A maximum likelihood approach for estimating growth from tag–recapture data

The Fabens method is commonly used to estimate growth parameters k and l infinity in the von Bertalanffy model from tag-recapture data. However, the Fabens method of estimation has an inherent bias when individual growth is variable. This paper presents an asymptotically unbiassed method using a maximum likelihood approach that takes account of individual variability in both maximum length and age-at-tagging. It is assumed that each individual's growth follows a von Bertalanffy curve with its own maximum length and age-at-tagging. The parameter k is assumed to be a constant to ensure that the mean growth follows a von Bertalanffy curve and to avoid overparameterization. Our method also makes more efficient use nf thp measurements at tno and recapture and includes diagnostic techniques for checking distributional assumptions. The method is reasonably robust and performs better than the Fabens method when individual growth differs from the von Bertalanffy relationship. When measurement error is negligible, the estimation involves maximizing the profile likelihood of one parameter only. The method is applied to tag-recapture data for the grooved tiger prawn (Penaeus semisulcatus) from the Gulf of Carpentaria, Australia.

Accounting for individual variability in the von Bertalanffy growth model

Estimation of von Bertalanffy growth parameters has received considerable attention in fisheries research. Since Sainsbury (1980, Can. J. Fish. Aquat. Sci. 37: 241-247) much of this research effort has centered on accounting for individual variability in the growth parameters. In this paper we demonstrate that, in analysis of tagging data, Sainsbury's method and its derivatives do not, in general, satisfactorily account for individual variability in growth, leading to inconsistent parameter estimates (the bias does not tend to zero as sample size increases to infinity). The bias arises because these methods do not use appropriate conditional expectations as a basis for estimation. This bias is found to be similar to that of the Fabens method. Such methods would be appropriate only under the assumption that the individual growth parameters that generate the growth increment were independent of the growth parameters that generated the initial length. However, such an assumption would be unrealistic. The results are derived analytically, and illustrated with a simulation study. Until techniques that take full account of the appropriate conditioning have been developed, the effect of individual variability on growth has yet to be fully understood.

A simple method for estimating growth parameters from multiple length-frequency data in presence of continuous recruitment

The extended recruitment season for short-lived species such as prawns biases the estimation of growth parameters from length-frequency data when conventional methods are used. We propose a simple method for overcoming this bias given a time series of length-frequency data. The difficulties arising from extended recruitment are eliminated by predicting the growth of the succeeding samples and the length increments of the recruits in previous samples. This method requires that some maximum size at recruitment can be specified. The advantages of this multiple length-frequency method are: it is simple to use; it requires only three parameters; no specific distributions need to be assumed; and the actual seasonal recruitment pattern does not have to be specified. We illustrate the new method with length-frequency data on the tiger prawn Penaeus esculentus from the north-western Gulf of Carpentaria, Australia.

Unbiased estimating equations from working correlation models for irregularly timed repeated measures

The method of generalized estimating equation-, (GEEs) has been criticized recently for a failure to protect against misspecification of working correlation models, which in some cases leads to loss of efficiency or infeasibility of solutions. However, the feasibility and efficiency of GEE methods can be enhanced considerably by using flexible families of working correlation models. We propose two ways of constructing unbiased estimating equations from general correlation models for irregularly timed repeated measures to supplement and enhance GEE. The supplementary estimating equations are obtained by differentiation of the Cholesky decomposition of the working correlation, or as score equations for decoupled Gaussian pseudolikelihood. The estimating equations are solved with computational effort equivalent to that required for a first-order GEE. Full details and analytic expressions are developed for a generalized Markovian model that was evaluated through simulation. Large-sample ".sandwich" standard errors for working correlation parameter estimates are derived and shown to have good performance. The proposed estimating functions are further illustrated in an analysis of repeated measures of pulmonary function in children.

Confucian education and enlightenment for the masses in the manner of Guwen guanzhi

The topic of this study is the most renowned anthology of essays written in Literary Chinese, Guwen guanzhi, compiled and edited by Wu Chengquan (Chucai) and Wu Dazhi (Diaohou), and first published during the Qing dynasty, in 1695. Because of the low social standing of the compilers, their anthology remained outside the recommended study materials produced by members of the established literati and used for preparing students in the imperial civil-service examinations. However, since the end of the imperial era, Guwen guanzhi has risen to a position as the classical anthology par excellence. Today it is widely used as required or supplementary reading material of Literary Chinese in middle-schools both in Mainland China and on Taiwan. The goal of this study is to explain the persistent longevity of the anthology. So far, Guwen guanzhi has not been a topic of any published academic study, and the opinions expressed on it in various sources are widely discrepant. Through a comparative study with a dozen classical Chinese anthologies in use during the early Qing dynasty, this study reveals the extent to which the compilers of Guwen guanzhi modelled their work after other selections. Altogether 86 % of the texts in Guwen guanzhi originate from another Qing era anthology, Guwen xiyi, often copied character by character. However, the notes and commentaries are all different. Concentrating on the special characteristics unique to Guwen guanzhi—the commentaries and certain peculiarities in the selection of texts—this study then discusses the possible reasons for the popularity of Guwen guanzhi over the competing readers during the Qing era. Most remarkably, Guwen guanzhi put in practise the equalitarian, educational ideals of the Ming philosopher Wang Shouren (Yangming). Thus Guwen guanzhi suited the self-enlightenment needs of the ”subordinate classes”, in particular the rising middle-class comprised mainly of merchants. The lack of moral teleology, together with the compact size, relative comprehensiveness of the selection and good notes and comments, have made Guwen guanzhi well suited for the new society since the abolition of the imperial examination system. Through a content analysis, based on a sample of the texts, this study measures the relative emphasis on centralism and localism (both in concrete and spiritual terms) expressed in the texts of Guwen guanzhi. The analysis shows that the texts manifest some bias towards emphasising innate virtue on the expense of state-defined moral. This may reflect hidden critique towards intellectual oppression by the centralised imperial rule. During the early decades of the Qing era, such critique was often linked to Ming-loyalism. Finally, this study concludes that the kind of ”spiritual localism” that Guwen guanzhi manifests gives it the potential to undermine monolithic orthodoxy even in today’s Chinese societies. This study has progressed hand in hand with the translation of a selection of texts from Guwen guanzhi into Finnish, published by Gaudeamus Helsinki University Press: Jadekasvot – Valittuja tarinoita Kiinan muinaisajoilta (2005), Jadelähde – Valittuja kirjoituksia Kiinan keskiajalta (2007) and Jadepeili – Valittuja kirjoituksia keisarillisen Kiinan kulta-ajoilta (2008). All translations are critical editions, complete with extensive notation. The trilogy is the first comprehensive translation based on Guwen guanzhi in a European language.

Low-intensity differential photocapacitance of MOS structures

Some new observations on the phenomenon of photocapacitane on n-type silicon MOS structures under low intensities of illumination are reported. The difference between the illuminated and dark C---characteristics is automatically followed as a function of the applied bias thereby obtaining the differential photocapacitance and the resulting characteristics has been termed as the Low Intensity Differential Photocapacitance (LIDP). For an MOS capacitor, the LIDP characteristics is seen to go through a well defined maximum. The phenomenon has been investigated under different ambient conditions like light intensity, temperature, dependance of the frequency of the light etc. and it has been found that the phenomenon is due to a band excband excitation. In this connection, a novel sensitive technique for the measurement of the capacitance based upon following the frequency changes of a tank circuit is also described in some detail. It is also shown that the phenomenon can be understood by a simple theoretical model.

Given and News : Media discourse and the construction of community on national days

National anniversaries such as independence days demand precise coordination in order to make citizens change their routines to forego work and spend the day at rest or at festivities that provide social focus and spectacle. The complex social construction of national days is taken for granted and operates as a given in the news media, which are the main agents responsible for coordinating these planned disruptions of normal routines. This study examines the language used in the news to construct the rather unnatural idea of national days and to align people in observing them. The data for the study consist of news stories about the Fourth of July in the New York Times, sampled over 150 years and are supplemented by material from other sources and other countries. The study is multidimensional, applying concepts from pragmatics (speech acts, politeness, information structure), systemic functional linguistics (the interpersonal metafunction and the Appraisal framework) and cognitive linguistics (frames, metaphor) as well as journalism and communications to arrive at an interdisciplinary understanding of how resources for meaning are used by writers and readers of the news stories. The analysis shows that on national anniversaries, nations tend to be metaphorized as persons having birthdays, to whom politeness should be shown. The face of the nation is to be respected in the sense of identifying the nation's interests as one's own (positive face) and speaking of citizen responsibilities rather than rights (negative face). Resources are available for both positive and negative evaluations of events and participants and the newspaper deftly changes footings (Goffman 1981) to demonstrate the required politeness while also heteroglossically allowing for a certain amount of disattention and even protest - within limits, for state holidays are almost never construed as Bakhtinian festivals, as they tend to reaffirm the hierarchy rather than invert it. Celebrations are evaluated mainly for impressiveness, and for the essentially contested quality of appropriateness, which covers norms of predictability, size, audience response, aesthetics, and explicit reference to the past. Events may also be negatively evaluated as dull ("banal") or inauthentic ("hoopla"). Audiences are evaluated chiefly in terms of their enthusiasm, or production of appropriate displays for emotional response, for national days are supposed to be occasions of flooding-out of nationalistic feeling. By making these evaluations, the newspaper reinforces its powerful position as an independent critic, while at the same time playing an active role in the construction and reproduction of emotional order embodied in "the nation's birthday." As an occasion for mobilization and demonstrations of power, national days may be seen to stand to war in the relation of play to fighting (Bateson 1955). Evidence from the newspaper's coverage of recent conflicts is adduced to support this analysis. In the course of the investigation, methods are developed for analyzing large collections of newspaper content, particularly topical soft news and feature materials that have hitherto been considered less influential and worthy of study than so-called hard news. In his work on evaluation in newspaper stories, White (1998) proposed that the classic hard news story is focused on an event that threatens the social order, but news of holidays and celebrations in general does not fit this pattern, in fact its central event is a reproduction of the social order. Thus in the system of news values (Galtung and Ruge 1965), national holiday news draws on "ground" news values such as continuity and predictability rather than "figure" news values such as negativity and surprise. It is argued that this ground helps form a necessary space for hard news to be seen as important, similar to the way in which the information structure of language is seen to rely on the regular alternation of given and new information (Chafe 1994).

Subsampling multi-species trawl catches from tropical northern Australia: Does it matter which part of the catch is sampled?

Subsampling is a common method for estimating the abundance of species in trawl catches. However, the accuracy of subsampling in representing the total catch has not been assessed. To estimate one possible source of bias due to subsampling, we tested whether the position on trawler sorting trays from which subsamples were taken affected their ability to represent species in catches. This was done by sorting catches into 10 kg subsamples and comparing subsamples taken from different positions on the sorting tray. Comparisons were made after species were grouped into three categories of abundance, either 'rare', 'common' or 'abundant'. A generalised linear model analysis showed that taking subsamples from different positions on the sorting tray had no major effect on estimating the total numbers or weights of fish or invertebrates, or the total number of fish or invertebrate taxa, recorded in each position. Some individual taxa showed differences between positions on the sorting tray (11.5% of taxa ina three-position design; 25% in a five-position design). But consistent and meaningful patterns in the position of these taxa on the sorting tray could only be seen for the pony fish Leiognathus moretoniensis and the saucer scallop Amusium pleuronectes. Because most bycatch laxa are well mixed throughout the catch, subsamples can be taken from any position on trawler sorting trays without introducing bias.

Estimating equations for parameters in stochastic growth models from tag-recapture data

James (1991, Biometrics 47, 1519-1530) constructed unbiased estimating functions for estimating the two parameters in the von Bertalanffy growth curve from tag-recapture data. This paper provides unbiased estimating functions for a class of growth models that incorporate stochastic components and explanatory variables. a simulation study using seasonal growth models indicates that the proposed method works well while the least-squares methods that are commonly used in the literature may produce substantially biased estimates. The proposed model and method are also applied to real data from tagged rack lobsters to assess the possible seasonal effect on growth.

Effect of individual variability on estimation of population parameters from length-frequency data

We consider estimation of mortality rates and growth parameters from length-frequency data of a fish stock when there is individual variability in the von Bertalanffy growth parameter L-infinity and investigate the possible bias in the estimates when the individual variability is ignored. Three methods are examined: (i) the regression method based on the Beverton and Holt's (1956, Rapp. P.V. Reun. Cons. Int. Explor. Mer, 140: 67-83) equation; (ii) the moment method of Powell (1979, Rapp. PV. Reun. Int. Explor. Mer, 175: 167-169); and (iii) a generalization of Powell's method that estimates the individual variability to be incorporated into the estimation. It is found that the biases in the estimates from the existing methods are, in general, substantial, even when individual variability in growth is small and recruitment is uniform, and the generalized method performs better in terms of bias but is subject to a larger variation. There is a need to develop robust and flexible methods to deal with individual variability in the analysis of length-frequency data.

Growth curves with explanatory variables and estimation of the effect of tagging

The von Bertalanffy growth model is extended to incorporate explanatory variables. The generalized model includes the switched growth model and the seasonal growth model as special cases, and can also be used to assess the tagging effect on growth. Distribution-free and consistent estimating functions are constructed for estimation of growth parameters from tag-recapture data in which age at release is unknown. This generalizes the work of James (1991, Biometrics 47 1519-1530) who considered the classical model and allowed for individual variability in growth. A real dataset from barramundi (Lates calcarifer) is analysed to estimate the growth parameters and possible effect of tagging on growth.

Non-invasive assessment of pineapple and mango fruit quality using near infra-red spectroscopy

The potential of near infra-red (NIR) spectroscopy for non-invasive measurement of fruit quality of pineapple (Ananas comosus var. Smooth Cayenne) and mango (Magnifera indica var. Kensington) fruit was assessed. A remote reflectance fibre optic probe, placed in contact with the fruit skin surface in a light-proof box, was used to deliver monochromatic light to the fruit, and to collect NIR reflectance spectra (760–2500 nm). The probe illuminated and collected reflected radiation from an area of about 16 cm2. The NIR spectral attributes were correlated with pineapple juice Brix and with mango flesh dry matter (DM) measured from fruit flesh directly underlying the scanned area. The highest correlations for both fruit were found using the second derivative of the spectra (d2 log 1/R) and an additive calibration equation. Multiple linear regression (MLR) on pineapple fruit spectra (n = 85) gave a calibration equation using d2 log 1/R at wavelengths of 866, 760, 1232 and 832 nm with a multiple coefficient of determination (R2) of 0.75, and a standard error of calibration (SEC) of 1.21 °Brix. Modified partial least squares (MPLS) regression analysis yielded a calibration equation with R2 = 0.91, SEC = 0.69, and a standard error of cross validation (SECV) of 1.09 oBrix. For mango, MLR gave a calibration equation using d2 log 1/R at 904, 872, 1660 and 1516 nm with R2 = 0.90, and SEC = 0.85% DM and a bias of 0.39. Using MPLS analysis, a calibration equation with R2 = 0.98, SEC = 0.54 and SECV = 1.19 was obtained. We conclude that NIR technology offers the potential to assess fruit sweetness in intact whole pineapple and DM in mango fruit, respectively, to within 1° Brix and 1% DM, and could be used for the grading of fruit in fruit packing sheds.