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                <text>Application of Equal Local Levels to Improve Q-Q Plot Testing Bands with R Package qqconf</text>
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                <text>: Q-Q plots, equal local levels, Kolmogorov-Smirnov, GWAS, multiple testing, global&#13;
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                <text>Quantile-quantile (Q-Q) plots are often difficult to interpret because it is unclear&#13;
how large the deviation from the theoretical distribution must be to indicate a lack of&#13;
fit. Most Q-Q plots could benefit from the addition of meaningful global testing bands,&#13;
but the use of such bands unfortunately remains rare because of the drawbacks of current&#13;
approaches and packages. These drawbacks include incorrect global type-I error rate, lack&#13;
of power to detect deviations in the tails of the distribution, relatively slow computation&#13;
for large data sets, and limited applicability. To solve these problems, we apply the&#13;
equal local levels global testing method, which we have implemented in the R Package&#13;
qqconf, a versatile tool to create Q-Q plots and probability-probability (P-P) plots in a&#13;
wide variety of settings, with simultaneous testing bands rapidly created using recentlydeveloped algorithms. qqconf can easily be used to add global testing bands to Q-Q plots&#13;
made by other packages. In addition to being quick to compute, these bands have a variety&#13;
of desirable properties, including accurate global levels, equal sensitivity to deviations in&#13;
all parts of the null distribution (including the tails), and applicability to a range of null&#13;
distributions. We illustrate the use of qqconf in several applications: assessing normality&#13;
of residuals from regression, assessing accuracy of p values, and use of Q-Q plots in&#13;
genome-wide association studies.</text>
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                <text>University of Chicago</text>
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                <text>bootstrap, R, time series, unit roots</text>
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                <text>Unit root tests form an essential part of any time series analysis. We provide practitioners with a single, unified framework for comprehensive and reliable unit root testing&#13;
in the R package bootUR. The package’s backbone is the popular augmented DickeyFuller test paired with a union of rejections principle, which can be performed directly on&#13;
single time series or multiple (including panel) time series. Accurate inference is ensured&#13;
through the use of bootstrap methods. The package addresses the needs of both novice&#13;
users, by providing user-friendly and easy-to-implement functions with sensible default&#13;
options, as well as expert users, by giving full user-control to adjust the tests to one’s&#13;
desired settings. Our parallelized C++ implementation ensures that all unit root tests&#13;
are scalable to datasets containing many time series.</text>
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                <text>Stephan Smeekes</text>
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                <text>https://www.jstatsoft.org/article/view/v106i12</text>
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                <text>Broken Stick Model for Irregular Longitudinal Data</text>
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                <text>brokenstick, R, linear mixed model, repeated measures, linear B-spline, personalized estimation, growth curve analysis, critical periods, time-to-time correlation, profile&#13;
analysis, curve interpolation, multiple imputation, curve matching, two-step method, KasimRaudenbush method</text>
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                <text>Many longitudinal studies collect data that have irregular observation times, often&#13;
requiring the application of linear mixed models with time-varying outcomes. This paper&#13;
presents an alternative that splits the quantitative analysis into two steps. The first step&#13;
converts irregularly observed data into a set of repeated measures through the broken stick&#13;
model. The second step estimates the parameters of scientific interest from the repeated&#13;
measurements at the subject level. The broken stick model approximates each subject’s&#13;
trajectory by a series of connected straight lines. The breakpoints, specified by the user,&#13;
divide the time axis into consecutive intervals common to all subjects. Specification of&#13;
the model requires just three variables: time, measurement and subject. The model is&#13;
a special case of the linear mixed model, with time as a linear B-spline and subject as&#13;
the grouping factor. The main assumptions are: Subjects are exchangeable, trajectories&#13;
between consecutive breakpoints are straight, random effects follow a multivariate normal&#13;
distribution, and unobserved data are missing at random. The R package brokenstick&#13;
v2.5.0 offers tools to calculate, predict, impute and visualize broken stick estimates. The&#13;
package supports two optimization methods, including options to constrain the variancecovariance matrix of the random effects. We demonstrate six applications of the model:&#13;
Detection of critical periods, estimation of the time-to-time correlations, profile analysis,&#13;
curve interpolation, multiple imputation and personalized prediction of future outcomes&#13;
by curve matching</text>
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                <text>Stef van Buuren</text>
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                <text>https://www.jstatsoft.org/article/view/v106i07</text>
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                <text>Netherlands Organization for Applied Scientific Research TNO, Leiden&#13;
University of Utrecht</text>
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                <text>Fajar bagus W</text>
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                <text>Disaggregation modeling, or downscaling, has become an important discipline in epidemiology. Surveillance data, aggregated over large regions, is becoming more common,&#13;
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understand spatial patterns. Disaggregation regression models use response data aggregated over large heterogeneous regions to make predictions at fine-scale over the region by&#13;
using fine-scale covariates to inform the heterogeneity. This paper presents the R package&#13;
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                <text>curve fitting, dose-response, drug sensitivity, logistic function, nonlinear regression.</text>
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                <text>Analysis of dose-response data is an important step in many scientific disciplines,&#13;
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drda is designed to facilitate the analysis of dose-response data by implementing efficient&#13;
and accurate functions with a familiar interface. With drda it is possible to fit models by&#13;
the method of least squares, perform goodness-of-fit tests, and conduct model selection.&#13;
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in the least-squares sense. This result is achieved by a smart choice of the starting point&#13;
in the optimization algorithm and by implementing the Newton method with a trust&#13;
region with analytical gradients and Hessian matrices. In this article, drda is presented&#13;
through the description of its methodological components and examples of its user-friendly&#13;
functions. Performance is evaluated using both synthetic data and a real, large-scale drug&#13;
sensitivity screening dataset</text>
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                <text>University of Helsinki</text>
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                <text>: lasso, elastic net, ℓ1 penalty, regularization path, coordinate descent, generalized&#13;
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                <text>The lasso and elastic net are popular regularized regression models for supervised&#13;
learning. Friedman, Hastie, and Tibshirani (2010) introduced a computationally efficient&#13;
algorithm for computing the elastic net regularization path for ordinary least squares&#13;
regression, logistic regression and multinomial logistic regression, while Simon, Friedman,&#13;
Hastie, and Tibshirani (2011) extended this work to Cox models for right-censored data.&#13;
We further extend the reach of the elastic net-regularized regression to all generalized&#13;
linear model families, Cox models with (start, stop] data and strata, and a simplified&#13;
version of the relaxed lasso. We also discuss convenient utility functions for measuring&#13;
the performance of these fitted models</text>
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                <text>gfpop: An R Package for Univariate Graph-Constrained Change-Point Detection</text>
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                <text>change-point detection, constrained inference, maximum likelihood inference, dynamic programming, robust losses</text>
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                <text>In a world with data that change rapidly and abruptly, it is important to detect those&#13;
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version of an algorithm recently proposed by Hocking, Rigaill, Fearnhead, and Bourque&#13;
(2020) for penalized maximum likelihood inference of constrained multiple change-point&#13;
models. This algorithm can be used to pinpoint the precise locations of abrupt changes&#13;
in large data sequences. There are many application domains for such models, such as&#13;
medicine, neuroscience or genomics. Often, practitioners have prior knowledge about the&#13;
changes they are looking for. For example in genomic data, biologists sometimes expect&#13;
peaks: up changes followed by down changes. Taking advantage of such prior information&#13;
can substantially improve the accuracy with which we can detect and estimate changes.&#13;
Hocking et al. (2020) described a graph framework to encode many examples of such&#13;
prior information and a generic algorithm to infer the optimal model parameters, but&#13;
implemented the algorithm for just a single scenario. We present the gfpop package that&#13;
implements the algorithm in a generic manner in R/C++. gfpop works for a user-defined&#13;
graph that can encode prior assumptions about the types of changes that are possible and&#13;
implements several loss functions (Gauss, Poisson, binomial, biweight, and Huber). We&#13;
then illustrate the use of gfpop on isotonic simulations and several applications in biology.&#13;
For a number of graphs the algorithm runs in a matter of seconds or minutes for 105 data&#13;
points.&#13;
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                <text>Université d’Évry</text>
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                <text>nearest neighbors, likelihood-based method, heterogeneous intrinsic dimension,&#13;
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for most dimensionality reduction techniques. In order to make these novel estimators&#13;
easily accessible, the package contains a small number of high-level functions that rely on&#13;
a broader set of efficient, low-level routines. Generally speaking, intRinsic encompasses&#13;
models that fall into two categories: homogeneous and heterogeneous intrinsic dimension&#13;
estimators. The first category contains the two nearest neighbors estimator, a method&#13;
derived from the distributional properties of the ratios of the distances between each data&#13;
point and its first two closest neighbors. The functions dedicated to this method carry out&#13;
inference under both the frequentist and Bayesian frameworks. In the second category, we&#13;
find the heterogeneous intrinsic dimension algorithm, a Bayesian mixture model for which&#13;
an efficient Gibbs sampler is implemented. After presenting the theoretical background,&#13;
we demonstrate the performance of the models on simulated datasets. This way, we can&#13;
facilitate the exposition by immediately assessing the validity of the results. Then, we&#13;
employ the package to study the intrinsic dimension of the Alon dataset, obtained from a&#13;
famous microarray experiment. Finally, we show how the estimation of homogeneous and&#13;
heterogeneous intrinsic dimensions allows us to gain valuable insights into the topological&#13;
structure of a dataset.</text>
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                <text>Università Cattolica del Sacro Cuore</text>
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                <text>penalized regression, correlated variables, hierarchical clustering, group selection,&#13;
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                <text>The R package MLGL, standing for multi-layer group-Lasso, implements a new procedure of variable selection in the context of redundancy between explanatory variables,&#13;
which holds true with high-dimensional data. A sparsity assumption is made that postulates that only a few variables are relevant for predicting the response variable. In this&#13;
context, the performance of classical Lasso-based approaches strongly deteriorates as the&#13;
redundancy increases.&#13;
The proposed approach combines variables aggregation and selection in order to improve interpretability and performance. First, a hierarchical clustering procedure provides&#13;
at each level a partition of the variables into groups. Then, the set of groups of variables&#13;
from the different levels of the hierarchy is given as input to group-Lasso, with weights&#13;
adapted to the structure of the hierarchy. At this step, group-Lasso outputs sets of candidate groups of variables for each value of the regularization parameter.&#13;
The versatility offered by package MLGL to choose groups at different levels of the&#13;
hierarchy a priori induces a high computational complexity. MLGL, however, exploits the&#13;
structure of the hierarchy and the weights used in group-Lasso to greatly reduce the final&#13;
time cost. The final choice of the regularization parameter – and therefore the final choice&#13;
of groups – is made by a multiple hierarchical testing procedure.</text>
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                <text>Fajar bagus W</text>
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                <text>network meta-analysis, R, inconsistency, component network meta-analysis.&#13;
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                <text>Network meta-analysis compares different interventions for the same condition, by&#13;
combining direct and indirect evidence derived from all eligible studies. Network metaanalysis has been increasingly used by applied scientists and it is a major research topic for&#13;
methodologists. This article describes the R package netmeta, which adopts frequentist&#13;
methods to fit network meta-analysis models. We provide a roadmap to perform network&#13;
meta-analysis, along with an overview of the main functions of the package. We present&#13;
three worked examples considering different types of outcomes and different data formats&#13;
to facilitate researchers aiming to conduct network meta-analysis with netmeta</text>
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                <text>Universität Freiburg</text>
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                <text>Fajar bagus W</text>
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          </element>
          <element elementId="44">
            <name>Language</name>
            <description>A language of the resource</description>
            <elementTextContainer>
              <elementText elementTextId="88895">
                <text>English</text>
              </elementText>
            </elementTextContainer>
          </element>
          <element elementId="51">
            <name>Type</name>
            <description>The nature or genre of the resource</description>
            <elementTextContainer>
              <elementText elementTextId="88896">
                <text>Text</text>
              </elementText>
            </elementTextContainer>
          </element>
        </elementContainer>
      </elementSet>
    </elementSetContainer>
  </item>
</itemContainer>
