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*  Spreading of mood in social networks | Proceedings of the Royal Society of London B: Biological Sciences
Appendix A. Likelihood functions. The following likelihood function was constructed for the development of the 'depressive ... Appendix A outlines the construction of the likelihood functions used in the fitting process. Competing models were assessed ... An equivalent likelihood function was constructed for the 'recovery from depressive symptoms' scenario:. with yk corresponding ... by minimizing the negative log-likelihood -log(L) with respect to p and q using the MATLAB fmincon(). function. Confidence ...
http://rspb.royalsocietypublishing.org/content/282/1813/20151180/
*  Proceedings of the Royal Society of London B: Biological Sciences
Model fits were estimated using maximum likelihood (ML) with a logit-link function. Pungency was determined by tasting in the ... b) The proportion of pungent plants in each population increases as a function of precipitation (r2 = 0.83, F1,19 = 100.5, p ≪ ... which function concomitantly or even synergistically [20,21]. Such interactions make it difficult to ascribe fitness ...
http://rspb.royalsocietypublishing.org/content/279/1735/2012.full
*  A quantitative test of the relationship between parasite dose and infection probability across different host-parasite...
The likelihood functions defined above were programmed in the R language (R Development Core Team 2005), and maximum-likelihood ... The likelihood function for all three models can be defined as,. (2.6) ... These dynamics are described by the following population survival function:. (2.5). This survival function for the ... The optimization of the likelihood is technically easier done on its logarithm, the log likelihood,. (2.7) ...
http://rspb.royalsocietypublishing.org/content/275/1636/853
*  Trophic cascade: apex predator to soil | Proceedings of the Royal Society of London B: Biological Sciences
Rainfall events function as a 'trigger' for 'pulses' of plant growth. Flows of wind and water 'transfer' materials and ... 2006 A better lemon squeezer? Maximum-likelihood regression with beta-distributed dependent variables. Psychol. Methods 11, 54 ... Models were performed using the lme and lmer functions from the 'nlme' package [38] and 'lme4' package [39], respectively. A ... We fitted a beta regression model to predict the proportion of dingo scats containing kangaroo as a function of kangaroo ...
http://rspb.royalsocietypublishing.org/content/284/1854/20170111
*  Speciation along a depth gradient in a marine adaptive radiation | Proceedings of the Royal Society of London B: Biological...
This function is used to calculate the likelihood of ψ and given X, λ, μ, and the tree [30,35]. ... where X is the vector of species means and 1 is a column vector of ones [35]. The likelihood function is the multivariate ... To calculate the likelihoods of values of ψ and , I first calculated the phylogenetic variance-covariance matrix V for the ... Results of likelihood analysis of speciational versus gradual evolution. ML estimates of and ψ are shown for each character. ...
http://rspb.royalsocietypublishing.org/content/278/1705/613
*  Ecological correlates of extra-group paternity in mammals | Proceedings of the Royal Society of London B: Biological Sciences
Models were fit using restricted maximum likelihood, GLS analyses were carried out using the function gls. in the nlme. package ... using likelihood-ratio tests to see if including phylogeny improved model fit (Pagel 1997; Pinheiro & Bates 2000). Likelihood- ... 2002 Extra pair paternity in birds: a review of interspecific variation and adaptive function. Mol. Ecol. 11, 2195-2212. doi: ...
http://rspb.royalsocietypublishing.org/content/274/1607/219
*  Proceedings of the Royal Society of London B: Biological Sciences
d) Cumulative survival functions for Orco1 females. Likelihood ratio tests revealed no significant difference in remating ... b) Cumulative survival functions for wild-type females. Likelihood ratio tests revealed a significant difference in remating ... 1975 Individual odor differences and their social functions in insects. Proc. Natl Acad. Sci. USA 7, 2824-2828. (doi:10.1073/ ... The survival curves were compared using the likelihood ratio test. We used a general LM to test the difference in remating ...
http://rspb.royalsocietypublishing.org/content/280/1771/20131691.short
*  History of Plumage Carotenoids | Proceedings of the Royal Society of London B: Biological Sciences
Furthermore, each family MRCA has a proportional likelihood for plumage carotenoids, although we note that these likelihood ... function in the 'ape' package [31]; hidden rates reconstructions were calculated using the 'corHMM' function in the 'corHMM' ... nodes had proportional likelihood values that were more than 0.5. Nodes with high proportional likelihoods for carotenoid- ... proportional likelihoods for (0) and (1) were the sum of proportional likelihoods in each rate category. ...
http://rspb.royalsocietypublishing.org/content/281/1788/20140806
*  Sexual isolation through imprinting | Proceedings of the Royal Society of London B: Biological Sciences
... as well as father behaviour in a generalized linear model with a binomial distribution and logit link function with family as a ... We tested the significance of interactions between father traits and mate species using likelihood ratio tests. Mate throat ... an ethological analysis of cranial nerve functions regarding nest fanning activity and the zigzag dance. Behaviour 86, 100-166 ... Significance was determined via likelihood ratio tests. We included as fixed factors the father's identity (conspecific, ...
http://rspb.royalsocietypublishing.org/content/278/1718/2604
*  Microscale laser surgery reveals adaptive function of male intromittent genitalia | Proceedings of the Royal Society of London...
The null hypothesis of equal mating frequency between experimental categories was evaluated with a likelihood ratio test, ... 2001 Function of the mating plug in Drosophila hibisci Bock. Behav. Ecol. Sociobiol. 49, 196-205. (doi:10.1007/s002650000281). ... Microscale laser surgery reveals adaptive function of male intromittent genitalia Message Subject (Your Name) has sent you a ... Thus, the current view being promulgated is that the genital spines in D. bipectinata and related Drosophila species function ...
http://rspb.royalsocietypublishing.org/content/early/2010/01/05/rspb.2009.1720
*  Continental Carnivore Radiation | Proceedings of the Royal Society of London B: Biological Sciences
In Carnivoran evolution: new views on phylogeny, form, and function (eds A Goswami, AR Friscia), pp. 311-341. Cambridge, UK: ... of diversification can also derive from increased extinction as population sizes diminish thus increasing the likelihood of ... it can be modelled as a non-homogeneous Poisson process in which the rate parameter is a function of time and the expected ... can experiment with different forms and functions. ...
http://rspb.royalsocietypublishing.org/content/282/1817/20151952
*  Cooperative breeding and monogamy | Proceedings of the Royal Society of London B: Biological Sciences
2009 Structure and function in mammalian societies. Phil. Trans. R. Soc. B 364, 3229-3242. doi:10.1098/rstb.2009.0120 (doi: ... Likelihoods for all different models were estimated using 25 optimization attempts per run. Significance of results was ... The tree was pruned to match the species in the dataset using functions of the package 'APE' [26] in R. Reconstruction of ... Models assuming a dependent model were considered significant at α = 0.05 if the respective likelihood was 4.75 lower than the ...
http://rspb.royalsocietypublishing.org/content/279/1736/2151
*  Electroreception in the Guiana dolphin | Proceedings of the Royal Society of London B: Biological Sciences
1995 Structure and function of the vibrissae of the ringed seal (Phoca hispida). In Sensory systems of aquatic mammals (eds ... We therefore suggest that the electroreceptors on the dolphin's rostrum maximize the likelihood of close distance prey ... Like the gel in ampullary electroreceptors of fish, it is rich in glycoproteins and thus could function as an electrically ... we developed the hypothesis that the vibrissal crypts function as electroreceptors. We tested this hypothesis in a ...
http://rspb.royalsocietypublishing.org/content/early/2011/07/21/rspb.2011.1127
*  Ecological drivers of influenza in birds | Proceedings of the Royal Society of London B: Biological Sciences
... using Laplace approximation of the maximum-likelihood and a logit link function. We used an information-theoretic procedure and ... For each model i, we computed the Akaike weight (ωi) which can be interpreted as the likelihood that model i is the best model ... Models were run with the 'glmer' function in the 'lme4' package in the R environment, ... were considered as cyclic and were modelled using a cosine function of the form logit(prevalence) = a + cos(2πt/365). All the ...
http://rspb.royalsocietypublishing.org/content/early/2011/09/09/rspb.2011.1417
*  Thermal plasticity of quail bills | Proceedings of the Royal Society of London B: Biological Sciences
... and all models were fitted using a restricted maximum-likelihood function in JMP v. 10.0 (JMP, v. 10. SAS Institute Inc., Cary ... We tested whether the bill and tarsus of Japanese quail exhibit plasticity in growth and function in response to the post-hatch ... It remains unknown whether bill size and thermal function are reversibly plastic. We raised Japanese quail in warm (30°C) or ... parallels the morphological trends in terms of thermoregulatory function, but also retains a signal of the environmental ...
http://rspb.royalsocietypublishing.org/content/280/1767/20131436
*  Proceedings of the Royal Society of London B: Biological Sciences
Figure 5 shows the results of the simulations (PACC, HACC and HREJ) as a function of p, the probability of parasite detection ... In every case, as p increases, and with it the likelihood of multiple parasitism, acceptors enjoy increasingly higher own egg ... function describing the loss to a host's reproductive output caused by rearing a given number of parasite nestlings. Simply put ... while some fraction occurs with a lower likelihood per day during incubation, as is the case for shiny cowbirds parasitizing ...
http://rspb.royalsocietypublishing.org/content/early/2011/12/06/rspb.2011.2047.short?rss=1
*  Proceedings of the Royal Society of London B: Biological Sciences
... vaginal morphologies of waterfowl function in physically restricting forced intromission and reducing consequent likelihood of ... In Form and function in birds (eds King A. S., McLelland J.), pp. 107-148. New York, NY: Academic Press. ... The two spiral tubes we used differ only in the chirality of the spiral, supporting an antagonistic function for vaginal ... The curved, flexible penis of male waterfowl apparently functions in the navigation of the inside of the folded female vagina ...
http://rspb.royalsocietypublishing.org/content/early/2009/12/18/rspb.2009.2139.short?rss=1
*  Proceedings of the Royal Society of London B: Biological Sciences
However, we do know that because of anisogamy, male preference functions may diverge from female preference functions: under ... 1993 Generalized linear mixed models-a pseudo-likelihood approach. J. Statist. Comput. Simulation. 48, 233-243. doi:10.1080/ ... Information theory and an extension of the maximum likelihood principle. In Proceedings of the second international sumposium ... All analyses were performed using generalized linear mixed models (GLMMs) with restricted maximum-likelihood (REML) estimation ...
http://rspb.royalsocietypublishing.org/content/276/1659/1083.long
*  Resource availability and fitness traits | Proceedings of the Royal Society of London B: Biological Sciences
Generalized mixed effects models using the 'glmer' function with a binomial error distribution and logit link function in the ' ... Non-significant factors were removed from the model and tests of significance were based on likelihood-ratio tests following a ... 2003 Carotenoid modulation of immune function and sexual attractiveness in zebra finches. Science 300, 125-127. (doi:10.1126/ ... In detail, linear mixed effects models were fitted using the 'lme' function of the 'nlme' package. Models were constructed ...
http://rspb.royalsocietypublishing.org/content/282/1817/20151279
*  Bacillus Calmette-Guérin vaccination reduces the severity and progression of tuberculosis in badgers | Proceedings of the Royal...
The purpose of the analyses was to identify any effect of vaccination on the likelihood that an individual would change its ... The binomial data were analysed using a generalized linear model with a logit (log odds ratio) link function and binomial ... IM BCG in free-living, wild badgers significantly reduced their likelihood of yielding a positive result to a serological test ... errors, fitted by maximum quasi-likelihood with provision for over-dispersion (i.e. greater than expected binomial variability ...
http://rspb.royalsocietypublishing.org/content/early/2010/11/24/rspb.2010.1953
*  Antibody-mediated malaria vaccines | Proceedings of the Royal Society of London B: Biological Sciences
When fitting the model using Hill functions, an exponential function was retained for the LSA-1 dose-response curve as this was ... For individuals infected in the trial, the likelihood of them developing infection at time ti is ɛbi e−ɛbi(ti−tL) while for ... For a Hill function, dose-response in individual i with antibody titre to antigen j of xij, the probability that a sporozoite ... 95 per cent CI were estimated by calculating the inverse hessian of the log-likelihood surface at the maximum-likelihood ...
http://rspb.royalsocietypublishing.org/content/278/1710/1298
*  Genetic variation and covariation of susceptibility to parasitoids in the aphid Myzus persicae: no evidence for trade-offs |...
We used this approach that is provided by the pvals.fnc function in the languageR library of R. The same function also provides ... We therefore tested their significance by running models with and without the effects and calculating likelihood ratio ...
http://rspb.royalsocietypublishing.org/content/275/1638/1089
*  Vertical transmission as the key to the colonization of Madagascar by fungus-growing termites? | Proceedings of the Royal...
... by using the penalized likelihood function implemented on the program r8s v. 1.7 (Sanderson 2002). The analysis was based on ... 2002 Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. ... Long-distance dispersal is a stochastic process and the likelihood that the disperser arrives, survives and reproduces to ... Stationarity was confirmed by analysis of the log likelihoods and the consistency between runs. ...
http://rspb.royalsocietypublishing.org/content/277/1680/359
*  SIV transmission in a primate population | Proceedings of the Royal Society of London B: Biological Sciences
The likelihood of any model is the product of the probability of the individual histories and written as a function of the ... Yet, understanding the functioning of pathogen populations and that of their hosts within an ecosystem is crucial for ... For rM, we assumed that the frequency of mating in males was a Gaussian function:. ... Because we had access to quasi-exhaustive data on the SIVmnd-1 status of each individual, the likelihood of each transmission ...
http://rspb.royalsocietypublishing.org/content/early/2012/06/01/rspb.2012.0963
*  A seasnake's colour affects its susceptibility to algal fouling | Proceedings of the Royal Society of London B: Biological...
d) Survival rates as a function of snake colour. We used the program MARK (White & Burnham 1999) to estimate survival rates of ... Likelihood ratio tests from a logistic regression with algal score as the dependent variable showed significant annual ... 2004 The evolution, maintenance and adaptive function of genetic colour polymorphism in birds. Biol. Rev. 79, 815-848. (doi: ... d) Survival rates as a function of snake colour. Our mark-recapture data reveal temporal stability in morph frequencies; the ...
http://rspb.royalsocietypublishing.org/content/early/2010/04/06/rspb.2010.0255