Martin Mächler

Bio: Martin Mächler is an academic researcher from ETH Zurich. The author has contributed to research in topics: Generalized linear mixed model & Copula (probability theory). The author has an hindex of 15, co-authored 27 publications receiving 42993 citations. Previous affiliations of Martin Mächler include École Polytechnique Fédérale de Lausanne.

Parallel and other simulations in R made easy: An end-to-end study

Abstract: It is shown how to set up, conduct, and analyze large simulation studies with the new R package simsalapar = simulations simplified and launched parallel. A simulation study typically starts with determining a collection of input variables and their values on which the study depends, such as sample sizes, dimensions, types and degrees of dependence, estimation methods, etc. Computations are desired for all com- binations of these variables. If conducting these computations sequentially is too time- consuming, parallel computing can be applied over all combinations of select variables. The final result object of a simulation study is typically an array. From this array, sum- mary statistics can be derived and presented in terms of (flat contingency or LATEX) tables or visualized in terms of (matrix-like) figures. The R package simsalapar provides several tools to achieve the above tasks. Warnings and errors are dealt with correctly, various seeding methods are available, and run time is measured. Furthermore, tools for analyzing the results via tables or graphics are pro- vided. In contrast to rather minimal examples typically found in R packages or vignettes, an end-to-end, not-so-minimal simulation problem from the realm of quantitative risk management is given. The concepts presented and solutions provided by simsalapar may be of interest to students, researchers, and practitioners as a how-to for conducting real- istic, large-scale simulation studies in R. Also, the development of the package revealed useful improvements to R itself, which are available in R 3.0.0.

A Graphical Goodness-of-Fit Test for Dependence Models in Higher Dimensions

Abstract: This article introduces a graphical goodness-of-fit test for copulas in more than two dimensions. The test is based on pairs of variables and can thus be interpreted as a first-order approximation of the underlying dependence structure. The idea is to first transform pairs of data columns with the Rosenblatt transform to bivariate standard uniform distributions under the null hypothesis. This hypothesis can be graphically tested with a matrix of bivariate scatterplots, Q-Q plots, or other transformations. Furthermore, additional information can be encoded as background color, such as measures of association or (approximate) p-values of tests of independence. The proposed goodness-of-fit test is designed as a basic graphical tool for detecting deviations from a postulated, possibly high-dimensional, dependence model. Various examples are given and the methodology is applied to a financial dataset. An implementation is provided by the R package copula. Supplementary material for this article is available on...

Parallel and Other Simulations in R Made Easy: An End-to-End Study

Abstract: It is shown how to set up, conduct, and analyze large simulation studies with the new R package simsalapar (= simulations simplified and launched parallel). A simulation study typically starts with determining a collection of input variables and their values on which the study depends. Computations are desired for all combinations of these variables. If conducting these computations sequentially is too time-consuming, parallel computing can be applied over all combinations of select variables. The final result object of a simulation study is typically an array. From this array, summary statistics can be derived and presented in terms of flat contingency or LATEX tables or visualized in terms of matrix-like figures. The R package simsalapar provides several tools to achieve the above tasks. Warnings and errors are dealt with correctly, various seeding methods are available, and run time is measured. Furthermore, tools for analyzing the results via tables or graphics are provided. In contrast to rather minimal examples typically found in R packages or vignettes, an end-to-end, not-so-minimal simulation problem from the realm of quantitative risk management is given. The concepts presented and solutions provided by simsalapar may be of interest to students, researchers, and practitioners as a how-to for conducting realistic, large-scale simulation studies in R.

Likelihood inference for Archimedean copulas

Abstract: Explicit functional forms for the generator derivatives of well-known one-parameter Archimedean copulas are derived. These derivatives are essential for likelihood inference as they appear in the copula density, conditional distribution functions, or the Kendall distribution function. They are also required for several asymmetric extensions of Archimedean copulas such as Khoudraji-transformed Archimedean copulas. Access to the generator derivatives makes maximum-likelihood estimation for Archimedean copulas feasible in terms of both precision and run time, even in large dimensions. It is shown by simulation that the root mean squared error is decreasing in the dimension. This decrease is of the same order as the decrease in sample size. Furthermore, confidence intervals for the parameter vector are derived. Moreover, extensions to multi-parameter Archimedean families are given. All presented methods are implemented in the open-source R package nacopula and can thus easily be accessed and studied.

Estimating Distributions with a Fixed Number of Modes

Abstract: A new approach for non- or semi-parametric density estimation allows to specify modes and antimodes The new smoother is a Maximum Penalized Likelihood (MPL) estimate with a novel roughness penalty It penalizes a relative change of curvature which allows considering modes and inflection points For a given number of modes, the score function, \(l^\prime = (\log f)^\prime\) can be represented as \({l^\prime }\left( x \right) = \pm (x - {w_1}) \cdots (x - {w_m})\cdot{\text{ }}exp{h_l}(x)\), a semiparametric term with parameters w j (model order m) and nonparametric part h l(·) The MPL variational problem is equivalent to a differential equation with boundary conditions The exponential and normal distributions are smoothest limits of the new estimator for zero and one mode, respectively

lmerTest Package: Tests in Linear Mixed Effects Models

Abstract: One of the frequent questions by users of the mixed model function lmer of the lme4 package has been: How can I get p values for the F and t tests for objects returned by lmer? The lmerTest package extends the 'lmerMod' class of the lme4 package, by overloading the anova and summary functions by providing p values for tests for fixed effects. We have implemented the Satterthwaite's method for approximating degrees of freedom for the t and F tests. We have also implemented the construction of Type I - III ANOVA tables. Furthermore, one may also obtain the summary as well as the anova table using the Kenward-Roger approximation for denominator degrees of freedom (based on the KRmodcomp function from the pbkrtest package). Some other convenient mixed model analysis tools such as a step method, that performs backward elimination of nonsignificant effects - both random and fixed, calculation of population means and multiple comparison tests together with plot facilities are provided by the package as well.

glmmTMB Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling

Abstract: Count data can be analyzed using generalized linear mixed models when observations are correlated in ways that require random effects However, count data are often zero-inflated, containing more zeros than would be expected from the typical error distributions We present a new package, glmmTMB, and compare it to other R packages that fit zero-inflated mixed models The glmmTMB package fits many types of GLMMs and extensions, including models with continuously distributed responses, but here we focus on count responses glmmTMB is faster than glmmADMB, MCMCglmm, and brms, and more flexible than INLA and mgcv for zero-inflated modeling One unique feature of glmmTMB (among packages that fit zero-inflated mixed models) is its ability to estimate the Conway-Maxwell-Poisson distribution parameterized by the mean Overall, its most appealing features for new users may be the combination of speed, flexibility, and its interface’s similarity to lme4

brms: An R Package for Bayesian Multilevel Models Using Stan

Abstract: The brms package implements Bayesian multilevel models in R using the probabilistic programming language Stan. A wide range of distributions and link functions are supported, allowing users to fit - among others - linear, robust linear, binomial, Poisson, survival, ordinal, zero-inflated, hurdle, and even non-linear models all in a multilevel context. Further modeling options include autocorrelation of the response variable, user defined covariance structures, censored data, as well as meta-analytic standard errors. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. In addition, model fit can easily be assessed and compared with the Watanabe-Akaike information criterion and leave-one-out cross-validation.

The effect of human mobility and control measures on the COVID-19 epidemic in China.

Abstract: The ongoing coronavirus disease 2019 (COVID-19) outbreak expanded rapidly throughout China. Major behavioral, clinical, and state interventions were undertaken to mitigate the epidemic and prevent the persistence of the virus in human populations in China and worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, affected COVID-19 spread in China. We used real-time mobility data from Wuhan and detailed case data including travel history to elucidate the role of case importation in transmission in cities across China and to ascertain the impact of control measures. Early on, the spatial distribution of COVID-19 cases in China was explained well by human mobility data. After the implementation of control measures, this correlation dropped and growth rates became negative in most locations, although shifts in the demographics of reported cases were still indicative of local chains of transmission outside of Wuhan. This study shows that the drastic control measures implemented in China substantially mitigated the spread of COVID-19.

Qgraph: Network visualizations of relationships in psychometric data

Abstract: We present the qgraph package for R, which provides an interface to visualize data through network modeling techniques. For instance, a correlation matrix can be represented as a network in which each variable is a node and each correlation an edge; by varying the width of the edges according to the magnitude of the correlation, the structure of the correlation matrix can be visualized. A wide variety of matrices that are used in statistics can be represented in this fashion, for example matrices that contain (implied) covariances, factor loadings, regression parameters and p values. qgraph can also be used as a psychometric tool, as it performs exploratory and confirmatory factor analysis, using sem and lavaan; the output of these packages is automatically visualized in qgraph ,w hich may aid the interpretation of results. In this article, we introduce qgraph by applying the package functions to data from the NEO-PI-R, a widely used personality questionnaire.