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1.
GREEN  PETER J. 《Biometrika》1995,82(4):711-732
Markov chain Monte Carlo methods for Bayesian computation haveuntil recently been restricted to problems where the joint distributionof all variables has a density with respect to some fixed standardunderlying measure. They have therefore not been available forapplication to Bayesian model determination, where the dimensionalityof the parameter vector is typically not fixed. This paper proposesa new framework for the construction of reversible Markov chainsamplers that jump between parameter subspaces of differingdimensionality, which is flexible and entirely constructive.It should therefore have wide applicability in model determinationproblems. The methodology is illustrated with applications tomultiple change-point analysis in one and two dimensions, andto a Bayesian comparison of binomial experiments.  相似文献
2.
A new method for calculating evolutionary substitution rates   总被引:38,自引:0,他引:38  
Summary In this paper we present a new method for analysing molecular evolution in homologous genes based on a general stationary Markov process. The elaborate statistical analysis necessary to apply the method effectively has been performed using Monte Carlo technqiues. We have applied our method to the silent third position of the codon of the five mitochondrial genes coding for identified proteins of four mammalian species (rat, mouse, cow and man). We found that the method applies satisfactorily to the three former species, while the last appears to be outside the scope of the present approach. The method allows one to calculate the evolutionarily effective silent substitution rate (vs) for mitochondrial genes, which in the species mentioned above is 1.4×10–8 nucleotide substitutions per site per year. We have also determined the divergence time ratios between the couples mousecow/rat-mouse and rat-cow/rat-mouse. In both cases this value is approximately 1.4.  相似文献
3.
We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.  相似文献
4.
On Gibbs sampling for state space models   总被引:24,自引:0,他引:24  
CARTER  C. K.; KOHN  R. 《Biometrika》1994,81(3):541-553
We show how to use the Gibbs sampler to carry out Bayesian inferenceon a linear state space model with errors that are a mixtureof normals and coefficients that can switch over time. Our approachsimultaneously generates the whole of the state vector giventhe mixture and coefficient indicator variables and simultaneouslygenerates all the indicator variables conditional on the statevectors. The states are generated efficiently using the Kalmanfilter. We illustrate our approach by several examples and empiricallycompare its performance to another Gibbs sampler where the statesare generated one at a time. The empirical results suggest thatour approach is both practical to implement and dominates theGibbs sampler that generates the states one at a time.  相似文献
5.
Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.  相似文献
6.
Tests for trend in life table analysis   总被引:18,自引:0,他引:18  
TARONE  ROBERT E. 《Biometrika》1975,62(3):679-690
7.
Divergence population genetics of chimpanzees   总被引:18,自引:0,他引:18  
The divergence of two subspecies of common chimpanzees (Pan troglodytes troglodytes and P. t. verus) and the bonobo (P. paniscus) was studied using a recently developed method for analyzing population divergence. Under the isolation with migration model, the posterior probability distributions of divergence time, migration rates, and effective population sizes were estimated for large multilocus DNA sequence data sets drawn from the literature. The bonobo and the common chimpanzee are estimated to have diverged approximately 0.86 to 0.89 MYA, and the divergence of the two common chimpanzee subspecies is estimated to have occurred 0.42 MYA. P. t. troglodytes appears to have had a larger effective population size (22,400 to 27,900) compared with P. paniscus, P. t. verus, and the ancestral populations of these species. No evidence of gene flow was found in the comparisons involving P. paniscus; however a clear signal of unidirectional gene flow was found from P. t. verus to P. t. troglodytes (2Nm = 0.51).  相似文献
8.
Owing to the exponential growth of genome databases, phylogenetic trees are now widely used to test a variety of evolutionary hypotheses. Nevertheless, computation time burden limits the application of methods such as maximum likelihood nonparametric bootstrap to assess reliability of evolutionary trees. As an alternative, the much faster Bayesian inference of phylogeny, which expresses branch support as posterior probabilities, has been introduced. However, marked discrepancies exist between nonparametric bootstrap proportions and Bayesian posterior probabilities, leading to difficulties in the interpretation of sometimes strongly conflicting results. As an attempt to reconcile these two indices of node reliability, we apply the nonparametric bootstrap resampling procedure to the Bayesian approach. The correlation between posterior probabilities, bootstrap maximum likelihood percentages, and bootstrapped posterior probabilities was studied for eight highly diverse empirical data sets and were also investigated using experimental simulation. Our results show that the relation between posterior probabilities and bootstrapped maximum likelihood percentages is highly variable but that very strong correlations always exist when Bayesian node support is estimated on bootstrapped character matrices. Moreover, simulations corroborate empirical observations in suggesting that, being more conservative, the bootstrap approach might be less prone to strongly supporting a false phylogenetic hypothesis. Thus, apparent conflicts in topology recovered by the Bayesian approach were reduced after bootstrapping. Both posterior probabilities and bootstrap supports are of great interest to phylogeny as potential upper and lower bounds of node reliability, but they are surely not interchangeable and cannot be directly compared.  相似文献
9.
1. Destructive subsampling or restrictive sampling are often standard procedures to obtain independence of spatial observations in home range analyses. We examined whether home range estimators based upon kernel densities require serial independence of observations, by using a Monte Carlo simulation, antler flies and snapping turtles as models.
2. Home range size, time partitioning and total straight line distances travelled were tested to determine if subsampling improved kernel performance and estimation of home range parameters.
3. The accuracy and precision of home range estimates from the simulated data set improved at shorter time intervals despite the increase in autocorrelation among the observations.
4. Subsampling did not reduce autocorrelation among locational observations of snapping turtles or antler flies, and home range size, time partitioning and total distance travelled were better represented by autocorrelated observations.
5. We found that kernel densities do not require serial independence of observations when estimating home range, and we recommend that researchers maximize the number of observations using constant time intervals to increase the accuracy and precision of their estimates.  相似文献
10.
Rao-Blackwellisation of sampling schemes   总被引:15,自引:0,他引:15  
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