Mosaic Plots Research Articles

An Empirical Study of R Applications for Data Analysis in Marine Geology

The study focuses on the application of R programming language towards marine geological research with a case study of Mariana Trench. Due to its logical and straightforward syntax, multi–functional standard libraries, R is especially attractive to the geologists for the scientific computing. Using R libraries, the unevenness of various factors affecting Mariana Trench geomorphic structure has been studied. These include sediment thickness, slope steepness, angle aspect, depth at the basement and magmatism of the nearby areas. Methods includes using following R libraries: {ggplot2} for regression analysis, Kernel density curves, compositional charts; {ggalt} for Dumbbell charts for data comparison by tectonic plates, ranking dot plots for correlation analysis; {vcd} for mosaic plots, silhouette plots for compositional similarities among the bathymetric profiles, association plots; {car} for ANOVA. Bathymetric GIS data processing was done in QGIS and LaTeX. The innovativeness of the work consists in the multi–disciplinary approach combining GIS analysis and statistical methods of R which contributes towards studies of ocean trenches, aimed at geospatial analysis of big data.

Framed! Reproducing and Revisiting 150-Year-Old Charts

The Statistical Atlases published by the Census Bureau in the late 1800s utilized a number of novel methods for displaying data. In this paper, we examine the use of framed spine and mosaic plots used in two plates of the Statistical Atlas of 1870. We use forensic statistics to recreate the data using available census information, and then use that data to create framed charts using modern plotting methods. We then examine the effectiveness of the framed charts compared to other alternatives with a user study. The data and code for this study are available online.

Intrapartum Foetal Heart Rate Monitoring and Rate of Caesarean Section: A National Survey

The rate of Caesarean section has dramatically increased in recent decades. Foetal scalp blood sampling and computer software analysing foetal heart rate detection should help in the decision-making for or against Caesarean section. The main aim of this study was to examine how these 2 factors influence the Caesarean section rate. A national survey of all maternity units in Germany was undertaken using a self-reported questionnaire via crowd sourcing. All variables were collected as categorised data sets. Using these data sets, correlation coefficients were calculated. The correlations were additionally analysed using visual mosaic plots. 97 questionnaires were analysed. There were several strong correlations between variables in the data set. Particularly, hospitals that assessed the foetal heart rate in the normal range (110-160 bpm) according to the current FIGO guidelines had a lower C-section rate. Computer-assisted foetal heart rate assessment that is based on the FIGO guidelines correlated with a lower Caesarean section rate. The use and further development of computer-based cardiotocograph assessment analysis should be continued.

An assessment of the effectiveness of virginiamycin on liver abscess incidence and growth performance in feedlot cattle: a comprehensive statistical analysis.

The judicious use of commercial products in livestock operations can be part of a sustainable and environmentally friendly production scenario. This study was designed to gather published data of virginiamycin (VM) used in feedlot conditions of the United States and analyze its effectiveness and optimum dosage in reducing the liver abscess incidence (LAI). The dataset contained 26 studies that evaluated more than 7,156 animals of diverse breeds fed in several regions in the United States under different management. Statistical analyses included contingency tables to assess the nonparametric independence of the LAI, meta regression analysis to remove study effects and to evaluate LAI and animal performance, broken-line analysis to determine thresholds of VM dosage on LAI, and residual-based shading mosaic plots to illustrate the contingency analysis. There were 1,391 of 5,430 animals with LAI scores 1, 2, or 3 (LAI1-3) and 651 of 4,690 animals with LAI A+ (score 3). Our analyses suggested that there was a significant dependency (χ2P-value < 0.001) and significant asymmetry (McNemar's test P-value < 0.001) between LAI and VM treatment for both LAI1-3 and LAI A+. For the LAI1-3 group, only 22.5% of the treated animals had liver abscesses compared with 31.7% of the control animals. The metaregression analysis indicated that LAI1-3 was linearly reduced (P < 0.001) by about 0.42% per mg/kg of DM of VM. The lower 95% confidence interval of the intercept for LAI1-3 and LAI A+ obtained with a generalized nonlinear mixed regression was 18.7 and 20.3 mg/kg of DM, respectively. The broken-line regression analysis identified 2 thresholds for LAI (23.9 and 12.3 mg/kg of DM) at which the reduction in total LAI1-3 and LAI A+, respectively, would decrease faster as VM dosage increases (from 2.14% to 6% and from 1.91% to 4.33% per mg of VM per kg of DM, respectively). Additionally, our analyses indicated that after accounting for the study effects, VM significantly increased ADG at 2.08 g BW/d per mg/kg DM compared with 0.92 g BW/d per mg/kg DM for monensin (P < 0.001), suggesting that VM was about 2.3 times more effective in increasing ADG for the same dosage and feeding period length. All analyses yielded consistent results that led us to conclude that VM is effective in reducing LAI when fed between approximately 12 and 24 mg/kg of DM, and the maximum reduction might occur at approximately 24 mg/kg of DM or higher.

Land use changes and development of the non-forest woody vegetation in the Danubian Lowland in Slovakia

AbstractThe aim of this paper is to assess the changes in the landscape structure of the Žitný Ostrov territory and in the woody species of the non-forest woody vegetation (NFWV) over the past 120 years. Within the assessed periods of 1892, 1949, 1969 and 2015, the shares of arable land increased by 17% while the ratio of the built-up areas with gardens increased by 3.7%. At the same time, natural habitats, grassland, waterlogged meadows and wetlands decreased by 26%. These changes, concerning small mosaic plots as well as large cultural blocks, were caused by the intensification of agriculture after 1948. Ecological stability and biodiversity of these areas has decreased. Thereafter 60 windbreaks were planted from 1951–1952 in an area of 30 ha. In total, 37 woody species were planted, of which 22 were alien species. After 25 years (in 1976), 19 of the same windbreaks were surveyed, observing 16 native and 12 alien woody species. During these periods, many rare alien and coniferous species died. In 2015, 13 windbreaks with 39 woody species were identified, both in the tree and the shrubby layer. The downside is that four of the long-time surviving species are invasive trees.

Film Writing Adapted for Game Narrative: Myth or Error?

Film Writing Adapted for Game Narrative: Myth or Error?

Nomograms to predict survival after colorectal cancer resection without preoperative therapy.

BackgroundThe predictive accuracy of the American Joint Committee on Cancer (AJCC) stages of colorectal cancer (CRC) is mediocre. This study aimed to develop postoperative nomograms to predict cancer-specific survival (CSS) and overall survival (OS) after CRC resection without preoperative therapy.MethodsEligible patients with stage I to IV CRC (n = 56072) diagnosed from 2004 to 2010 were selected from the Surveillance, Epidemiology, and End Results (SEER) database. The patients were allocated into training (n = 27,700), contemporary (n = 3158), and prospective (n = 25,214) validation cohorts. Clinically important variables were incorporated and selected using the Akaike information criterion in multivariate Cox regressions to derive nomograms with the training cohort. The performance of the nomograms was assessed and externally testified using the concordance index (c-index), bootstrap validation, calibration, time-dependent receiver-operating characteristic curves, Kaplan–Meier curves, mosaic plots, and decision curve analysis (DCA). Performance of the conventional AJCC stages was also compared with the nomograms using similar statistics.ResultsThe nomograms for CSS and OS shared common predictors: sex, age, race, marital status, preoperative carcinoembryonic antigen status, surgical extent, tumor size, location, histology, differentiation, infiltration depth, lymph node count, lymph node ratio, and metastasis. The c-indexes of the nomograms for CSS and OS were 0.816 (95 % CI 0.810–0.822) and 0.777 (95 % CI 0.772–0.782), respectively. Performance evaluations showed that the nomograms achieved considerable predictive accuracy, appreciable reliability, and significant clinical validity with wide practical threshold probabilities, while the results remained reproducible when applied to the validation cohorts. Additionally, model comparisons and DCA proved that the nomograms excelled in stratifying each AJCC stage into three significant prognostic subgroups, allowing for more robust risk classification with an improved net benefit.ConclusionsWe propose two prognostic nomograms that exhibit improved predictive accuracy and net benefit for patients who have undergone CRC resection. The established nomograms are intended for risk assessment and selection of suitable patients who may benefit from adjuvant therapy and intensified follow-up after surgery. Independent external validations may still be required.

Methods to Quantify Regional Differences in Land Cover Change

This paper describes and illustrates methods for quantifying regional differences in land use/land cover changes. A series of approaches are used to analyse differences in land cover change from data held in change matrices. These are contingency tables and are commonly used in remote sensing to describe the spatial coincidence of land cover recorded over two time periods. Comparative analyses of regional change are developed using odds ratios to analyse data in two regions. These approaches are extended using generalised linear models to analyse data for three or more regions. A generalised Poisson regression model is used to generate a comparative index of change based on differences in change likelihoods. Mosaic plots are used to provide a visual representation of statistically surprising land use losses and gains. The methods are explored using a hypothetical but tractable dataset and then applied to a national case study of coastal land use changes over 50 years conducted for the National Trust. The suitability of the different approaches to different types of problem and the potential for their application to land cover accuracy measures are briefly discussed.

American Woodcock and Golden-Winged Warbler Abundance and Associated Vegetation in Managed Habitats

Abstract Vermivora chrysoptera (Golden-winged Warbler) and Scolopax minor (American Woodcock, hereafter, Woodcock) are 2 young-forest-dependent species of eastern North America that are experiencing population declines due to loss of breeding habitat. The goals of our study were to compare avian abundance and habitat similarities and differences in sites used by the 2 species. A portion of our survey plots were manipulated under Woodcock or Golden-winged Warbler habitat prescriptions in managed shrublands, and others were on regenerating timber-harvest sites. In north-central PA, we compared Woodcock abundance in 10-ha experimental plots assigned to one of 3 habitat prescriptions: uncut controls, Woodcock strip plots, and Golden-winged Warbler mosaic plots. We also quantified vegetation characteristics in each 10-ha study plot. Woodcock density was higher in the strip (4.8 males/10 ha) and mosaic (5.1 males/10 ha) plots compared to the uncut reference plots (3.3 males/10 ha). Woodcock density was negative...

MOSAICISM OF HYALINE CARTILAGE: QUANTITATIVE MORPHOLOGICAL STUDY ON RABBIT ELBOW JOINT

To study the heterogenecity of hyaline cartilage we have analyzed the tissues of elbow joint received from six intact Chinchilla rabbits. Classic histological assays, step-by-step scanning, and quantitative morphological analysis were performed. The revealed phenomenon at least concluded in an available of mosaic plots (microclusters), different from the environment of the numerical density of chondrocytes, structure and optical density of cartilage matrix. These microclusters took up to 40% of cartilage volume, they could be described as a polygon truncated pyramids with a diameter cross section about 60-100 microns near the basophil line and extending to 100-150 microns by superficial zone of the cartilage. The revealed phenomenon was matched to the biomechanics of the joints to provide for optimal redistribution of static and dynamic loads on the articular surface.

Saprolegnia species affecting the salmonid aquaculture in Chile and their associations with fish developmental stage

article The rapid increase in the aquaculture production of salmonids has been followed by a rise in several diseases. In particular, saprolegniosis can account for at least 10% of the annual economic loss in salmonids. In this study, we investigated the main Saprolegnia species involved in saprolegniosis of salmonids in Chile, and their association with specific developmental stages of the host fish. For this purpose, we studied 244 isolates of Saprolegnia- affected Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and king salmon (Oncorhynchus tshawytscha) from the salmon farming regions, using a recently developed identification strategy based on mo- lecular taxonomical operational units. We found that the Saprolegnia species associated with diseased salmon were Saprolegnia australis, Saprolegnia delica, Saprolegnia diclina, Saprolegnia ferax, Saprolegnia parasitica and two new Saprolegnia species observed during this study. In order to determine whether there were any specific species associations with different stages in the fish life cycle, we applied mosaic plots and correspondence anal- yses for categorical data. These analyses showed a strong association of S. parasitica with samples from the adult stage of the fish (χ 2 = 196.29, p b 0.0001), while the species S. australis, S. diclina and Saprolegnia sp. 2 were

Mosaic Plots are Useful for Visualizing Low-Order Projections of Factorial Designs

Factorial experiments are widely used in industrial experimentation and other fields. Whenever a factorial experiment is not designed as a full factorial, but as a regular or nonregular fraction thereof, choice between competing designs and interpretation of experimental results should take into consideration how the experimental plan will confound experimental effects. This article proposes mosaic plots of low-order projections of factorial designs for visualizing confounding of low-order effects. Mosaic plots are particularly useful for design and analysis of orthogonal main effect plans. The R code for the creation of the plots in this article is available online in the supplementary material.

Smart Visualization of Urban Area Earthquake Simulation

Smart visualization of output from Integrated Earthquake Simulation (IES) performed for various earthquake scenarios is studied by taking advantage of existing methodology of big data visualization and by developing our own methodology which is suitable for earthquake disaster assessment. A key issue of being smart is to deliver information generated by IES to not only professional earthquake engineers, but also non-professional government officials and city residents. Simple visualization for city residents, wide area visualization for government officials, and dual visualization for professional engineers are proposed to bring common recognition to IES users. As a trial of smart visualization, both structure-wise and scenariowise damage condition statistics are graphed by means of histograms and mosaic plots; spatial clustering analysis for damaged structures is introduced and the distance between the damage conditions of earthquake scenarios is defined and visualized, accompanied by scenario cluster analysis.

Capturing the Design Space of Sequential Space-Filling Layouts.

We characterize the design space of the algorithms that sequentially tile a rectangular area with smaller, fixed-surface, rectangles. This space consist of five independent dimensions: Order, Size, Score, Recurse and Phrase. Each of these dimensions describe a particular aspect of such layout tasks. This class of layouts is interesting, because, beyond encompassing simple grids, tables and trees, it also includes all kinds of treemaps involving the placement of rectangles. For instance, Slice and dice, Squarified, Strip and Pivot layouts are various points in this five dimensional space. Many classic statistics visualizations, such as 100% stacked bar charts, mosaic plots and dimensional stacking, are also instances of this class. A few new and potentially interesting points in this space are introduced, such as spiral treemaps and variations on the strip layout. The core algorithm is implemented as a JavaScript prototype that can be used as a layout component in a variety of InfoViz toolkits.

Generating a Close-to-Reality Synthetic Population of Ghana

The purpose of this research is to generate a close-to-reality synthetic human population for use in a geosimulation of urban dynamics. Two commonly accepted approaches to generating synthetic human populations are Iterative Proportional Fitting (IPF) and Resampling with Replacement. While these methods are effective at reproducing one instance of the probability model describing the survey, it is an instance with extremely small variability amongst subgroups and is very unlikely to be the real population. IPF and Resampling with Replacement also rely on pure replication of units from the underlying sample which can increase unrealistic model behavior. In this work we present a sequential logic for estimating variables using multinomial logistic regressions and the conditional probabilities amongst each variable in order to generate combinations which were not represented in the original survey but are likely to occur in the real population. We also present a model based approach to imputing missing observation responses and apply the methodology to the Ghana Living Standard Survey 5 (GLSS5) in order to generate a comprehensive synthetic population for the Republic of Ghana, including such household and person variables as household size, tribal affiliation, educational attainment and annual income, amongst others. The R language and environment for statistical computing was used as well as the packages VIM and simPopulation in developing and executing the code. Contingency coefficients, cumulative distributions, mosaic plots, and box plots are presented for evaluation in order to demonstrate the effectiveness of the new method in its application to Ghana.

Descriptive epidemiological study of the use of antimicrobial drugs by companion animal veterinarians in New Zealand

AIM: To describe the patterns of use of antimicrobial drugs by veterinary surgeons treating commonly presented bacterial infections in companion animals in New Zealand. METHODS: A postal survey of 800 randomly selected companion animal veterinarians practicing in New Zealand was conducted between August and December 2008. Data were collected regarding the antimicrobials prescribed for recent cases of skin, ear and urinary tract infections; the use of culture and susceptibility testing; and veterinarian characteristics such as proportion of time spent treating companion animals and recent attendance at continuing professional development (CPD) events. Potential associations within the data were explored using extended mosaic plots and multivariable regression models. RESULTS:Completed surveys from 393 respondents were available for analysis, providing data on systemic antimicrobial drug use for 1,799 cases of presumptive bacterial infections. The most frequently prescribed drugs were amoxicillin-clavulanic acid (864 cases, 48%), cephalexin (558, 31%), and fluoroquinolones (198, 11%). Of 359 cases of canine superficial pyoderma, 157 (44%) were treated with amoxicillin-clavulanic acid and 155 (43%) were treated with cephalexin with median reported treatment durations of 7 and 10 days, for these two drugs respectively. Culture and susceptibility tests had been used in 376 of 1,984 (19%) of all reported cases and 160 (43%) of these were suspected urinary tract infections. Practitioners that spent 100% of their time treating companion animals and who had attended a CPD course related to companion animals within the 12 months prior to completing the survey were more likely to submit a sample for culture and susceptibility testing and to prescribe longer courses of antimicrobials for the treatment of canine pyoderma than practitioners who spent less than 100% of their time treating companion animals and had not attended a CPD course in the last 12 months. CONCLUSIONS: Broad-spectrum drugs considered by the World Health Organisation to be critically important for human health, such as fluoroquinolones and amoxicillin-clavulanic acid, are amongst the most frequently prescribed antimicrobials in companion animal medicine, and these drugs are often prescribed without submitting a sample for culture and susceptibility testing. CLINICAL RELEVANCE: Many cases of superficial pyoderma were treated for less than the recommended duration of 21 days, which may contribute to a higher rate of recurrent pyoderma and the development of drug resistance within the causal bacteria. Veterinarians should be aware that the use of fluoroquinolones, in particular, should be based upon the results of a culture and susceptibility test.

Mosaic plots

AbstractMosaic plots are a recursive generalization of barcharts to visualize multivariate categorical data. Mosaic plots were first introduced by Hartigan and Kleiner and are the de‐facto standard for advanced visualizations of categorical data.This review explains the general construction and the successful application of mosaic plots. Recent implementations of mosaic plots offer various generalizations which can effectively cope with almost any kind of categorical data. Besides plotting expected values of a proposed model, these variations include the doubledecker plot, the empty bin display and fluctuation diagrams. Within an interactive graphical analysis tool, subgroups reflecting a certain property can easily be linked into mosaic plots to effectively visualize the relationship between this property and the categorical variables in the plot. Mosaic plots are most powerful when investigating associations between categorical variables, conditioned by other categorical variables. This is illustrated along with an explanation of how Simpson's Paradox for categorical data can be explained using mosaic plots. WIREs Comput Stat 2012, 4:191–198. doi: 10.1002/wics.1192This article is categorized under: Statistical and Graphical Methods of Data Analysis &gt; Statistical Graphics and Visualization

Product Plots

We propose a new framework for visualising tables of counts, proportions and probabilities. We call our framework product plots, alluding to the computation of area as a product of height and width, and the statistical concept of generating a joint distribution from the product of conditional and marginal distributions. The framework, with extensions, is sufficient to encompass over 20 visualisations previously described in fields of statistical graphics and infovis, including bar charts, mosaic plots, treemaps, equal area plots and fluctuation diagrams.

Relationship between clock and star drawing and the degree of hepatic encephalopathy

Purpose of the studyCurrent hepatic encephalopathy grading tools are limited because of complexity or subjectivity. The degree of constructional apraxia could serve as a simple, objective and reproducible tool to...

모자이크 플롯에서 변수와 범주의 순서화

Hartigan과 Kleiner (1981, 1984)에 의해 제안된 모자이크 플롯은 범주형 자료의 탐색에 매우 유용한 시각화 도구이다. 모자이크 플롯은 범주 셀의 빈도를 사각형의 기에 비례하게 나타내므로 이해가 쉽고 데이터에 포함된 정보를 유지하지만 실제 모습은 변수 순서와 변수 내 범주의 순서에 따라 상당히 달라진다. 이에 우리는 본 연구에서 모자이크 플롯에서 크래머(Cramer)의 V 계수를 활용한 변수의 순서화 방법과 감마 계수를 활용한 범주의 순서화 방법을 제안하고 Titanic, Housing, PreSex 등 공개 자료에 적용한 결과를 제시한다. Mosaic plots, proposed by Hartigan and Kleiner (1981, 1984), are very useful in visualizing categorical data. In mosaic plot, multi-way classified cell frequencies are represented by rectangles with proportional area. The plot is easy to understand while preserving the information contained in the data. Plot's appearance, however, does change substantially depending on the order of variables and the orders of categories with variable put into the plot. In this study, we propose the algorithms for ordering variables and categories of the categorical data to be explored via mosaic plots. We demonstrate our methods to three well-known datasets: Titanic, Housing and PreSex.