A comparison of hierarchical models for relative catch efficiency based on paired-gear data for US Northwest Atlantic fish stocks

2013 ◽  
Vol 70 (9) ◽  
pp. 1306-1316 ◽  
Author(s):  
Timothy J. Miller
Keyword(s):  
Size Effects ◽  
Hierarchical Models ◽  
Northwest Atlantic ◽  
Fish Stocks ◽  
Gear Design ◽  
The Us ◽  
Conditional Beta ◽  
Binomial Models ◽  
Random Pair ◽  
Better Than

Selectivity and catch comparison studies are important for surveys that use two or more gears to collect relative abundance information. Prevailing model-based analytical methods for studies using a paired-gear design assume a binomial model for the data from each pair of gear sets. Important generalizations include nonparametric smooth size effects and normal random pair and size effects, but current methods for fitting models that account for random smooth size effects are restrictive, and observations within pairs may exhibit extra-binomial variation. I propose a hierarchical model that accounts for random smooth size effects among pairs and extra-binomial variation within pairs with a conditional beta-binomial distribution. I compared relative performance of models with different conditional distribution and random effects assumptions fit to data on 16 species from an experiment carried out in the US Northwest Atlantic Ocean comparing a new and a retiring vessel. For more than half of the species, conditional beta-binomial models performed better than binomial models, and accounting for random variation among pairs in the relative efficiency was important for all species.

Martin Shapiro: An Appreciation

The Forum ◽  
2016 ◽  
Vol 14 (2) ◽  
Author(s):  
R. Shep Melnick
Keyword(s):  
Institutional Environment ◽  
Empirical Studies ◽  
The Political ◽  
Public Officials ◽  
Thick Description ◽  
Past Half Century ◽  
The Us ◽  
The Matrix ◽  
The One ◽  
Better Than

AbstractOver the past half century no judicial politics scholar has been more respected or influential than Martin Shapiro. Yet it is hard to identify a school of thought one could call “Shapiroism.” Rather than offer convenient methodologies or grand theories, Shapiro provides rich empirical studies that show us how to think about the relationship between law and courts on the one hand and politics and governing on the other. Three key themes run through Shapiro’s impressive oevre. First, rather than study courts in isolation, political scientists should view them as “one government agency among many,” and seek to “integrate the judicial system in the matrix of government and politics in which it actually operates.” Law professors may understand legal doctrines better than political scientists, but we know (or should know) the rest of the political system better than they do. Second, although judges inevitably make political decisions, their institutional environment leads them to act differently from other public officials. Most importantly, their legitimacy rests on their perceived impartiality within the plaintiff-defendant-judge triad. The conflict between judges’ role as impartial arbiter and enforcer of the laws of the regime can never be completely resolved and places powerful constraints on their actions. Third, the best way to understand the complex relationship between courts and other elements of the regime is comparative analysis. Shapiro played a major role in resuscitating comparative law, especially in his work comparing the US and the EU. All this he did with a rare combination of thick description and crisp, jargon-free analysis, certainly a rarity the political science of our time.

scholarly journals Fast effect size shrinkage software for beta-binomial models of allelic imbalance

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 2024
Author(s):  
Joshua P. Zitovsky ◽  
Michael I. Love
Keyword(s):  
Allelic Imbalance ◽  
Real Data ◽  
Shrinkage Estimators ◽  
Data Set ◽  
Bayesian Shrinkage ◽  
In Cis ◽  
Posterior Estimation ◽  
Binomial Models ◽  
Better Than ◽  
Diploid Organism

Allelic imbalance occurs when the two alleles of a gene are differentially expressed within a diploid organism and can indicate important differences in cis-regulation and epigenetic state across the two chromosomes. Because of this, the ability to accurately quantify the proportion at which each allele of a gene is expressed is of great interest to researchers. This becomes challenging in the presence of small read counts and/or sample sizes, which can cause estimators for allelic expression proportions to have high variance. Investigators have traditionally dealt with this problem by filtering out genes with small counts and samples. However, this may inadvertently remove important genes that have truly large allelic imbalances. Another option is to use pseudocounts or Bayesian estimators to reduce the variance. To this end, we evaluated the accuracy of four different estimators, the latter two of which are Bayesian shrinkage estimators: maximum likelihood, adding a pseudocount to each allele, approximate posterior estimation of GLM coefficients (apeglm) and adaptive shrinkage (ash). We also wrote C++ code to quickly calculate ML and apeglm estimates and integrated it into the apeglm package. The four methods were evaluated on two simulations and one real data set. Apeglm consistently performed better than ML according to a variety of criteria, and generally outperformed use of pseudocounts as well. Ash also performed better than ML in one of the simulations, but in the other performance was more mixed. Finally, when compared to five other packages that also fit beta-binomial models, the apeglm package was substantially faster and more numerically reliable, making our package useful for quick and reliable analyses of allelic imbalance. Apeglm is available as an R/Bioconductor package at http://bioconductor.org/packages/apeglm.

scholarly journals The impact of alternative rebuilding strategies to rebuild overfished stocks

2016 ◽  
Vol 73 (9) ◽  
pp. 2190-2207 ◽  
Author(s):  
Chantel R. Wetzel ◽  
André E. Punt ◽  
Keyword(s):  
West Coast ◽  
Life Histories ◽  
Estimation Error ◽  
The United States ◽  
Fish Stocks ◽  
Strategy Evaluation ◽  
The Us ◽  
History Of ◽  
The Impact ◽  
Us West

Abstract Ending overfishing and rebuilding fish stocks to levels that provide for optimum sustainable yield is a concern for fisheries management worldwide. In the United States, fisheries managers are legally mandated to end overfishing and to implement rebuilding plans for fish stocks that fall below minimum stock size thresholds. Rebuilding plans should lead to recovery to target stock sizes within 10 years, except in situations where the life history of the stock or environmental conditions dictate otherwise. Federally managed groundfish species along the US West Coast have diverse life histories where some are able to rebuild quickly from overfished status, while others, specifically rockfish (Sebastes spp.), may require decades for rebuilding. A management strategy evaluation which assumed limited estimation error was conducted to evaluate the performance of alternative strategies for rebuilding overfished stocks for these alternative US West Coast life histories. Generally, the results highlight the trade-off between the reduction of catches during rebuilding vs. the length of rebuilding. The most precautionary rebuilding plans requiring the greatest harvest reduction resulted in higher average catches over the entire projection period compared with strategies that required a longer rebuilding period with less of a reduction in rebuilding catch. Attempting to maintain a 50% probability of rebuilding was the poorest performing rebuilding strategy for all life histories, resulting in a large number of changes to the rebuilding plan, increased frequency of failing to meet rebuilding targets, and higher variation in catch. The rebuilding plans that implemented a higher initial rebuilding probability (≥60%) for determining rebuilding fishing mortality and targets generally resulted in fewer changes to the rebuilding plans and rebuilt by the target rebuilding year, particularly for stocks with the longer rebuilding plans (e.g. rockfishes).

scholarly journals Understanding the Average Impact of Microcredit Expansions: A Bayesian Hierarchical Analysis of Seven Randomized Experiments

2019 ◽  
Vol 11 (1) ◽  
pp. 57-91 ◽  
Author(s):  
Rachael Meager
Keyword(s):  
External Validity ◽  
Hierarchical Models ◽  
Hierarchical Analysis ◽  
Randomized Experiments ◽  
Average Effect ◽  
Bayesian Hierarchical ◽  
Heterogeneous Effects ◽  
Average Impact ◽  
The Impact ◽  
Better Than

Despite evidence from multiple randomized evaluations of microcredit, questions about external validity have impeded consensus on the results. I jointly estimate the average effect and the heterogeneity in effects across seven studies using Bayesian hierarchical models. I  find the impact on household business and consumption variables is unlikely to be transformative and may be negligible. I find reasonable external validity: true heterogeneity in effects is moderate, and approximately 60 percent of observed heterogeneity is sampling variation. Households with previous business experience have larger but more heterogeneous effects. Economic features of microcredit interventions predict variation in effects better than studies’ evaluation protocols. (JEL D14, G21, I38, O12, O16, P34, P36)

Frequency Distributions for Hourly and Daily Clearness Indices

2001 ◽  
Author(s):  
Manuel Ibañez ◽  
William A. Beckman ◽  
Sanford A. Klein
Keyword(s):  
Solar Radiation ◽  
Recent Literature ◽  
Weather Data ◽  
Clearness Index ◽  
Frequency Distributions ◽  
The Us ◽  
Daily Frequency ◽  
Better Than ◽  
Exponential Probability

Abstract The clearness index for hourly and daily radiation is an important parameter in describing solar radiation. Liu and Jordan demonstrated that the monthly average daily clearness index could be used to predict the long-term distribution of daily solar radiation in a month. This paper reviews recent literature on the prediction of hourly and daily frequency distributions and cumulative frequency distributions of clearness indices. Ten years of measured weather data for six cities in the US are used to investigate the nature of the hourly and daily frequency distributions. A second set of ten years of data for six cities is used to verify the predictions. A bi-exponential probability density function is proposed that fits the observed bimodal nature of the data better than existing models. A case is made for the function being universal.

Disease in commercially valuable fish stocks in the Northwest Atlantic

1987 ◽  
Vol 18 (9) ◽  
pp. 496-504 ◽  
Author(s):  
John J Ziskowski ◽  
Linda Despres-Patanjo ◽  
Robert A Murchelano ◽  
Arnold B Howe ◽  
Daniel Ralph ◽  
...  
Keyword(s):  
Northwest Atlantic ◽  
Fish Stocks

Evaluating the potential for trophodynamic control of fish by the longfin inshore squid (Loligo pealeii) in the Northwest Atlantic Ocean

2008 ◽  
Vol 65 (11) ◽  
pp. 2524-2535 ◽  
Author(s):  
Mary E. Hunsicker ◽  
Timothy E. Essington
Keyword(s):  
Published Data ◽  
Apex Predator ◽  
Northwest Atlantic ◽  
Fish Stocks ◽  
Juvenile Mortality ◽  
Fish Recruitment ◽  
Juvenile Stages ◽  
Commercially Important ◽  
A Minor ◽  
Loligo Pealeii

Many marine apex predator populations have been depleted via targeted fishing, potentially enhancing the productivity of lower trophic-level species such as squid. Squid may be predators of juvenile stages of fish stocks, so fishing could induce depensatory juvenile mortality. Here we evaluate the energetic potential of the longfin inshore squid ( Loligo pealeii ) to exert trophodynamic control on recruitment of several commercially important fish populations. We estimated the population prey consumption of L. pealeii by developing bioenergetics and population models based on previously published data. Our predictions of population consumption showed that squid consume high quantities of prey on daily and seasonal time scales. Further, comparisons between our estimates of population consumption and fish recruitment biomass indicate that L. pealeii may potentially exert a trophodynamic control on the recruitment success of commercially exploited fish species even if these species are only a minor prey item of squid. Overall, our findings suggest that the predation interactions of L. pealeii should be considered when managing and rebuilding fish stocks in the northwest Atlantic continental shelf ecosystem.

Temporal, spatial, and body size effects on growth rates of loggerhead sea turtles (Caretta caretta) in the Northwest Atlantic

2013 ◽  
Vol 160 (10) ◽  
pp. 2711-2721 ◽  
Author(s):  
Karen A. Bjorndal ◽  
Barbara A. Schroeder ◽  
Allen M. Foley ◽  
Blair E. Witherington ◽  
Michael Bresette ◽  
...  
Keyword(s):  
Body Size ◽  
Growth Rates ◽  
Size Effects ◽  
Sea Turtles ◽  
Caretta Caretta ◽  
Loggerhead Sea Turtles ◽  
Northwest Atlantic

scholarly journals Effect of message congruency on attention and recall in pictorial health warning labels

2017 ◽  
Vol 27 (3) ◽  
pp. 266-271 ◽  
Author(s):  
Kirsten Lochbuehler ◽  
Melissa Mercincavage ◽  
Kathy Z Tang ◽  
C Dana Tomlin ◽  
Joseph N Cappella ◽  
...  
Keyword(s):  
Dwell Time ◽  
Design Feature ◽  
Incongruent Condition ◽  
Congruent Condition ◽  
Warning Labels ◽  
Textual Information ◽  
Health Warning ◽  
The Us ◽  
Label Content ◽  
Better Than

ObjectiveThe nine pictorial health warning labels (PWLs) proposed by the US Food and Drug Administration vary in format and feature of visual and textual information. Congruency is the degree to which visual and textual features reflect a common theme. This characteristic can affect attention and recall of label content. This study investigates the effect of congruency in PWLs on smoker’s attention and recall of label content.Methods120 daily smokers were randomly assigned to view either congruent or incongruent PWLs, while having their eye movements recorded. Participants were asked to recall label content immediately after exposure and 5 days later.ResultsOverall, the image was viewed more and recalled better than the text. Smokers in the incongruent condition spent more time focusing on the text than smokers in the congruent condition (p=0.03), but dwell time of the image did not differ. Despite lower dwell time on the text, smokers in the congruent condition were more likely to correctly recall it on day 1 (p=0.02) and the risk message of the PWLs on both day 1 (p=0.01) and day 5 (p=0.006) than smokers in the incongruent condition.ConclusionsThis study identifies an important design feature of PWLs and demonstrates objective differences in how smokers process PWLs. Our results suggest that message congruency between visual and textual information is beneficial to recall of label content. Moreover, images captured and held smokers’ attention better than the text.

scholarly journals A literature review of drugs for the treatment of COVID-19

2020 ◽  
Author(s):  
Yuri Clement ◽  
Satish Jankie ◽  
Shalini Pooransingh ◽  
Diane Ignacio ◽  
Avril Reid ◽  
...  
Keyword(s):  
Literature Review ◽  
Clinical Evidence ◽  
Search Terms ◽  
Published Evidence ◽  
Overwhelming Evidence ◽  
The Us ◽  
Repurposed Drugs ◽  
Robust Evidence ◽  
Food And Drugs Administration ◽  
Better Than

Objectives: To review the published evidence of repurposed drugs, antivirals and biologics for the treatment of COVID-19. Materials and Methods: A literature review was conducted in several databases and research portals. Search terms included COVID-19, SARS-Cov-2, MERS, MERS-CoV, SARS, SARS-CoV, coronavirus, beta-coronavirus, influenza, pneumonia and several drugs considered for use in COVID-19. Results: There is a paucity of clinical evidence regarding the safety and efficacy of most agents being considered for the treatment of COVID-19. However, based on promising preliminary research the US Food and Drugs Administration has authorized the emergency use of hydroxychloroquine and remdesivir for hospitalized COVID-19 patients. To date, the most robust evidence for lopinavir-ritonavir (LPV/r) found that it was no better than standard care. Overwhelming evidence suggests that corticosteroids increase mortality, nosocomial infections and lengthen hospitalization in SARS and MERS patients, and should be used cautiously in patients with severe respiratory symptoms. Additionally, low level evidence suggests that tocilizumab may be useful to reduce the cytokine storm precipitated by SARS-CoV-2 infection. Conclusions: Hydroxychloroquine and remdesivir have surged to the front of the race to repurpose drugs in the fight against COVID-19. With hundreds of ongoing trials it is envisaged that indisputable evidence would be provided for prophylactic and therapeutic use of drugs and biologics within the next few months. However, in our setting it would be worthwhile to consider the availability and accessibility of some of these agents.

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