PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data

Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth-death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open-source command-line Python program available at http://sourceforge.net/projects/pyrate/.

Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.

The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.

Three essays in incomplete contracts

General Introduction These three chapters, while fairly independent from each other, study economic situations in incomplete contract settings. They are the product of both the academic freedom my advisors granted me, and in this sense reflect my personal interests, and of their interested feedback. The content of each chapter can be summarized as follows: Chapter 1: Inefficient durable-goods monopolies In this chapter we study the efficiency of an infinite-horizon durable-goods monopoly model with a fmite number of buyers. We find that, while all pure-strategy Markov Perfect Equilibria (MPE) are efficient, there also exist previously unstudied inefficient MPE where high valuation buyers randomize their purchase decision while trying to benefit from low prices which are offered once a critical mass has purchased. Real time delay, an unusual monopoly distortion, is the result of this attrition behavior. We conclude that neither technological constraints nor concern for reputation are necessary to explain inefficiency in monopolized durable-goods markets. Chapter 2: Downstream mergers and producer's capacity choice: why bake a larger pie when getting a smaller slice? In this chapter we study the effect of downstream horizontal mergers on the upstream producer's capacity choice. Contrary to conventional wisdom, we find anon-monotonic relationship: horizontal mergers induce a higher upstream capacity if the cost of capacity is low, and a lower upstream capacity if this cost is high. We explain this result by decomposing the total effect into two competing effects: a change in hold-up and a change in bargaining erosion. Chapter 3: Contract bargaining with multiple agents In this chapter we study a bargaining game between a principal and N agents when the utility of each agent depends on all agents' trades with the principal. We show, using the Potential, that equilibria payoffs coincide with the Shapley value of the underlying coalitional game with an appropriately defined characteristic function, which under common assumptions coincides with the principal's equilibrium profit in the offer game. Since the problem accounts for differences in information and agents' conjectures, the outcome can be either efficient (e.g. public contracting) or inefficient (e.g. passive beliefs).

Open Environmental Information Upon Disclosure Request in China: The Paradox of Legal Mobilization

Taking a realist view that law is one form of politics, this dissertation studies the roles of citizens and organizations in mobilizing the law to request government agencies to disclose environmental information in China, and during this process, how the socio-legal field interacts with the political-legal sphere, and what changes have been brought about during their interactions. This work takes a socio-legal approach and applies methodologies of social science and legal analysis. It aims to understand the paradox of why and how citizens and entities have been invoking the law to access environmental information despite the fact that various obstacles exist and the effectiveness of the new mechanism of environmental information disclosure still remains low. The study is largely based on the 28 cases and eight surveys of environmental information disclosure requests collected by the author. The cases and surveys analysed in this dissertation all occurred between May 2008, when the OGI Regulations and the OEI Measures came into effect, and August 2012 when the case collection was completed. The findings of this study have shown that by invoking the rules of law made by the authorities to demand government agencies disclosing environmental information, the public, including citizens, organizations, law firms, and the media, have strategically created a repercussive pressure upon the authorities to act according to the law. While it is a top-down process that has established the mechanism of open government information in China, it is indeed the bottom-up activism of the public that makes it work. Citizens and organizations’ use of legal tactics to push government agencies to disclose environmental information have formed not only an end of accessing the information but more a means of making government agencies accountable to their legal obligations. Law has thus played a pivotal role in enabling citizen participation in the political process. Against the current situation in China that political campaigns, or politicization, from general election to collective actions, especially contentious actions, are still restrained or even repressed by the government, legal mobilization, or judicialization, that citizens and organizations use legal tactics to demand their rights and push government agencies to enforce the law, become de facto an alternative of political participation. During this process, legal actions have helped to strengthen the civil society, make government agencies act according to law, push back the political boundaries, and induce changes in the relationship between the state and the public. In the field of environmental information disclosure, citizens and organizations have formed a bottom-up social activism, though limited in scope, using the language of law, creating progressive social, legal and political changes. This study emphasizes that it is partial and incomplete to understand China’s transition only from the top-down policy-making and government administration; it is also important to observe it from the bottom-up perspective that in a realistic view law can be part of politics and legal mobilization, even when utterly apolitical, can help to achieve political aims as well. This study of legal mobilization in the field of environmental information disclosure also helps us to better understand the function of law: law is not only a tool for the authorities to regulate and control, but inevitably also a weapon for the public to demand government agencies to work towards their obligations stipulated by the laws issued by themselves.

Loan sales under asymmetric information

Loans are illiquid assets that can be sold in a secondary market even that buyers have no certainty about their quality. I study a model in which a lender has access to new investment opportunities when all her assets are illiquid. To raise funds, the lender may either borrow using her assets as collateral, or she can sell them in a secondary market. Given asymmetric information about assets quality, the lender cannot recover the total value of her assets. There is then a role for the government to correct the information problem using fiscal tools.

When enough is not enough: information overload and metacognitive decisions to stop studying information

People are often exposed to more information than they can actually remember. Despite this frequent form of information overload, little is known about how much information people choose to remember. Using a novel “stop” paradigm, the current research examined whether and how people choose to stop receiving new—possibly overwhelming—information with the intent to maximize memory performance. Participants were presented with a long list of items and were rewarded for the number of correctly remembered words in a following free recall test. Critically, participants in a stop condition were provided with the option to stop the presentation of the remaining words at any time during the list, whereas participants in a control condition were presented with all items. Across five experiments, we found that participants tended to stop the presentation of the items to maximize the number of recalled items, but this decision ironically led to decreased memory performance relative to the control group. This pattern was consistent even after controlling for possible confounding factors (e.g., task demands). The results indicated a general, false belief that we can remember a larger number of items if we restrict the quantity of learning materials. These findings suggest people have an incomplete understanding of how we remember excessive amounts of information.

How much flower-rich habitat is enough for wild pollinators? Answering a key policy question with incomplete knowledge

In 2013, an opportunity arose in England to develop an agri-environment package for wild pollinators, as part of the new Countryside Stewardship scheme launched in 2015. It can be understood as a 'policy window', a rare and time-limited opportunity to change policy, supported by a narrative about pollinator decline and widely supported mitigating actions. An agri-environment package is a bundle of management options that together supply sufficient resources to support a target group of species. This paper documents information that was available at the time to develop such a package for wild pollinators. Four questions needed answering: (1) Which pollinator species should be targeted? (2) Which resources limit these species in farmland? (3) Which management options provide these resources? (4) What area of each option is needed to support populations of the target species? Focussing on wild bees, we provide tentative answers that were used to inform development of the package. There is strong evidence that floral resources can limit wild bee populations, and several sources of evidence identify a set of agri-environment options that provide flowers and other resources for pollinators. The final question could only be answered for floral resources, with a wide range of uncertainty. We show that the areas of some floral resource options in the basic Wild Pollinator and Farmland Wildlife Package (2% flower-rich habitat and 1 km flowering hedgerow), are sufficient to supply a set of six common pollinator species with enough pollen to feed their larvae at lowest estimates, using minimum values for estimated parameters where a range was available. We identify key sources of uncertainty, and stress the importance of keeping the Package flexible, so it can be revised as new evidence emerges about how to achieve the policy aim of supporting pollinators on farmland.

Macroeconomic announcements, price discovery, and order flow efects in the stock market: evidence from incomplete data and multiple financial markets

This paper investigates heterogeneity in the market assessment of public macro- economic announcements by exploring (jointly) two main mechanisms through which macroeconomic news might enter stock prices: instantaneous fundamental news im- pacts consistent with the asset pricing view of symmetric information, and permanent order ow e¤ects consistent with a microstructure view of asymmetric information related to heterogeneous interpretation of public news. Theoretical motivation and empirical evidence for the operation of both mechanisms are presented. Signi cant in- stantaneous news impacts are detected for news related to real activity (including em- ployment), investment, in ation, and monetary policy; however, signi cant order ow e¤ects are also observed on employment announcement days. A multi-market analysis suggests that these asymmetric information e¤ects come from uncertainty about long term interest rates due to heterogeneous assessments of future Fed responses to em- ployment shocks.

Organizations redesign and building of information systems

Develop software is still a risky business. After 60 years of experience, this community is still not able to consistently build Information Systems (IS) for organizations with predictable quality, within previously agreed budget and time constraints. Although software is changeable we are still unable to cope with the amount and complexity of change that organizations demand for their IS. To improve results, developers followed two alternatives: Frameworks that increase productivity but constrain the flexibility of possible solutions; Agile ways of developing software that keep flexibility with less upfront commitments. With strict frameworks, specific hacks have to be put in place to get around the framework construction options. In time this leads to inconsistent architectures that are harder to maintain due to incomplete documentation and human resources turnover. The main goals of this work is to create a new way to develop flexible IS for organizations, using web technologies, in a faster, better and cheaper way that is more suited to handle organizational change. To do so we propose an adaptive object model that uses a new ontology for data and action with strict normalizing rules. These rules should bound the effects of changes that can be better tested and therefore corrected. Interfaces are built with templates of resources that can be reused and extended in a flexible way. The “state of the world” for each IS is determined by all production and coordination acts that agents performed over time, even those performed by external systems. When bugs are found during maintenance, their past cascading effects can be checked through simulation, re-running the log of transaction acts over time and checking results with previous records. This work implements a prototype with part of the proposed system in order to have a preliminary assessment its feasibility and limitations.

Where do Latin America and the Caribbean stand in relation to the eLAC2007 Plan of Action?: evidence from available information

Includes bibliography

Using incomplete citation data for MEDLINE results ranking.

Information overload is a significant problem for modern medicine. Searching MEDLINE for common topics often retrieves more relevant documents than users can review. Therefore, we must identify documents that are not only relevant, but also important. Our system ranks articles using citation counts and the PageRank algorithm, incorporating data from the Science Citation Index. However, citation data is usually incomplete. Therefore, we explore the relationship between the quantity of citation information available to the system and the quality of the result ranking. Specifically, we test the ability of citation count and PageRank to identify "important articles" as defined by experts from large result sets with decreasing citation information. We found that PageRank performs better than simple citation counts, but both algorithms are surprisingly robust to information loss. We conclude that even an incomplete citation database is likely to be effective for importance ranking.

Using incomplete citation data for MEDLINE results ranking.

Information overload is a significant problem for modern medicine. Searching MEDLINE for common topics often retrieves more relevant documents than users can review. Therefore, we must identify documents that are not only relevant, but also important. Our system ranks articles using citation counts and the PageRank algorithm, incorporating data from the Science Citation Index. However, citation data is usually incomplete. Therefore, we explore the relationship between the quantity of citation information available to the system and the quality of the result ranking. Specifically, we test the ability of citation count and PageRank to identify "important articles" as defined by experts from large result sets with decreasing citation information. We found that PageRank performs better than simple citation counts, but both algorithms are surprisingly robust to information loss. We conclude that even an incomplete citation database is likely to be effective for importance ranking.

A group decision-making methodology with incomplete individual beliefs applied to e-Democracy

We consider the situation where there are several alternatives for investing a quantity of money to achieve a set of objectives. The choice of which alternative to apply depends on how citizens and political representatives perceive that such objectives should be achieved. All citizens with the right to vote can express their preferences in the decision-making process. These preferences may be incomplete. Political representatives represent the citizens who have not taken part in the decision-making process. The weight corresponding to political representatives depends on the number of citizens that have intervened in the decision-making process. The methodology we propose needs the participants to specify for each alternative how they rate the different attributes and the relative importance of attributes. On the basis of this information an expected utility interval is output for each alternative. To do this, an evidential reasoning approach is applied. This approach improves the insightfulness and rationality of the decision-making process using a belief decision matrix for problem modeling and the Dempster?Shafer theory of evidence for attribute aggregation. Finally, we propose using the distances of each expected utility interval from the maximum and the minimum utilities to rank the alternative set. The basic idea is that an alternative is ranked first if its distance to the maximum utility is the smallest, and its distance to the minimum utility is the greatest. If only one of these conditions is satisfied, a distance ratio is then used.

Invitation to contractors, information for contractors and forms of contract, bond and contractor's proposal for construction of station finish for a part of the ... rapid transit railroad ... Form finally adopted by the Commission ...

No. 36/37 & 50, sect. 1-3. Queensboro subway.--No. 39, sect. 2. Broadway - Fourth avenue (New Utrecht avenue) - No. 43, 4/38, see no. 4/38, 43.--No. 48, sect. 1-2. Seventh avenue - Lexington avenue.--No. 50. Queensboro subway (Hunters Point avenue station