Comparison experiments by using IF.

Performance of DynGPE.

This article proposes a new graphical tool, the magnitude-shape (MS) plot, for visualizing both the magnitude and shape outlyingness of multivariate functional data. The proposed tool builds on the recent notion of functional directional outlyingness, which measures the centrality of functional data by simultaneously considering the level and the direction of their deviation from the central region. The MS-plot intuitively presents not only levels but also directions of magnitude outlyingness on the horizontal axis or plane, and demonstrates shape outlyingness on the vertical axis. A dividing curve or surface is provided to separate nonoutlying data from the outliers. Both the simulated data and the practical examples confirm that the MS-plot is superior to existing tools for visualizing centrality and detecting outliers for functional data. Supplementary material for this article is available online.

Categorical scatterplots with R for biologists: a step-by-step guide

Benjamin Petre1, Aurore Coince2, Sophien Kamoun1

1 The Sainsbury Laboratory, Norwich, UK; 2 Earlham Institute, Norwich, UK

Weissgerber and colleagues (2015) recently stated that ‘as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies’. They called for more scatterplot and boxplot representations in scientific papers, which ‘allow readers to critically evaluate continuous data’ (Weissgerber et al., 2015). In the Kamoun Lab at The Sainsbury Laboratory, we recently implemented a protocol to generate categorical scatterplots (Petre et al., 2016; Dagdas et al., 2016). Here we describe the three steps of this protocol: 1) formatting of the data set in a .csv file, 2) execution of the R script to generate the graph, and 3) export of the graph as a .pdf file.

Protocol

• Step 1: format the data set as a .csv file. Store the data in a three-column excel file as shown in Powerpoint slide. The first column ‘Replicate’ indicates the biological replicates. In the example, the month and year during which the replicate was performed is indicated. The second column ‘Condition’ indicates the conditions of the experiment (in the example, a wild type and two mutants called A and B). The third column ‘Value’ contains continuous values. Save the Excel file as a .csv file (File -> Save as -> in ‘File Format’, select .csv). This .csv file is the input file to import in R.

• Step 2: execute the R script (see Notes 1 and 2). Copy the script shown in Powerpoint slide and paste it in the R console. Execute the script. In the dialog box, select the input .csv file from step 1. The categorical scatterplot will appear in a separate window. Dots represent the values for each sample; colors indicate replicates. Boxplots are superimposed; black dots indicate outliers.

• Step 3: save the graph as a .pdf file. Shape the window at your convenience and save the graph as a .pdf file (File -> Save as). See Powerpoint slide for an example.

Notes

• Note 1: install the ggplot2 package. The R script requires the package ‘ggplot2’ to be installed. To install it, Packages & Data -> Package Installer -> enter ‘ggplot2’ in the Package Search space and click on ‘Get List’. Select ‘ggplot2’ in the Package column and click on ‘Install Selected’. Install all dependencies as well.

• Note 2: use a log scale for the y-axis. To use a log scale for the y-axis of the graph, use the command line below in place of command line #7 in the script.

7 Display the graph in a separate window. Dot colors indicate

replicates

graph + geom_boxplot(outlier.colour='black', colour='black') + geom_jitter(aes(col=Replicate)) + scale_y_log10() + theme_bw()

References

Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, et al. (2016) An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife 5:e10856.

Petre B, Saunders DGO, Sklenar J, Lorrain C, Krasileva KV, Win J, et al. (2016) Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE 11(2):e0149035

Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4):e1002128

https://cran.r-project.org/

http://ggplot2.org/

This data package includes the underlying data and files to replicate the calculations, charts, and tables presented in United States Is Outlier in Tax Trends in Advanced and Large Emerging Economies, PIIE Policy Brief 17-29. If you use the data, please cite as: Djankov, Simeon. (2017). United States Is Outlier in Tax Trends in Advanced and Large Emerging Economies. PIIE Policy Brief 17-29. Peterson Institute for International Economics.

Additional file 2.

Identifying and dealing with outliers is an important part of data analysis. A new visualization, the O3 plot, is introduced to aid in the display and understanding of patterns of multivariate outliers. It uses the results of identifying outliers for every possible combination of dataset variables to provide insight into why particular cases are outliers. The O3 plot can be used to compare the results from up to six different outlier identification methods. There is anRpackage OutliersO3 implementing the plot. The article is illustrated with outlier analyses of German demographic and economic data. Supplementary materials for this article are available online.

TopologyBench is a systematic graph theoretical approach to benchmarking optical network topologies. Network datasets are combined with their corresponding graph theoretical analysis to provide a systematic methodology for selecting diverse sets of optical networks for benchmarking. This topology benchmark is comprised of a network dataset and a systematic graph theoretic analysis. The dataset provides (a) 105 real optical networks and (b) synthetic topologies, generated by the SNR-BA model, divided into (i) Syn-small of 900 synthetic networks and (ii) Syn-large of 270,000 synthetic networks. The systematic graph theoretical analysis identifies and analyses structural, spatial and spectral properties of both the real world and synthetic networks. The graph theoretical correlation analysis reveal network design strategies leading to sparse yet efficient networks. An outlier analysis identifies networks that deviate from standard network designs. The analysis also identifies the limitations of real data in terms of network diversity and provides a justification for using synthetic data to complement the real dataset. We conclude the paper by providing a systematic methodology to cluster networks based on unsupervised machine learning and to select a diverse set of topologies for benchmarking. TopologyBench is a novel, high-quality and unified benchmark designed to facilitate research collaborations in long-haul fibre infrastructure by providing a systematic graph theoretical approach to benchmarking optical networks.

This dataset represents the CHANGE in the number of jobs per industry category and sub-category from the previous month, not the raw counts of actual jobs. The data behind these monthly change values is from the Bureau of Labor Statistics (BLS) Current Employment Statistics (CES) program. CES data represents businesses and government agencies, providing detailed industry data on employment on nonfarm payrolls.

This is the repository for the scripts and data of the study "Building and updating software datasets: an empirical assessment".

Data collected

The data generated for the study it can be downloaded as a zip file. Each folder inside the file corresponds to one of the datasets of projects employed in the study (qualitas, currentSample and qualitasUpdated). Every dataset comprised three files "class.csv", "method.csv" and "sample.csv", with class metrics, method metrics and repository metadata of the projects respectively. Here is a description of the datasets:

• qualitas: includes code metrics and repository metrics from the projects in the release 20130901r of the Qualitas Corpus.
• currentSample: includes code metrics and repository metrics from a recent sample collected with our sampling procedure.
• qualitasUpdated: includes code metrics and repository metrics from an updated version of the Qualitas Corpus applying our maintenance procedure.

Plot graphics

To plot the results and graphics in the article there is a Jupyter Notebook "Experiment.ipynb". It is initially configured to use the data in "datasets" folder.

Replication Kit

For replication purposes, the datasets containing recent projects from Github can be re-generated. To do so, the virtual environment must have installed the dependencies in "requirements.txt" file, add Github's tokens in "./token" file, re-define or leave as is the paths declared in the constants (variables written in caps) in the main method, and finally run "main.py" script. The source code scanner Sourcemeter for Windows is already installed in the project. If a new release becomes available or if the tool needs to be run on a different OS, it can be replaced in "./Sourcemeter/tool" directory.

The script comprise 5 steps:

1. Project retrieval from Github: at first the sampling frame with projects complying with a specific quality criteria are retrieved from Github's API.
2. Create samples: with the sampling frame retrieved, the current samples are selected (currentSample and qualitasUpdated). In the case of qualitasUpdated, it is important to have first the "sample.csv" file inside the qualitas folder of the dataset originally created for the study. This file contains the metadata of the projects in Qualitas Corpus.
3. Project download and analysis: when all the samples are selected from the sampling frame (currentSample and qualitasUpdated), the repositories are downloaded and scanned with SourceMeter. In the cases in which the analysis is not possible, the projects are replaced with another one with similar size.
4. Outlier detection: once the datasets are collected, it is necessary to manually look for possible outliers in the code metrics under study. In the notebook "Experiment.ipynb" there are specific sections dedicated for it ("Outlier detection (Section 4.2.2)").
5. Outlier replacement: when the outliers are detected, in the same notebook there is also a section for outlier replacement ("Replace Outliers") where the outliers' url have to be listed to find the appropriate replacement.

• If it is required, the metrics from the Qualitas Corpus can also be re-generated. First, it is necessary to download the release 20130901r from its official webpage. Second, decompress the .tar files downloaded. Third, make sure that the compressed files with source code from the projects (.java files) are placed in the "compressed" folder, in some cases it is necessary to read the "QC_README" file in the project's folder. Finally, run the original main script "Generate metrics for the Qualitas Corpus (QC) dataset" part of the code.

In robot localisation and mapping, outliers are unavoidable when loop-closure measurements are taken into account. A single false-positive loop-closure can have a very negative impact on SLAM problems causing an inferior trajectory to be produced or even for the optimisation to fail entirely. To address this issue, popular existing approaches define a hard switch for each loop-closure constraint. This paper presents AEROS, a novel approach to adaptively solve a robust least-squares minimisation problem by adding just a single extra latent parameter. It can be used in the back-end component of the SLAM system to enable generalised robust cost minimisation by simultaneously estimating the continuous latent parameter along with the set of sensor poses in a single joint optimisation. This leads to a very closely curve fitting on the distribution of the residuals, thereby reducing the effect of outliers. Additionally, we formulate the robust optimisation problem using standard Gaussian factors so that it can be solved by direct application of popular incremental estimation approaches such as iSAM. Experimental results on publicly available synthetic datasets and real LiDAR-SLAM datasets collected from the 2D and 3D LiDAR systems show the competitiveness of our approach with the state-of-the-art techniques and its superiority on real world scenarios.

Two Variable Artificial Dataset.

With the rapid increase of large-scale datasets, biomedical data visualization is facing challenges. The data may be large, have different orders of magnitude, contain extreme values, and the data distribution is not clear. Here we present an R package ggbreak that allows users to create broken axes using ggplot2 syntax. It can effectively use the plotting area to deal with large datasets (especially for long sequential data), data with different magnitudes, and contain outliers. The ggbreak package increases the available visual space for a better presentation of the data and detailed annotation, thus improves our ability to interpret the data. The ggbreak package is fully compatible with ggplot2 and it is easy to superpose additional layers and applies scale and theme to adjust the plot using the ggplot2 syntax. The ggbreak package is open-source software released under the Artistic-2.0 license, and it is freely available on CRAN (https://CRAN.R-project.org/package=ggbreak) and Github (https://github.com/YuLab-SMU/ggbreak).

The Pulp-fibre Dataset.

The crcc T2 Revised statistics.

Metric multidimensional scaling (MDS) is a widely used multivariate method with applications in almost all scientific disciplines. Eigenvalues obtained in the analysis are usually reported in order to calculate the overall goodness-of-fit of the distance matrix. In this paper, we refine MDS goodness-of-fit calculations, proposing additional point and pairwise goodness-of-fit statistics that can be used to filter poorly represented observations in MDS maps. The proposed statistics are especially relevant for large data sets that contain outliers, with typically many poorly fitted observations, and are helpful for improving MDS output and emphasizing the most important features of the dataset. Several goodness-of-fit statistics are considered, and both Euclidean and non-Euclidean distance matrices are considered. Some examples with data from demographic, genetic and geographic studies are shown.

IntroductionCreating training and testing datasets for machine learning algorithms to measure linear dimensions of organs is a tedious task. There are no universally accepted methods for evaluating outliers or anomalies in such datasets. This can cause errors in machine learning and compromise the quality of end products. The goal of this study is to identify optimal methods for detecting organ anomalies and outliers in medical datasets designed to train and test neural networks in morphometrics.MethodsA dataset was created containing linear measurements of the spleen obtained from CT scans. Labelling was performed by three radiologists. The total number of studies included in the sample was N = 197 patients. Using visual methods (1.5 interquartile range; heat map; boxplot; histogram; scatter plot), machine learning algorithms (Isolation forest; Density-Based Spatial Clustering of Applications with Noise; K-nearest neighbors algorithm; Local outlier factor; One-class support vector machines; EllipticEnvelope; Autoencoders), and mathematical statistics (z-score, Grubb’s test; Rosner’s test).ResultsWe identified measurement errors, input errors, abnormal size values and non-standard shapes of the organ (sickle-shaped, round, triangular, additional lobules). The most effective methods included visual techniques (including boxplots and histograms) and machine learning algorithms such is OSVM, KNN and autoencoders. A total of 32 outlier anomalies were found.DiscussionCuration of complex morphometric datasets must involve thorough mathematical and clinical analyses. Relying solely on mathematical statistics or machine learning methods appears inadequate.

Addition-point OLS matrix, B.

Values in parentheses are 95% credible intervals. Results are listed for a range of prior weights on the null model.

Augmented Projector.