE)&#13;
distribution. The module is an extension to the open-source program JAGS by which a&#13;
Gibbs sampler can be applied without requiring the derivation of complete conditionals&#13;
and the subsequent implementation of strategies to draw samples from unknown distributions. The PE distribution is widely used in the fields of survival analysis and reliability.&#13;
Currently, it can only be implemented in JAGS through methods to indirectly specify the&#13;
likelihood based on the Poisson or Bernoulli probabilities. Our module provides a more&#13;
straightforward implementation and is thus more attractive to the researchers aiming to&#13;
spend more time exploring the results from the Bayesian inference rather than implementing the Markov Chain Monte Carlo algorithm. For those interested in extending JAGS,&#13;
this work can be seen as a tutorial including important information not well investigated&#13;
or organized in other materials. Here, we describe how to use the module taking advantage&#13;
of the interface between R and JAGS. A short simulation study is developed to ensure&#13;
that the module behaves well and a real illustration, involving two PE models, exhibits a&#13;
context where the module can be used in practice.&#13;
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                <text>Vinícius D. Mayrink</text>
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                <text>Generalized additive models (GAMs) are flexible non-linear regression models, which&#13;
can be fitted efficiently using the approximate Bayesian methods provided by the mgcv R&#13;
package. While the GAM methods provided by mgcv are based on the assumption that&#13;
the response distribution is modeled parametrically, here we discuss more flexible methods&#13;
that do not entail any parametric assumption. In particular, this article introduces the&#13;
qgam package, which is an extension of mgcv providing fast calibrated Bayesian methods&#13;
for fitting quantile GAMs (QGAMs) in R. QGAMs are based on a smooth version of the&#13;
pinball loss of Koenker (2005), rather than on a likelihood function, hence jointly achieving&#13;
satisfactory accuracy of the quantile point estimates and coverage of the corresponding&#13;
credible intervals requires adopting the specialized Bayesian fitting framework of Fasiolo,&#13;
Wood, Zaffran, Nedellec, and Goude (2021b). Here we detail how this framework is&#13;
implemented in qgam and we provide examples illustrating how the package should be&#13;
used in practi</text>
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                <text>: Bayesian inference, diversity patterns, hierarchical models, generalized linear models, Markov chain Monte Carlo, structured residual variance, variance patterns</text>
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                <text>Traditional regression models, including generalized linear mixed models, focus on understanding the deterministic factors that affect the mean of a response variable. Many&#13;
biological studies seek to understand non-deterministic patterns in the variance or dispersion of a phenotypic or ecological response variable. We describe a new R package,&#13;
dalmatian, that provides methods for fitting double hierarchical generalized linear models&#13;
incorporating fixed and random predictors of both the mean and variance. Models are&#13;
fit via Markov chain Monte Carlo sampling implemented in either JAGS or nimble and&#13;
the package provides simple functions for monitoring the sampler and summarizing the&#13;
results. We illustrate these functions through an application to data on food delivery by&#13;
breeding pied flycatchers (Ficedula hypoleuca). Our intent is that this package makes it&#13;
easier for practitioners to implement these models without having to learn the intricacies&#13;
of Markov chain Monte Carlo methods.</text>
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            <description>An entity responsible for making the resource available</description>
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                <text>University of Western&#13;
Ontario&#13;
</text>
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                <text>: seemingly unrelated regression, Bayesian multivariate regression, structured covariance matrix, Markov random field prior, multi-omics data.</text>
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                <text>In molecular biology, advances in high-throughput technologies have made it possible to study complex multivariate phenotypes and their simultaneous associations with&#13;
high-dimensional genomic and other omics data, a problem that can be studied with&#13;
high-dimensional multi-response regression, where the response variables are potentially&#13;
highly correlated. To this purpose, we recently introduced several multivariate Bayesian&#13;
variable and covariance selection models, e.g., Bayesian estimation methods for sparse&#13;
seemingly unrelated regression for variable and covariance selection. Several variable selection priors have been implemented in this context, in particular the hotspot detection&#13;
prior for latent variable inclusion indicators, which results in sparse variable selection for&#13;
associations between predictors and multiple phenotypes. We also propose an alternative,&#13;
which uses a Markov random field (MRF) prior for incorporating prior knowledge about&#13;
the dependence structure of the inclusion indicators. Inference of Bayesian seemingly unrelated regression (SUR) by Markov chain Monte Carlo methods is made computationally&#13;
feasible by factorization of the covariance matrix amongst the response variables.&#13;
In this paper we present BayesSUR, an R package, which allows the user to easily&#13;
specify and run a range of different Bayesian SUR models, which have been implemented in&#13;
C++ for computational efficiency. The R package allows the specification of the models in&#13;
a modular way, where the user chooses the priors for variable selection and for covariance&#13;
selection separately. We demonstrate the performance of sparse SUR models with the&#13;
hotspot prior and spike-and-slab MRF prior on synthetic and real data sets representing&#13;
eQTL or mQTL studies and in vitro anti-cancer drug screening studies as examples for&#13;
typical applications.&#13;
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                <text>Zhi Zhao&#13;
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                <text>https://www.jstatsoft.org/article/view/v100i11</text>
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                <text>Fajar bagus W</text>
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