ANALYSING ASSOCIATIONS AMONG MORE THAN TWO SPECIES

This article attempts to fill two gaps in the literature on individual party choice. First, it deals with hitherto unanswered questions about relationships between social cleavages and party choice in Israel. Second, the article attempts to overcome methodological problems arising in the multivariate analysis of multiparty systems by utilizing Goodman's method of log-linear contingency table analysis. In the sample, occupation is not as strongly related to party choice as is a nonhierarchical dimension of economic position, sector of the economy. Ethnicity is modestly related to party choice, but hypotheses that the relationship is affected by place of birth, age, or other variables are disconfirmed. Hypotheses that the relationship between religiosity and party choice is affected by economic position are also disconfirmed. The advantages of using log linear contingency table analysis are demonstrated.

This article compares the advantages and disadvantages of two multivariate methods for the analysis of small grolup communication data, log-linear contingency table analysis and multivariate analysis of variance, in the context of ani experimental design. The independent conditions were discussion procedure, task solution multiplicity, and discussion topic. Participant communication behaviors, the dependent variables, were coded into a mix of 15 task social, and procedural categories. The analyses of communication indicated that log-linzear analyasis produced thle most complex models for various behaviors, including both single-factor and multifactor termns. Multivariate analysis of variance (MANOVA) findings at tlte grolup level provided the most parsimonious explanations, with a main effect of discussion procedure. Some MANOVA results at the individual level were similar to loglitnear mnodels in their complexity, whereas others duplicated the results of the group-level MANOVA. The differing outcomes from these methods point to several design considerations that should be taken account when choosing a statistical test for group communication data.

The protection of endangered species is a hot topic for scholars worldwide, and interspecific association and community stability analysis are important methods with which to explore the structure and function of the endangered species community. Thuja sutchuenensis Franch. is an endangered species; however, studies on the T. sutchuenensis community remain insufficient. Here, based on the data of the plot survey of the T. sutchuenensis community in the Ta-pa Mountains and Xuebao Mountains, we analyzed the interspecific associations, niche width, and niche overlap of major species in the arborous and shrub layers, as well as community stability. The results showed that the overall interspecies association between the species of the arbor layer was non-significantly negatively associated, while the shrub layer was non-significantly positively associated. The Chi-square test results showed that the species pairs without interspecific association in the arbor layer and the shrub layer were much higher than those with significant interspecific association; in other words, the interspecific association of species in the T. sutchuenensis community was loose. The results of interspecific association coefficient analysis showed that the number of negatively associated species pairs was significantly higher than that of positive association species pairs, but Pearson’s correlation coefficient and Morisita’s niche overlap index analysis showed that the degree of competition between species in the community was small. In the arbor layer, the niche width of T. sutchuenensis was the widest, while in the shrub layer, the niche width of T. sutchuenensis was relatively high, indicating that T. sutchuenensis had a strong ability to adapt to the environment and use available resources. In addition, the intersection point of community stability (32.11, 67.89) in the vegetative community of T. sutchuenensis suggested that the community displayed a better stability. The survival strategy of T. sutchuenensis is based on its strong adaptability to the harsh environment to escape the competition among species, and this knowledge can provide a reference for the protection and restoration of endangered species.

The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co‐occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co‐occur either due to environmental filtering or due to competitive exclusion of inferior competitors (hereafter hierarchical competition).We used a fully mapped 50‐ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering, and hierarchical competition on species co‐occurrence.We found that trait dissimilarity was generally negatively related to interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co‐occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages.This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co‐occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co‐occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.

In analyses of contingency tables made up of categorical variables, the study of relationship between the variables is usually the major objective. So far, many association measures and association models have been used to measure the association structure present in the table. Although the association measures merely determine the degree of strength of association between the study variables, the association models illustrate the details and components of association structure. These measure and models have found vast application in many disciplines. For more details see Goodman and Kruskal (1954, 1979), Leibetrau (1983), Goodman (1972, 1979, 1985, 1991) and Ghoreishi and Meshkani (2006, 2008).

This paper reviews the contributions Jerome Cornfield made to epidemiologic methodology. Section 2 discusses his development of the odds ratio obtained in a case-control study as an estimate of the relative risk of the disease under study. Section 3 presents Cornfield's introduction of the multiple logistic risk function as a smoothing function for data classified in a multi-way contingency table in order to determine the joint effects of several risk factors on the incidence of a disease. Section 4 gives a brief description of his work in the analysis of contingency tables. In Section 5, there is a summary of his views on a number of issues relating to the research, mostly case-control studies, on the relationship between smoking and lung cancer. The discussion in this section is selective and undoubtedly does not reflect all the important things he had to say on the subject. Finally, in Section 6, there is a discussion, based on only one of his papers on the subject, of some very significant thoughts on intervention studies in coronary disease.

This paper introduces the method of log-linear analysis for performing hypothesis testing on contingency tables. The reader will see a brief development of this topic beginning with Pearson's classic chi-square test and examples of analyses on two and three dimensional tables. The idea of hierarchical models and backward elimination are discussed. Finally, the APL2 implementation of the Newton-Raphson algorithm is described. Newton-Raphson is an iterative procedure for finding the roots of a function. It is used in log-linear analysis to find the maximum-likelihood estimation of expected frequencies that cannot be calculated from expressions in closed form.

Log-linear analysis was used to investigate the relationships between spouse isonymy and parental isonymy, time, endogamy/exogamy and groom's occupation in a total of 6266 first marriages of parish-born spouses in the civil parishes of Harris, Barra and Stornoway, between 1855 and 1990. Stornoway was divided into rural and urban (Burgh) components. Spouse isonymy comprised between 6% and 12% of all marriages; parental isonymy was generally slightly more frequent, due probably to the occurrence of occasional families in which both sets of parents were isonymous. Between 38% and 51% of marriages were endogamous. In the multi-way contingency tables, good fits between observed and expected cell numbers were obtained by a simple model, comprising the main effect of spouse isonymy and the first-order interactions between spouse isonymy and the independent variables. Inspection of the coefficients showed that in all four populations spouse isonymy was positively related to parental isonymy (doubtfully so in the case of Barra). The other independent variables showed less clear-cut relationships-endogamy/exogamy in Barra, and groom's occupation in Stornoway Rural; time period showed no significant relationships. It is concluded that the occurrence of this 'two-generational marital isonymy' might have an effect on the breeding structure of the population.Mittels einer Log-linear-Analyse sollten die Beziehungen zwischen Ehepartner-Isonymie und Eltern-Isonymie, der Zeit, Endogamie/Exogamie und dem Beruf der Brautleute in einer Gruppe von insgesamt 6266 Erstverheirateten Ehepaaren, welche zwischen 1855 und 1990 in den Gemeinden Harris, Barra und Stornoway geboren wurden, untersucht werden. Stornoway wurde in einen ländlichen und einen städtischen (Burgh) Teil unterteilt. Die Ehepartner-Isonymie umfasste zwischen 6% und 12% aller Ehen; die Ehepartner-Isonymie war generell leicht häufiger, vielleicht verursacht durch das Vorhandensein von vereinzelten Familien, in welchen beide Elternteile isonym waren. Zwischen 38% und 51% der Ehepaare waren endogam. In den Mehrfelder-Kontingenztafeln wurde eine gute Übereinstimmung zwischen den bobachteten und den erwarteten Zellzahlen durch ein einfaches Modell beobachtet, das den Haupteffekt der Ehepartner-Isonymie und die Interaktionen erster Ordnung zwischen der Ehepartner-Isonymie und den unabhängigen Variablen einschließt. Die Inspektion der Koeffizienten zeigte, dass in allen 4 Populationen die Ehepartner-Isonymie mit der Eltern-Isonymie in einem positiven Zusammenhang stand (fraglich im Falle von Barra). Die anderen unabhängigen Variablen zeigten weniger klare Beziehungen - Endogamie/Exogamie in Barra und Beruf der Brautleute in Stornoway (Landregion); die Zeitperiode zeigte keine signifikanten Beziehungen. Es ist abschließend zu sagen, dass das Vorkommen dieser 2 Generations-Ehegatten-Isonymie möglicherweise einen Effekt auf die Fortpflanzungsstruktur der Population hat.On a employé l'analyse log-linéaire pour explorer la relation entre l'isonymie maritale, l'isonymie parentale, la chronologie, l'endogamie/exogamie et la profession du conjoint dans un ensemble de 2266 premiers mariages d'époux nés dans les paroisses civiles de Harris, Barra et Stornoway entre 1855 et 1990. Stornoway a été divisée en composants rural et urbain (bourg). L'isonymie maritale représente entre 6 et 12% de tous les mariages; l'isonymie parentale est généralement un peu plus fréquente, probablement par suite de l'existence de certaines familles dans lesquelles les deux ensembles de parents sont isonymiques. De 38 à 51% de tous les mariages sont endogames. Dans les tables de contingence à entrées multiples on a obtenu un bon ajustement entre valeurs attendues et valeurs observées au moyen d'un modèle simple comprenant l'effet majeur de l'isonymie maritale et les interactions de premier ordre entre isonymie maritale et variables indépendantes. L'examen des coefficients montre que l'isonymie maritale est positivement liée à l'isonymie parentale (avec un doute dans le cas de Barra), dans les quatre populations. Les autres variables indépendantes montrent des relations moins nettes.. l'endogamie/exogamie à Barra et la profession du conjoint à Stornoway; on ne trouve pas d'association significative selon la pé

BackgroundIt is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic associations aggregate in specific functional groups as defined by the Gene Ontology (GO).ResultsWe first estimated all pairwise additive and nonadditive genetic effects using the multifactor dimensionality reduction (MDR) method that makes few assumptions about the underlying genetic model. Statistical significance was evaluated using permutation testing in two genome-wide association studies of ALS. The detection data consisted of 276 subjects with ALS and 271 healthy controls while the replication data consisted of 221 subjects with ALS and 211 healthy controls. Both studies included genotypes from approximately 550,000 single-nucleotide polymorphisms (SNPs). Each SNP was mapped to a gene if it was within 500 kb of the start or end. Each SNP was assigned a p-value based on its strongest joint effect with the other SNPs. We then used the Exploratory Visual Analysis (EVA) method and software to assign a p-value to each gene based on the overabundance of significant SNPs at the α = 0.05 level in the gene. We also used EVA to assign p-values to each GO group based on the overabundance of significant genes at the α = 0.05 level. A GO category was determined to replicate if that category was significant at the α = 0.05 level in both studies. We found two GO categories that replicated in both studies. The first, ‘Regulation of Cellular Component Organization and Biogenesis’, a GO Biological Process, had p-values of 0.010 and 0.014 in the detection and replication studies, respectively. The second, ‘Actin Cytoskeleton’, a GO Cellular Component, had p-values of 0.040 and 0.046 in the detection and replication studies, respectively.ConclusionsPathway analysis of pairwise genetic associations in two GWAS of sporadic ALS revealed a set of genes involved in cellular component organization and actin cytoskeleton, more specifically, that were not reported by prior GWAS. However, prior biological studies have implicated actin cytoskeleton in ALS and other motor neuron diseases. This study supports the idea that pathway-level analysis of GWAS data may discover important associations not revealed using conventional one-SNP-at-a-time approaches.

In 2005, Chen et al. introduced a sequential importance sampling (SIS) procedure to analyze zero-one two-way tables with given fixed marginal sums (row and column sums) via the conditional Poisson (CP) distribution. They showed that compared with Monte Carlo Markov chain (MCMC)-based approaches, their importance sampling method is more efficient in terms of running time and also provides an easy and accurate estimate of the total number of contingency tables with fixed marginal sums. In this paper, we extend their result to zero-one multi-way ( $$d$$ -way, $$d \ge 2$$ ) contingency tables under the no $$d$$ -way interaction model, i.e., with fixed $$d-1$$ marginal sums. Also, we show by simulations that the SIS procedure with CP distribution to estimate the number of zero-one three-way tables under the no three-way interaction model given marginal sums works very well even with some rejections. We also applied our method to Samson’s monks data set.

An assessment is made of the repeatability of parasite community structure in space for a marine fish, and in space and time for a freshwater fish from south-eastern Mexico. The marine fish species was the red grouper, Epinephelus morio (collected from 9 localities), and the freshwater species was the cichlid, Cichlasoma urophthalmus (collected from 6 localities: including monthly at 2 localities for 1 year, and bimonthly at 1 locality in 1990 and 1999). Pairwise interspecific associations and analyses of nested patterns in the distributions of parasite species among hosts were used in both fish species, with comparisons over time made only with the cichlid. Positive interspecific associations, and nested patterns were noted in some localities for both fish species, and/or at some sampling times for the cichlid fish. However, non-random patterns in the structure of parasite communities in these 2 host species only were observed sporadically. When present, nestedness in both fish species was apparently linked with a positive association between total infection intensities and fish size. Additionally, adjacent localities were more likely to display similar parasite community structure than distant ones. This preliminary result suggests that distance between localities is an important determinant of predictability in parasite community structure.

This paper analyses the distribution of longline catches of swordfish, Xiphias gladius, and six species of pelagic elasmobranchs, during a fishing voyage in the tropical eastern Atlantic. Seven scales of sampling units, ranging from about 0.72 to 7.2 km were used. Observed frequencies of appearance of each species in the basic sampling unit, were compared with theoretical frequencies obtained from the Poisson and negative binomial distributions. For the study of the interspecific relationships, contingency tables were used and the degree of association was estimated using the χ2test and the coefficient v of Kendall. The catch distribution of the swordfish and the devil ray (Mobula sp.) can be explained by both randomness and a slight trend to association. For the pelagic sharks, a clear trend towards intraspecific clustering was found. Catches of two species of the genus Carcharhinus showed the most positive trends to interspecific association, especially in short ranges, probably due to attraction to previously hooked fish. The possible causes of these distributions are discussed.

To evaluate the impact cirrhosis has on survival the records of 40 cirrhotic trauma victims from the registries of two Level 1 trauma centers were reviewed and probability of survival calculated using the TRISS methodology. Mechanism of injury, anatomic location, involvement of single or multiple sites, presence of ascites, elevations in serum glutamic oxaloacetic transaminase (SGOT), alkaline phosphatase, serum bilirubin, prothrombin time (PT), and hypoalbuminemia were tabulated for each patient. Contingency tables were created for injury and hepatic parameters, as related to survival, and subjected to chi square analysis. Loglinear analysis was performed on all significant parameters to evaluate the independent effects of injury characteristics and hepatic insufficiency on survival. Predicted survival was 93%; observed survival was 70% (Z = -6.92; p less than 0.001). Cause of death was multiple-system organ failure (9) and closed head injury (3). Admission markers of poor outcome included one or more of the following: ascites, elevated PT or bilirubin, history of motor vehicle accident, multiple trauma, or blunt abdominal trauma requiring laparotomy. Loglinear analysis revealed that the presence of ascites, elevated PT, or bilirubin, further diminished the rate of survival for any individual injury characteristic. We concluded that survival among cirrhotic trauma victims was significantly lower than predicted. In addition the presence of hepatic insufficiency further diminishes survival, regardless of the injury sustained.

Correspondence analysis, association analysis, and generalized nonindependence analysis of contingency tables: Saturated and unsaturated models, and appropriate graphical displays

Configural frequency analysis and association analyses in contingency tables