Search Results - "Fitzjohn, Richard"

Diversitree: comparative phylogenetic analyses of diversification in R by FitzJohn, Richard G.

“…Summary 1. The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary…”
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Quantitative Traits and Diversification by FitzJohn, Richard G.

“…Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be…”
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How functional traits influence plant growth and shade tolerance across the life cycle by Falster, Daniel S., Duursma, Remko A., FitzJohn, Richard G.

“…Plant species differ in many functional traits that drive differences in rates of photosynthesis, biomass allocation, and tissue turnover. However, it remains…”
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geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees by Pennell, Matthew W, Eastman, Jonathan M, Slater, Graham J, Brown, Joseph W, Uyeda, Josef C, FitzJohn, Richard G, Alfaro, Michael E, Harmon, Luke J

“…Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased…”
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Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies by FitzJohn, Richard G., Maddison, Wayne P., Otto, Sarah P.

“…Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits…”
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Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study by Sonabend, Raphael, Whittles, Lilith K, Imai, Natsuko, Perez-Guzman, Pablo N, Knock, Edward S, Rawson, Thomas, Gaythorpe, Katy A M, Djaafara, Bimandra A, Hinsley, Wes, FitzJohn, Richard G, Lees, John A, Kanapram, Divya Thekke, Volz, Erik M, Ghani, Azra C, Ferguson, Neil M, Baguelin, Marc, Cori, Anne

“…England's COVID-19 roadmap out of lockdown policy set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as…”
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Model Adequacy and the Macroevolution of Angiosperm Functional Traits by Pennell, Matthew W., FitzJohn, Richard G., Cornwell, William K., Harmon, Luke J.

“…Making meaningful inferences from phylogenetic comparative data requires a meaningful model of trait evolution. It is thus important to determine whether the…”
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Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England by Perez-Guzman, Pablo N., Knock, Edward, Imai, Natsuko, Rawson, Thomas, Elmaci, Yasin, Alcada, Joana, Whittles, Lilith K., Thekke Kanapram, Divya, Sonabend, Raphael, Gaythorpe, Katy A. M., Hinsley, Wes, FitzJohn, Richard G., Volz, Erik, Verity, Robert, Ferguson, Neil M., Cori, Anne, Baguelin, Marc

“…As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were…”
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Three keys to the radiation of angiosperms into freezing environments by Zanne, Amy E., Tank, David C., Cornwell, William K., Eastman, Jonathan M., Smith, Stephen A., FitzJohn, Richard G., McGlinn, Daniel J., O’Meara, Brian C., Moles, Angela T., Reich, Peter B., Royer, Dana L., Soltis, Douglas E., Stevens, Peter F., Westoby, Mark, Wright, Ian J., Aarssen, Lonnie, Bertin, Robert I., Calaminus, Andre, Govaerts, Rafaël, Hemmings, Frank, Leishman, Michelle R., Oleksyn, Jacek, Soltis, Pamela S., Swenson, Nathan G., Warman, Laura, Beaulieu, Jeremy M.

“…This large comparative phylogenetic study across angiosperms shows that species that are herbaceous or have small conduits evolved these traits before…”
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Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England by Knock, Edward S, Whittles, Lilith K, Lees, John A, Perez-Guzman, Pablo N, Verity, Robert, FitzJohn, Richard G, Gaythorpe, Katy A M, Imai, Natsuko, Hinsley, Wes, Okell, Lucy C, Rosello, Alicia, Kantas, Nikolas, Walters, Caroline E, Bhatia, Sangeeta, Watson, Oliver J, Whittaker, Charlie, Cattarino, Lorenzo, Boonyasiri, Adhiratha, Djaafara, Bimandra A, Fraser, Keith, Fu, Han, Wang, Haowei, Xi, Xiaoyue, Donnelly, Christl A, Jauneikaite, Elita, Laydon, Daniel J, White, Peter J, Ghani, Azra C, Ferguson, Neil M, Cori, Anne, Baguelin, Marc

“…We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Compared with other approaches, our…”
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The Unsolved Challenge to Phylogenetic Correlation Tests for Categorical Characters by Maddison, Wayne P., FitzJohn, Richard G.

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How much of the world is woody? by FitzJohn, Richard G, Pennell, Matthew W, Zanne, Amy E, Stevens, Peter F, Tank, David C, Cornwell, William K, Shefferson, Richard

“…The question posed by the title of this study is a basic one, and it is surprising that the answer is not known. Recently, assembled trait data sets provide an…”
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Shedding light on the ‘dark side’ of phylogenetic comparative methods by Cooper, Natalie, Thomas, Gavin H., FitzJohn, Richard G., O'Hara, Robert B.

“…Summary Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are…”
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Author Correction: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England by Perez-Guzman, Pablo N., Knock, Edward, Imai, Natsuko, Rawson, Thomas, Elmaci, Yasin, Alcada, Joana, Whittles, Lilith K., Thekke Kanapram, Divya, Sonabend, Raphael, Gaythorpe, Katy A. M., Hinsley, Wes, FitzJohn, Richard G., Volz, Erik, Verity, Robert, Ferguson, Neil M., Cori, Anne, Baguelin, Marc

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Dietary innovations spurred the diversification of ruminants during the Caenozoic by Cantalapiedra, Juan L., FitzJohn, Richard G., Kuhn, Tyler S., Fernández, Manuel Hernández, DeMiguel, Daniel, Azanza, Beatriz, Morales, Jorge, Mooers, Arne Ø.

“…Global climate shifts and ecological flexibility are two major factors that may affect rates of speciation and extinction across clades. Here, we connect past…”
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Partitioning mortality into growth-dependent and growth-independent hazards across 203 tropical tree species by Camac, James S., Condit, Richard, FitzJohn, Richard G., McCalman, Lachlan, Steinberg, Daniel, Westoby, Mark, Wright, S. Joseph, Falster, Daniel S.

“…Tree death drives population dynamics, nutrient cycling, and evolution within plant communities. Mortality variation across species is thought to be influenced…”
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Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria by Watson, Oliver J., Alhaffar, Mervat, Mehchy, Zaki, Whittaker, Charles, Akil, Zack, Brazeau, Nicholas F., Cuomo-Dannenburg, Gina, Hamlet, Arran, Thompson, Hayley A., Baguelin, Marc, FitzJohn, Richard G., Knock, Edward, Lees, John A., Whittles, Lilith K., Mellan, Thomas, Winskill, Peter, Howard, Natasha, Clapham, Hannah, Checchi, Francesco, Ferguson, Neil, Ghani, Azra, Beals, Emma, Walker, Patrick

“…The COVID-19 pandemic has resulted in substantial mortality worldwide. However, to date, countries in the Middle East and Africa have reported considerably…”
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Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe by Flaxman, Seth, Mishra, Swapnil, Gandy, Axel, Unwin, H. Juliette T., Mellan, Thomas A., Coupland, Helen, Whittaker, Charles, Zhu, Harrison, Berah, Tresnia, Eaton, Jeffrey W., Monod, Mélodie, Ghani, Azra C., Donnelly, Christl A., Riley, Steven, Vollmer, Michaela A. C., Ferguson, Neil M., Okell, Lucy C., Bhatt, Samir

“…Following the detection of the new coronavirus 1 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its spread outside of China, Europe has…”
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A simple approach for maximizing the overlap of phylogenetic and comparative data by Pennell, Matthew W., FitzJohn, Richard G., Cornwell, William K., Kembel, Steven

“…Summary Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch…”
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Conspecific density modulates the effect of predation on dispersal rates by Hammill, Edd, Fitzjohn, Richard G, Srivastava, Diane S

“…Dispersal decisions underlie the spatial dynamics of metacommunities. Prey individuals may disperse to reduce the risk of either predation or starvation, and…”
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