A comparison of methods for estimating mean fecundity

Four computational methods for estimating mean fecundity are compared by Monte Carlo simulation. One of the four methods is the simple expedient of estimating fecundity at sample mean length, a method known to be downwardly biassed. The Monte Carlo study shows that the other three methods reduce bias and provide worthwhile efficiency gains. For small samples, the most efficient of the four methods is a 'bias adjustment', proposed here, that uses easily calculated sample statistics. For large samples, a numerical integration method has the highest efficiency. The fourth method, a 'direct summation' procedure which can be done easily in many statistical or spreadsheet programs, performs well for all sample sizes.     

Bayesian methods for estimating GEBVs of threshold traits

Estimation of genomic breeding values is the key step in genomic selection (GS). Manymethods have been proposed for continuous traits, but methods for threshold traits arestill scarce. Here we introduced threshold model to the framework of GS, and specifically,we extended the three Bayesian methods BayesA, BayesB and BayesCπ on the basis ofthreshold model for estimating genomic breeding values of threshold traits, and theextended methods are correspondingly termed BayesTA, BayesTB and BayesTCπ. Computingprocedures of the three BayesT methods using Markov Chain Monte Carlo algorithm werederived. A simulation study was performed to investigate the benefit of the presentedmethods in accuracy with the genomic estimated breeding values (GEBVs) for thresholdtraits. Factors affecting the performance of the three BayesT methods were addressed. Asexpected, the three BayesT methods generally performed better than the correspondingnormal Bayesian methods, in particular when the number of phenotypic categories was small.In the standard scenario (number of categories=2, incidence=30%,number of quantitative trait loci=50, h²=0.3), theaccuracies were improved by 30.4%, 2.4%, and 5.7% points,respectively. In most scenarios, BayesTB and BayesTCπ generated similar accuracies andboth performed better than BayesTA. In conclusion, our work proved that threshold modelfits well for predicting GEBVs of threshold traits, and BayesTCπ is supposed to be themethod of choice for GS of threshold traits.     

A comparison of methods for estimating plant population size

Assessing local population size is one of the most common tasks in biodiversity monitoring. Population size estimates are not only important for conservation management and population threat assessment; they also enter many other analyses in landscape ecology and conservation. It is therefore concerning that methods for estimating plant population sizes are not standardized. We surveyed the literature and found that the most commonly used methods are counting either all or only flowering individuals on a site, as well as counting individuals in random plots or plots on transects. Sometimes, these methods are combined in the same study, without assurance that they produce comparable results. We therefore conducted a field study, in which we obtained population size estimates from all four methods for six different calcareous grassland species at 18 study sites. Our results demonstrate not only substantial differences between overall count rates generated by the different methods, but methods that surveyed the whole population also systematically yielded lower counts when species were less visible and when the area was larger, suggesting that these methods suffer from biases that could distort species and site comparisons. We conclude that estimates from different methods should not be mixed, and that plot or transect based surveys have likely smaller biases for large areas or poorly visible individuals, and are therefore preferable.     

A comparison of different methods for estimating single-trial P300 latencies

Inferences from comparative analyses of reaction time and P300 latency are stronger when the various aspects of the distribution across trials are treated in the same way for both variables. To this end, a number of studies have resorted to estimation of P300 latency at the single-trial level. This report presents a comparative evaluation of two common methods for such single-trial analysis, i.e., peak-picking and template-matching. Both methods were applied to a representative set of real data, comprising different task conditions and two age groups. Relevant scoring parameters were varied: low-pass filter settings (down to 0.94 Hz) for peak-picking, template duration (250–970 msec) and use of covariance vs. correlation for template-matching, and use of a noise-range criterion for both methods. It is concluded that peak-picking with a 3.4 Hz filter, and template-matching using covariance and template duration between 600 and 800 msec, are best in terms of sensitivity and reliability, with peak-picking surpassing template-matching. Also, the marked increase in the number of rejected trials when the noise-range criterion was applied resulted in unwanted modulation of behavioral effects of task conditions and age groups.     

A comparison of two methods for estimating measurement repeatability in morphometric studies

1. Measurement repeatability is often reported in morphometric studies as an index of the contribution of measurement error to trait measurements. However, the common method of remeasuring a mounted specimen fails to capture some components of measurement error and could therefore yield inflated repeatability estimates. Remounting specimens between successive measurements is likely to provide more realistic estimates of repeatability, particularly for structures that are difficult to measure.
2. Using measurements of 22 somatic and genitalic traits of the neriid fly Telostylinus angusticollis, we compared repeatability estimates obtained via remeasurement of a specimen that is mounted once (single‐mounted method) versus remeasurement of a specimen that is remounted between measurements (remounted method). We also asked whether the difference in repeatability estimates obtained via the two methods depends on trait size, trait type (somatic vs. genitalic), sclerotization, or sex.
3. Repeatability estimates obtained via the remounted method were lower than estimates obtained via the single‐mounted method for each of the 22 traits, and the difference between estimates obtained via the two methods was generally greater for small structures (such as genitalic traits) than for large structures (such as legs and wings). However, the difference between estimates obtained via the two methods did not depend on trait type (genitalic or somatic), tissue type (soft or sclerotized) or sex.
4. Remounting specimens between successive measurements can provide more accurate estimates of measurement repeatability than remeasuring from a single mount, especially for small structures that are difficult to measure.

     

A comparison of methods for estimating the transition:transversion ratio from DNA sequences

Estimation of the ratio of the rates of transitions to transversions (TI:TV ratio) for a collection of aligned nucleotide sequences is important because it provides insight into the process of molecular evolution and because such estimates may be used to further model the evolutionary process for the sequences under consideration. In this paper, we compare several methods for estimating the TI:TV ratio, including the pairwise method [TREE 11 (1996) 158], a modification of the pairwise method due to Ina [J. Mol. Evol. 46 (1998) 521], a method based on parsimony (TREE 11 (1996) 158), a method due to Purvis and Bromham [J. Mol. Evol. 44 (1997) 112] that uses phylogenetically independent pairs of sequences, the maximum likelihood method, and a Bayesian method [Bioinformatics 17 (2001) 754]. We examine the performance of each estimator under several conditions using both simulated and real data.     

A comparison of methods for estimating raccoon abundance: Implications for disease vaccination programs

Accurate estimates of demographic parameters are critical to the management of wildlife populations, including management programs focused on controlling the spread of zoonotic diseases. Rabies managers in the United States Department of Agriculture (USDA) have applied a simple raccoon (Procyon lotor) abundance index (RAI) based on cumulative catch of unique raccoons per unit area to determine vaccine-bait distribution densities. This approach was designed to allow for both the collection of biological samples and to index raccoon abundance to determine bait densities for oral rabies programs. However, post-baiting surveillance data indicate that, on average, only 30% of raccoons sampled have vaccine induced rabies antibody titers, suggesting that bait densities may not be well calibrated to raccoon densities. We trapped raccoons using both capture-mark-recapture (CMR) and the standard RAI to evaluate the accuracy of the current index-based methodology for estimating raccoon density. We then developed a resource selection function from spatial data collected from radio-collared raccoons to standardize trap placement within the existing RAI protocol, and evaluated the performance of this modified RAI approach relative to CMR for estimating raccoon population size. Both abundance and density estimates derived using the RAI consistently underestimated raccoon population sizes compared with CMR methods. Similarly, although the use of resource selection models to inform trap placement appeared to improve the accuracy of the RAI, the effectiveness of this method was inconsistent because of an inability to account for variance in detection probabilities. Despite the logistical advantages of using indices to estimate population parameters to determine vaccine bait distribution densities, our results suggest that adjustments may be necessary to more accurately quantify raccoon abundance, which should improve the effectiveness of rabies management in the United States. In particular, estimates of detection probabilities are needed to more precisely quantify abundance estimates and ensure appropriate vaccine coverage rates. © 2012 The Wildlife Society.     

A comparison of some quick and simple threshold selection methods for stained cells

The segmentation accuracy of four fast and simple gray-scale threshold selection methods were compared using a data base of stained cervical cell images. Some postprocessing was applied to the segmented images to increase the accuracy of the nuclear segmentation. The most accurate method correctly segmented the cytoplasm of 81% of the cell images and the nuclei of 78% of the cell images in the data base.     

A comparison of methods for estimating the kinetic parameters of two simple types of transport process

Sets of experimental data, with known characteristics and error structures, have been simulated for the Michaelis-Menten equation plus a second term, either for linear transport or for competitive inhibition. The Michaelis-Menten equation plus linear term was fitted by several methods and the accuracy and the precision of the parameter estimates from the several methods were compared. The model-fitting methods were: three for least-squares non-linear regression, computer versions of two graphical methods and of two non-parametric methods. The most precise and accurate method was that of D.W. Marquardt (J. Soc. Ind. Appl. Math. 11 (1963) 431–441). The Michaelis-Menten equation with competitive inhibition was also fitted by several methods, viz., two for least-squared non-linear regression, a non-parametric method and four variants of the Preston-Schaeffer-Curran plot (Preston, R.L. et al. (1974) J. Gen. Physiol. 64, 443–467). The most precise and accurate of these was the non-linear regression method of W.W. Cleland (Adv. Enzymol. 29 (1967) 1–32). For both these models, the various graphical methods and non-parametric methods gave poor results and are not recommended.     

A comparison of survey and focal follow methods for estimating individual activity budgets of cetaceans

Activity budget data are essential for determining behavioral responses to physiological and ecological variables. Yet, few studies are available to investigate the robustness, accuracy, and biases of the methods used to estimate activity budgets for cetaceans. In this study, we compare activity budgets of 55 adult female bottlenose dolphins in Shark Bay, Australia derived from two methods: surveys (n = 6,903) and focal follows (n = 1,185, totaling 2,721 h of observation). Activity budgets estimated from survey data differed in all behavioral states compared to focal follow data. However, when controlling for temporal autocorrelation, only time spent socializing and time spent traveling remained disparate between the methods. To control for biases associated with assigning group‐level behavior to individuals, we also compared survey and focal follow activity budgets for lone females. Here we found differences between methods in time spent foraging and traveling regardless of whether we controlled for temporal autocorrelation, which suggests detection biases likely play a role in explaining differences in activity budget estimates between the two methodologies. Our results suggest that surveys are less representative of individual‐level activity budgets, and thus, when individual‐level knowledge about behavior is needed, focal follows are preferred.     

A comparison of in situ and simulated in situ methods for estimating oceanic primary production

Primary production data measured by in situ (IS) and ‘simulated’in situ (SIS) incubations were compared. To minimize differencesbetween the two types of incubations, SIS experiments were conductedin temperature-controlled incubators in which the spectral distributionand irradiance were adjusted to approximate IS conditions. ISavailable irradiance (I_Is) was computed from vertical attenuationof integrated surface irradiance. Vertical attenuation was estimatedusing a spectral irradiance model, validated by measured profilesof the vertical attenuation coefficient. IS incubations werecarried out using two methods. The first involved deploymentof bottles on a drifting array for whole-day (dawn to dusk)incubations. The second method employed an autonomous submersibleincubation device that performed short term (<1 h) incubationsat multiple depths. Differences between whole-day IS and SISincubation estimates were attributed partially to differencesbetween I_IS and SIS-available irradiance (I_SIS). Photosynthesis-irradiance(P-I) properties of IS and SIS populations from the whole-dayincubations were not significantly different. P-I propertiesof the short-term IS and SIS populations were significantlydifferent, although estimates of P^B (mg C mg Chl^–1 h^–1)from contemporaneous IS and SIS incubations did not differ by>40%. Integrated water-column primary production (IPP) estimatedusing P-I models derived from SIS data were within 15% of ISestimates of IPP.     

数据点选择与参数估计方法对杉木人工林自疏边界线的影响

自疏边界线是指植物种群发生密度依赖死亡时种群最大收获量的上边界线。已有研究由于在拟合自疏边界线的过程中对数据点的选择和参数估计的方法存在诸多的差异,进而导致产生对自疏法则的争议。该研究采用26年生杉木(Cunninghamia lanceolata)人工林的定位观测数据,对视觉法、死亡率法、等距区间法和相对密度法等4种数据点选择方法以及最小二乘法、降维分析法、分位数回归法和随机边界方程等4种参数拟合方法进行对比分析,以探寻客观选择自疏拟合数据和正确拟合方法的途径。比较4种不同的数据选择方法得出:视觉法具有较强的主观性;对于没有发生非密度依赖死亡的林分,死亡率法可以准确地确定林分自疏的起始点;等距区间法可以减少非密度依赖死亡的影响,得到的数据点能充分反映林分的自疏过程;相对密度法可以保证临界密度阈值以上的数据点拟合林分自疏边界线的有效性,并能排除非密度依赖死亡的影响。比较分析4种不同的拟合方法发现:最小二乘法和降维分析法拟合的林分自疏边界线均从实测数据"中心"穿过,与林分自疏边界线为林分收获量上边界线的涵义不相符合,无法真实反映林分的自疏进程;分位数回归和随机边界方程的拟合结果均与实测数据一致,能够较为准确地反映林分自疏的真实过程,但二者的统计推断要求都比较严格。分位数值的正确选取和残差足够小且趋于0,是分位数回归法和随机边界方程能否正确反映林分自疏动态的前提。     

A fine line: a comparison of methods for estimating ages of linear enamel hypoplasia formation

It is accepted that linear enamel hypoplasias (LEHs), a specific type of enamel thickness deficiency, are related to periodic physiological disruptions to enamel matrix secretion during times that teeth are developing. Thus, LEHs are treated as general indicators of metabolic stress. Because the disruptions that cause LEHs affect only the portion of the crown that is in the process of forming, determining their locations allows researchers to reconstruct chronologies of stressful events. It is widely held that the many of the commonly used macroscopic methods for estimating the timing of LEHs are imprecise and do not conform to our current understanding of the process of enamel formation. The goal of the present study is to compare estimated ages of LEH formation produced by two of the most commonly used macroscopic methods to those derived from data in recent histological studies that include more precise information about the timing of crown formation across diverse human populations. These approaches are compared in two ways: 1) by creating a theoretical model using simulated LEHs and 2) empirically, by analyzing data collected on a sample of ancient Nubians from Semna South (present-day Sudan). Results indicate that the approach derived from histological studies provides significantly higher age estimates than the commonly used methods and this difference is particularly marked in early forming LEHs. The magnitude of this difference is large enough to produce divergent interpretation of bioarchaeological datasets and suggests that reevaluation of the methods used to estimate ages of LEH formation may be justified.     

A comparison of two indirect methods for estimating average levels of gene flow using microsatellite data

We compare the performance of Nm estimates based on FST and RST obtained from microsatellite data using simulations of the stepwise mutation model with range constraints in allele size classes. The results of the simulations suggest that the use of microsatellite loci can lead to serious overestimations of Nm, particularly when population sizes are large (N > 5000) and range constraints are high (K < 20). The simulations also indicate that, when population sizes are small (N /= 50) and many loci (nl >/= 20), RST performs better than FST for most of the parameter space. However, FST-based estimates are always better than RST when sample sizes are moderate or small (ns 相似文献