Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).
The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.
Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).
The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.
Internationally acclaimed play of cross-cultural friendship Paris in the 1960s. Thirteen-year-old Moses lives in the shadow of his less-than loving father. When he's caught stealing from wise old shopkeeper Monsieur Ibrahim, he discovers an unlikely friend and a whole new world. Together they embark on a journey that takes them from the streets of Paris to the whirling dervishes of the Golden Crescent. This delightful, moving play has already been a huge hit in Paris and New York. Performed in thirteen countries and published in twelve languages, it is also an award-winning film starring Omar Sharif. Monsieur Ibrahim and the Flowers of the Qur'an received its UK premiere at the Bush Theatre on 17 January 2006.
This book sheds a new light on the metafictional aspects of futuristic and science fiction novels, at the crossroads of information and media studies, possible worlds theories applied to cognitive narratology, questions related to the criticism of post-humanity, and, more broadly, contemporary French and Francophone literature. It examines the fictional minds of characters and their conceptions of resistance to the anticipated worlds they inhabit, particularly in novels by Pierre Bordage, Marie Darrieussecq, Michel Houellebecq, Amin Maalouf, Jean-Christophe Rufin, Antoine Volodine, and Élisabeth Vonarburg. It also explores how corporal postures serve as a matrix for philosophical quests in novels by Amélie Nothomb, Alain Damasio, and Romain Lucazeau. More specifically, from the fictional readers’ points of view, it provides a critical approach to the mythologies of writing, in the wake of the French philosophical tales by authors including Cyrano de Bergerac and Voltaire, to question the traditionally expressed formulations of the mythologies of writing, that is, of the metaphors of the book (the book of life, nature, and the world), to rethink the idea of a humanity within its limits.
From the acclaimed award-winning author Emmanuel Carrère, Lives Other Than My Own: A Memoir is an act of generous imagination that unflinchingly records devastating loss and, equally vividly, the wealth of human solace that follows in its wake. Selected by the New York Times as one of the 50 Best Memoirs of the Past 50 Years In Sri Lanka, a tsunami sweeps a child out to sea, her grand-father helpless against the onrushing water. In France, a young woman succumbs to illness, leaving her husband and small children bereft. Present at both events, Emmanuel Carrère sets out to tell the story of two families—shattered and ultimately restored. What he accomplishes is nothing short of a literary miracle: a heartrending narrative of endless love, a meditation on courage and decency in the face of adversity, an intimate and reverent look at the extraordinary beauty and nobility of ordinary lives. Precise, sober, and suspenseful, as full of twists and turns as any novel, Lives Other Than My Own confronts terrifying catastrophes to illuminate the astonishing richness of human connection: a grandfather who thought he had found paradise—too soon—and now devotes himself to helping his neighbors rebuild their village; a husband so in love with his ailing wife that he carries her in his arms like a knight does his princess; and finally, Carrère himself, longtime chronicler of the tormented self, who unexpectedly finds consolation and even joy as he immerses himself in the lives of others. “Moving...Carrère’s prose is precise and measured...Through interviews with friends and relatives of both families, he creates powerful portraits that celebrate ordinary lives.”—The New Yorker “You begin this memoir thinking it will be about one thing, and it turns into something else altogether—a book at once more ordinary and more extraordinary than any first impressions might allow.”—The New York Times
A phenomenal bestseller in France, Metronome presents a fascinating history of Paris through the lens of the city's iconic Metro system Did you know that the last Gallic warriors massacred by the Romans lie beneath the Eiffel Tower? That the remains of Paris's first cathedral are under a parking lot in the Fifth District? Metronome follows Loránt Deutsch, historian and lifelong Francophile, as he goes on a compelling journey through the ages, treating readers to Paris as they've never seen it before. Using twenty-one stops of the subway system as focal points—one per century—Deutsch shows, from the underground up, the unique, often violent, and always striking events that shaped one of the world's most romanticized city. Readers will find out which streets are hiding incredible historical treasures in plain sight; peer into forgotten nooks and crannies of the City of Lights and learn what used to be there; and discover that, however deeply buried, something always remains.
Rwanda, this small country located in the center of Africa, was filled with human blood in 1994. Extremist Rwandans killed about 1 million people in only one hundred days, about 3 million fled Rwanda into exile in Democratic Republic of Congo ( ex-Zaire) where they would be killed by the Rwandan Patriotic Army from 1996 until 1998. This book is about a testimony of two boys who survived these massacres in which they had lost both their parents who were killed in the forests of the Congo. The older boy, 7 years old at that time, had to take care of his little brother, a newborn whose mother was killed only a couple hours after his birth. Miraculously, they both traveled the entire country of the Congo and came back to Rwanda. Once in their home country of Rwanda, in their own home village, the neighbours, who wanted to keep their inheritance, accused them of committing genocide in 1994. But at the time of this heinous crime, the older brother was only 5 years old, and his little brother was not born yet. To survive the attacks, harassment, and terror of these neighbours, ancient refugees from Uganda, they became "street kids" where I met them.
The text offers a comprehensive and unique perspective on disaster risk associated with natural hazards. It covers a wide range of topics, reflecting the most recent debates but also older and pioneering discussions in the academic field of disaster studies as well as in the policy and practical areas of disaster risk reduction (DRR). This book will be of particular interest to undergraduate students studying geography and environmental studies/science. It will also be of relevance to students/professionals from a wide range of social and physical science disciplines, including public health and public policy, sociology, anthropology, political science and geology.
Named a Best Book of 2022 by The Guardian This is a book about yoga. Or at least, it was. Emmanuel Carrère is a renowned writer. After decades of emotional upheaval, he has begun to live successfully—he is healthy; he works; he loves. He practices meditation, striving to observe the world without evaluating it. In this state of heightened awareness, he sets out for a ten-day silent retreat in the French heartland, leaving his phone, his books, and his daily life behind. But he’s also gathering material for his next book, which he thinks will be a pleasant, useful introduction to yoga. Four days later, there’s a tap on the window: something has happened. Forced to leave the retreat early, he returns to a Paris in crisis. Life is derailed. His city is in turmoil. His work-in-progress falters. His marriage begins to unravel, as does his entanglement with another woman. He wavers between opposites—between self-destruction and self-control; sanity and madness; elation and despair. The story he has told about himself falls away. And still, he continues to live. This is a book about one man’s desire to get better, and to be better. It is laced with doubt, animated by the dangerous interplay between what is fiction and what is real. Loving, humorous, harrowing and profound, Yoga hurls us towards the outer edges of consciousness, where, finally, we can see things as they really are.
Postmodernism has had its day. Are we now in the era of epimodernism? Reinterpreting the six “memos” that Italo Calvino suggested more than thirty years ago for “the new Millennium”, in this acclaimed book Emmanuel Bouju identifies six new values for literature in the twenty-first century: Superficiality, Secrecy, Energy, Acceleration, Credit, and Follow Through. Based on the principal meanings of the Ancient Greek prefix epi – surface, contact, origin, extension, duration, authority, and finality – these values represent six different ways of relating to the legacy of modernist utopias, reorienting postmodern critique and rebooting, with all due irony, its various forms of engagement and empowerment. Equal parts cultural criticism and literary creation, this highly original essay both enacts and explores the epimodern turn in contemporary European literature. Rigorous and humorous, provocative and playful, Epimodernism helps us to understand what literature can describe, imagine, and invent in our challenging times.
From the Pharaohs to Fanon, Dictionary of African Biography provides a comprehensive overview of the lives of the men and women who shaped Africa's history. Unprecedented in scale, DAB covers the whole continent from Tunisia to South Africa, from Sierra Leone to Somalia. It also encompasses the full scope of history from Queen Hatsheput of Egypt (1490-1468 BC) and Hannibal, the military commander and strategist of Carthage (243-183 BC), to Kwame Nkrumah of Ghana (1909-1972), Miriam Makeba and Nelson Mandela of South Africa (1918 -).
Paris is commonly acknowledged as one of the world's great gourmet destinations. But how can food lovers find the gastronomic experience they are yearning for amongst the myriad of choices that confront them in this city? With its unique dish by dish guide, "Gourmet Paris" offers an original and practical way of finding exactly what you are looking for in the capital of great food. Craving for the finest applied tart? The most succulent "boeuf bourguignon"? Want to try North African cuisine, or sample the freshest sushi? Whether you are seeking out the tastiest "andouillette" or the most finely whipped zabaione, "Gourmet Paris" has the addresses you are looking for. Reviews over 1000 of Paris's restaurants, from the very finest in their field to those best avoided Includes restaurants in all districts of Paris and for all budgets Easy-to-follow alphabetical listing by dish covering over 60 local, regional, and international specialities Additional listings by theme: choice restaurants for children, with fireplaces, in museums, on the river . . . More than 100 new entries in this fully revised and updated edition for 2001
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