scholarly journals On the control of psychological networks

2020 ◽  
Author(s):  
Teague R Henry ◽  
Donald Robinaugh ◽  
Eiko I Fried
Keyword(s):  
Psychological Disorders ◽  
Real Data ◽  
R Package ◽  
Testing Procedure ◽  
Statistical Testing ◽  
Optimal Intervention ◽  
Potential Efficacy ◽  
Intervention Cost ◽  
Intervention Efficacy ◽  
Ema Data

The combination of network theory and network psychometric methods have opened up a variety of new ways to conceptualize and study psychological disorders. The idea of psychological disorders as dynamic systems has sparked interest in developing interventions based on results of network analytic tools. However, estimating a network model is not sufficient for determining which symptoms might be most effective to intervene upon, and is not sufficient for determining the potential efficacy of any given intervention. In this paper, we attempt to remedy this gap by introducing fundamental concepts in control theory to both methodologists and applied psychologists. We show how two controllability measures, average and modal controllability, can be used to select the best set of intervention targets. We provide a statistical testing procedure for determining if the dynamical systems of different people have the same optimal intervention targets. Following that, we show how intervention scientists can probe the effects of both theoretical and empirical interventions on networks derived from real data; demonstrate how simulations can be used to account for intervention cost and the desire to reduce specific symptoms; introduce a metric for evaluating intervention efficacy, the intervention efficacy ratio (IER); and showcase how between subject heterogeneity in intervention response can be evaluated. Every step is illustrated using rich clinical EMA data from a sample of subjects undergoing treatment for complicated grief, with a focus on the outcome `Suicidal Ideation'. All methods are implemented in an open-source R package ''netcontrol'', and complete code for replicating the analyses in this manuscript is available at https://osf.io/f268v/.

scholarly journals Testing Differences Between Pathogen Compositions with Small Samples and Sparse Data

2017 ◽  
Vol 107 (10) ◽  
pp. 1199-1208 ◽  
Author(s):  
Samuel Soubeyrand ◽  
Vincent Garreta ◽  
Caroline Monteil ◽  
Frédéric Suffert ◽  
Henriette Goyeau ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Statistical Tests ◽  
Puccinia Triticina ◽  
Real Data ◽  
R Package ◽  
Testing Procedure ◽  
Small Samples ◽  
Disease Epidemiology ◽  
Significant Difference ◽  
Pathogen Populations

The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791 . A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.

scholarly journals Using Least-Squares Residuals to Assess the Stochasticity of Measurements—Example: Terrestrial Laser Scanner and Surface Modeling

2021 ◽  
Vol 5 (1) ◽  
pp. 59
Author(s):  
Gaël Kermarrec ◽  
Niklas Schild ◽  
Jan Hartmann
Keyword(s):  
Least Squares ◽  
Laser Scanner ◽  
Real Data ◽  
Point Clouds ◽  
Statistical Testing ◽  
Normal Vector ◽  
Engineering Structures ◽  
3D Point Clouds ◽  
Least Squares Adjustment ◽  
Correlation Parameters

Terrestrial laser scanners (TLS) capture a large number of 3D points rapidly, with high precision and spatial resolution. These scanners are used for applications as diverse as modeling architectural or engineering structures, but also high-resolution mapping of terrain. The noise of the observations cannot be assumed to be strictly corresponding to white noise: besides being heteroscedastic, correlations between observations are likely to appear due to the high scanning rate. Unfortunately, if the variance can sometimes be modeled based on physical or empirical considerations, the latter are more often neglected. Trustworthy knowledge is, however, mandatory to avoid the overestimation of the precision of the point cloud and, potentially, the non-detection of deformation between scans recorded at different epochs using statistical testing strategies. The TLS point clouds can be approximated with parametric surfaces, such as planes, using the Gauss–Helmert model, or the newly introduced T-splines surfaces. In both cases, the goal is to minimize the squared distance between the observations and the approximated surfaces in order to estimate parameters, such as normal vector or control points. In this contribution, we will show how the residuals of the surface approximation can be used to derive the correlation structure of the noise of the observations. We will estimate the correlation parameters using the Whittle maximum likelihood and use comparable simulations and real data to validate our methodology. Using the least-squares adjustment as a “filter of the geometry” paves the way for the determination of a correlation model for many sensors recording 3D point clouds.

Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities

2019 ◽  
Vol 36 (7) ◽  
pp. 2017-2024
Author(s):  
Weiwei Zhang ◽  
Ziyi Li ◽  
Nana Wei ◽  
Hua-Jun Wu ◽  
Xiaoqi Zheng
Keyword(s):  
Real Data ◽  
R Package ◽  
Differential Methylation ◽  
Least Square ◽  
Epigenetic Mechanism ◽  
Supplementary Information ◽  
Cpg Sites ◽  
Tumor Purity ◽  
Different Sources ◽  
Normal Controls

Abstract Motivation Inference of differentially methylated (DM) CpG sites between two groups of tumor samples with different geno- or pheno-types is a critical step to uncover the epigenetic mechanism of tumorigenesis, and identify biomarkers for cancer subtyping. However, as a major source of confounding factor, uneven distributions of tumor purity between two groups of tumor samples will lead to biased discovery of DM sites if not properly accounted for. Results We here propose InfiniumDM, a generalized least square model to adjust tumor purity effect for differential methylation analysis. Our method is applicable to a variety of experimental designs including with or without normal controls, different sources of normal tissue contaminations. We compared our method with conventional methods including minfi, limma and limma corrected by tumor purity using simulated datasets. Our method shows significantly better performance at different levels of differential methylation thresholds, sample sizes, mean purity deviations and so on. We also applied the proposed method to breast cancer samples from TCGA database to further evaluate its performance. Overall, both simulation and real data analyses demonstrate favorable performance over existing methods serving similar purpose. Availability and implementation InfiniumDM is a part of R package InfiniumPurify, which is freely available from GitHub (https://github.com/Xiaoqizheng/InfiniumPurify). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bing Song ◽  
August E. Woerner ◽  
John Planz
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Genetic Markers ◽  
Software Package ◽  
Tandem Repeats ◽  
Population Data ◽  
Real Data ◽  
R Package ◽  
Nucleotide Polymorphisms ◽  
Mutual Independence

Abstract Background Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. Results This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. Conclusion The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. Availability The R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

scholarly journals Implementation of the Omega (ω) Index to detect large-scale systematic cheating

2019 ◽  
Author(s):  
Alvin Vista
Keyword(s):  
Standardized Testing ◽  
Large Scale ◽  
Type I Error ◽  
R Package ◽  
Statistical Testing ◽  
System Level ◽  
Control Group ◽  
Type I ◽  
Data Contamination ◽  
Cheating Detection

Cheating detection is an important issue in standardized testing, especially in large-scale settings. Statistical approaches are often computationally intensive and require specialised software to conduct. We present a two-stage approach that quickly filters suspected groups using statistical testing on an IRT-based answer-copying index. We also present an approach to mitigate data contamination and improve the performance of the index. The computation of the index was implemented through a modified version of an open source R package, thus enabling wider access to the method. Using data from PIRLS 2011 (N=64,232) we conduct a simulation to demonstrate our approach. Type I error was well-controlled and no control group was falsely flagged for cheating, while 16 (combined n=12,569) of the 18 (combined n=14,149) simulated groups were detected. Implications for system-level cheating detection and further improvements of the approach were discussed.

scholarly journals Hierarchical correction of p-values via an ultrametric tree running Ornstein-Uhlenbeck process

2021 ◽  
Author(s):  
Antoine Bichat ◽  
Christophe Ambroise ◽  
Mahendra Mariadassou
Keyword(s):  
Multiple Testing ◽  
R Package ◽  
Statistical Testing ◽  
Uhlenbeck Process ◽  
Explanatory Variables ◽  
New Associations ◽  
Penalized Estimation ◽  
Ultrametric Tree ◽  
Ornstein Uhlenbeck Process ◽  
The Mean

AbstractStatistical testing is classically used as an exploratory tool to search for association between a phenotype and many possible explanatory variables. This approach often leads to multiple testing under dependence. We assume a hierarchical structure between tests via an Ornstein-Uhlenbeck process on a tree. The process correlation structure is used for smoothing the p-values. We design a penalized estimation of the mean of the Ornstein-Uhlenbeck process for p-value computation. The performances of the algorithm are assessed via simulations. Its ability to discover new associations is demonstrated on a metagenomic dataset. The corresponding R package is available from https://github.com/abichat/zazou.

scholarly journals Categorical Functional Data Analysis. The cfda R Package

Mathematics ◽  
2021 ◽  
Vol 9 (23) ◽  
pp. 3074
Author(s):  
Cristian Preda ◽  
Quentin Grimonprez ◽  
Vincent Vandewalle
Keyword(s):  
Functional Data ◽  
Multiple Correspondence Analysis ◽  
Real Data ◽  
Jump Process ◽  
R Package ◽  
Finite Basis ◽  
Data Set ◽  
Stochastic Jump ◽  
Finite Set ◽  
Infinite Set

Categorical functional data represented by paths of a stochastic jump process with continuous time and a finite set of states are considered. As an extension of the multiple correspondence analysis to an infinite set of variables, optimal encodings of states over time are approximated using an arbitrary finite basis of functions. This allows dimension reduction, optimal representation, and visualisation of data in lower dimensional spaces. The methodology is implemented in the cfda R package and is illustrated using a real data set in the clustering framework.

The asymptotic distribution of the Net Benefit estimator in presence of right-censoring

2021 ◽  
pp. 096228022110370
Author(s):  
Brice Ozenne ◽  
Esben Budtz-Jørgensen ◽  
Julien Péron
Keyword(s):  
Asymptotic Distribution ◽  
Nuisance Parameter ◽  
Real Data ◽  
R Package ◽  
Right Censoring ◽  
Drop Out ◽  
Net Benefit ◽  
Asymptotic Results ◽  
Finite Samples ◽  
Benefit Risk Assessment

The benefit–risk balance is a critical information when evaluating a new treatment. The Net Benefit has been proposed as a metric for the benefit–risk assessment, and applied in oncology to simultaneously consider gains in survival and possible side effects of chemotherapies. With complete data, one can construct a U-statistic estimator for the Net Benefit and obtain its asymptotic distribution using standard results of the U-statistic theory. However, real data is often subject to right-censoring, e.g. patient drop-out in clinical trials. It is then possible to estimate the Net Benefit using a modified U-statistic, which involves the survival time. The latter can be seen as a nuisance parameter affecting the asymptotic distribution of the Net Benefit estimator. We present here how existing asymptotic results on U-statistics can be applied to estimate the distribution of the net benefit estimator, and assess their validity in finite samples. The methodology generalizes to other statistics obtained using generalized pairwise comparisons, such as the win ratio. It is implemented in the R package BuyseTest (version 2.3.0 and later) available on Comprehensive R Archive Network.

powmic: an R package for power assessment in microbiome case–control studies

2020 ◽  
Vol 36 (11) ◽  
pp. 3563-3565
Author(s):  
Li Chen
Keyword(s):  
Power Analysis ◽  
Real Data ◽  
Analytical Form ◽  
R Package ◽  
Case Control ◽  
Supplementary Information ◽  
Metagenomic Sequencing ◽  
Case Control Studies ◽  
Simulation Based ◽  
Over Dispersion

Abstract Summary Power analysis is essential to decide the sample size of metagenomic sequencing experiments in a case–control study for identifying differentially abundant (DA) microbes. However, the complexity of microbial data characteristics, such as excessive zeros, over-dispersion, compositionality, intrinsically microbial correlations and variable sequencing depths, makes the power analysis particularly challenging because the analytical form is usually unavailable. Here, we develop a simulation-based power assessment strategy and R package powmic, which considers the complexity of microbial data characteristics. A real data example demonstrates the usage of powmic. Availability and implementation powmic R package and online tutorial are available at https://github.com/lichen-lab/powmic. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Quantitative color profiling of images in a comparative framework using the R package colordistance

2018 ◽  
Author(s):  
Hannah Weller ◽  
Mark Westneat
Keyword(s):  
Profile Analysis ◽  
Color Space ◽  
Distance Matrix ◽  
R Package ◽  
Color Variation ◽  
Statistical Testing ◽  
Color Analysis ◽  
Color Histograms ◽  
Color Profile ◽  
Image Pixels

Color is a central aspect of biology, with important impacts on ecology and evolution. Organismal color may be adaptive or incidental, seasonal or permanent, species- or population-specific, or modified for breeding, defense or camouflage. Thus, measuring and comparing color among organisms provides important biological insights. However, color comparison is limited by color categorization methods, with few universal tools available for quantitative color profiling and comparison. We present a package of R tools for processing images of organisms (or other objects) in order to quantify color profiles, gather color trait data, and compare color palettes in a reproducible way. The package treats image pixels as 3D coordinates in “color space", producing a multidimensional color histogram for each image. Pairwise distances between histograms are computed using earth mover's distance or a combination of more conventional distance metrics. The user sets parameters for generating color histograms, and comparative color profile analysis is performed through pairwise comparisons to produce a color distance matrix for a set of images. The toolkit provided in the colordistance R package can be used for analyses involving quantitative color variation in organisms with statistical testing. We illustrate the use of colordistance with three biological examples: hybrid coloration in butterflyfishes; mimicry in wing coloration in Heliconius butterflies; and analysis of background matching in camouflaging flounder fish. The tools presented for quantitative color analysis may be applied to a broad range of questions in biology and other disciplines.

Sign in / Sign up

Export Citation Format

Share Document