Calculating the exclusion probability and paternity index for X-chromosomal loci in the presence of substructure

There has been recent interest in the use of X-chromosomal loci for forensic and relatedness testing casework, with many authors developing new X-linked short tandem repeat (STR) loci suitable for forensic use. Here we present formulae for two key quantities in paternity testing, the average probability of exclusion and the paternity index, which are suitable for Xchromosomal loci in the presence of population substructure.

Experimental verification of suction sampler capture efficiency in grasslands of differing vegetation height and structure

1. Suction sampling is a popular method for the collection of quantitative data on grassland invertebrate populations, although there have been no detailed studies into the effectiveness of the method. 2. We investigate the effect of effort (duration and number of suction samples) and sward height on the efficiency of suction sampling of grassland beetle, true bug, planthopper and spider Populations. We also compare Suction sampling with an absolute sampling method based on the destructive removal of turfs. 3. Sampling for durations of 16 seconds was sufficient to collect 90% of all individuals and species of grassland beetles, with less time required for the true bugs, spiders and planthoppers. The number of samples required to collect 90% of the species was more variable, although in general 55 sub-samples was sufficient for all groups, except the true bugs. Increasing sward height had a negative effect on the capture efficiency of suction sampling. 4. The assemblage structure of beetles, planthoppers and spiders was independent of the sampling method (suction or absolute) used. 5. Synthesis and applications. In contrast to other sampling methods used in grassland habitats (e.g. sweep netting or pitfall trapping), suction sampling is an effective quantitative tool for the measurement of invertebrate diversity and assemblage structure providing sward height is included as a covariate. The effective sampling of beetles, true bugs, planthoppers and spiders altogether requires a minimum sampling effort of 110 sub-samples of duration of 16 seconds. Such sampling intensities can be adjusted depending on the taxa sampled, and we provide information to minimize sampling problems associated with this versatile technique. Suction sampling should remain an important component in the toolbox of experimental techniques used during both experimental and management sampling regimes within agroecosystems, grasslands or other low-lying vegetation types.

Mixture models for capture-recapture count data

The contribution investigates the problem of estimating the size of a population, also known as the missing cases problem. Suppose a registration system is targeting to identify all cases having a certain characteristic such as a specific disease (cancer, heart disease, ...), disease related condition (HIV, heroin use, ...) or a specific behavior (driving a car without license). Every case in such a registration system has a certain notification history in that it might have been identified several times (at least once) which can be understood as a particular capture-recapture situation. Typically, cases are left out which have never been listed at any occasion, and it is this frequency one wants to estimate. In this paper modelling is concentrating on the counting distribution, e.g. the distribution of the variable that counts how often a given case has been identified by the registration system. Besides very simple models like the binomial or Poisson distribution, finite (nonparametric) mixtures of these are considered providing rather flexible modelling tools. Estimation is done using maximum likelihood by means of the EM algorithm. A case study on heroin users in Bangkok in the year 2001 is completing the contribution.

A jackknife variance estimator for unequal probability sampling

The jackknife method is often used for variance estimation in sample surveys but has only been developed for a limited class of sampling designs.We propose a jackknife variance estimator which is defined for any without-replacement unequal probability sampling design. We demonstrate design consistency of this estimator for a broad class of point estimators. A Monte Carlo study shows how the proposed estimator may improve on existing estimators.

Estimators in capture-recapture studies with two sources

This paper investigates the applications of capture-recapture methods to human populations. Capture-recapture methods are commonly used in estimating the size of wildlife populations but can also be used in epidemiology and social sciences, for estimating prevalence of a particular disease or the size of the homeless population in a certain area. Here we focus on estimating the prevalence of infectious diseases. Several estimators of population size are considered: the Lincoln-Petersen estimator and its modified version, the Chapman estimator, Chao's lower bound estimator, the Zelterman's estimator, McKendrick's moment estimator and the maximum likelihood estimator. In order to evaluate these estimators, they are applied to real, three-source, capture-recapture data. By conditioning on each of the sources of three source data, we have been able to compare the estimators with the true value that they are estimating. The Chapman and Chao estimators were compared in terms of their relative bias. A variance formula derived through conditioning is suggested for Chao's estimator, and normal 95% confidence intervals are calculated for this and the Chapman estimator. We then compare the coverage of the respective confidence intervals. Furthermore, a simulation study is included to compare Chao's and Chapman's estimator. Results indicate that Chao's estimator is less biased than Chapman's estimator unless both sources are independent. Chao's estimator has also the smaller mean squared error. Finally, the implications and limitations of the above methods are discussed, with suggestions for further development.

CAMCR: Computer assisted mixture model analysis for capture-recapture count data

Population size estimation with discrete or nonparametric mixture models is considered, and reliable ways of construction of the nonparametric mixture model estimator are reviewed and set into perspective. Construction of the maximum likelihood estimator of the mixing distribution is done for any number of components up to the global nonparametric maximum likelihood bound using the EM algorithm. In addition, the estimators of Chao and Zelterman are considered with some generalisations of Zelterman’s estimator. All computations are done with CAMCR, a special software developed for population size estimation with mixture models. Several examples and data sets are discussed and the estimators illustrated. Problems using the mixture model-based estimators are highlighted.

A capture-recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 x 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture-recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture-recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

Application of one-list capture-recapture models to scrapie surveillance data in Great Britain

In this paper, we apply one-list capture-recapture models to estimate the number of scrapie-affected holdings in Great Britain. We applied this technique to the Compulsory Scrapie Flocks Scheme dataset where cases from all the surveillance sources monitoring the presence of scrapie in Great Britain, the abattoir survey, the fallen stock survey and the statutory reporting of clinical cases, are gathered. Consequently, the estimates of prevalence obtained from this scheme should be comprehensive and cover all the different presentations of the disease captured individually by the surveillance sources. Two estimators were applied under the one-list approach: the Zelterman estimator and Chao's lower bound estimator. Our results could only inform with confidence the scrapie-affected holding population with clinical disease; this moved around the figure of 350 holdings in Great Britain for the period under study, April 2005-April 2006. Our models allowed the stratification by surveillance source and the input of covariate information, holding size and country of origin. None of the covariates appear to inform the model significantly. Crown Copyright (C) 2008 Published by Elsevier B.V. All rights reserved.

Adjusted jackknife for imputation under unequal probability sampling without replacement

Imputation is commonly used to compensate for item non-response in sample surveys. If we treat the imputed values as if they are true values, and then compute the variance estimates by using standard methods, such as the jackknife, we can seriously underestimate the true variances. We propose a modified jackknife variance estimator which is defined for any without-replacement unequal probability sampling design in the presence of imputation and non-negligible sampling fraction. Mean, ratio and random-imputation methods will be considered. The practical advantage of the method proposed is its breadth of applicability.

Seston capture by Hydropsyche siltalai and the accuracy of capture efficiency estimates

1. Suspension feeding by caseless caddisfly larvae (Trichoptera) constitutes a major pathway for energy flow, and strongly influences productivity, in streams and rivers. 2. Consideration of the impact of these animals on lotic ecosystems has been strongly influenced by a single study investigating the efficiency of particle capture of nets built by one species of hydropsychid caddisfly. 3. Using water sampling techniques at appropriate spatial scales, and taking greater consideration of local hydrodynamics than previously, we examined the size-frequency distribution of particles captured by the nets of Hydropsyche siltalai. Our results confirm that capture nets are selective in terms of particle size, and in addition suggest that this selectivity is for particles likely to provide the most energy. 4. By incorporating estimates of flow diversion around the nets of caseless caddisfly larvae, we show that capture efficiency (CE) is considerably higher than previously estimated, and conclude that more consideration of local hydrodynamics is needed to evaluate the efficiency of particle capture. 5. We use our results to postulate a mechanistic explanation for a recent example of interspecific facilitation, whereby a reduction of near-bed velocities seen in single species monocultures leads to increased capture rates and local depletion of seston within the region of reduced velocity.

API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives

Individual identification via DNA profiling is important in molecular ecology, particularly in the case of noninvasive sampling. A key quantity in determining the number of loci required is the probability of identity (PIave), the probability of observing two copies of any profile in the population. Previously this has been calculated assuming no inbreeding or population structure. Here we introduce formulae that account for these factors, whilst also accounting for relatedness structure in the population. These formulae are implemented in API-CALC 1.0, which calculates PIave for either a specified value, or a range of values, for F-IS and F-ST.

Thermoselective phase property of silica tethered with fluorinated chains for controlled 'release' and 'capture' of catalytic fluorous tin species

The temperature dependent mixing of organic and fluorous phases is one of the key principals of fluorous biphasic systems (FBS). Given the high cost of the perfluorous solvents and their impacts to the environment, it is apparent that elimination of these solvents in bulk quantity in the FBS is advantageous. We report for the first time, the surface coverage of silica with a fluorous solvent like material that traps (at ambient temperatures) and releases (at elevated temperatures) a fluorous tin bromide in organic solvent. Here, we demonstrate the catalytic utilisation of this species for the hydrocyclisation of 6-bromo-1-hexene with NaBH4. (C) 2002 Elsevier Science B.V. All rights reserved.