Sentence examples for fixed effects likelihood from inspiring English sources

To further infer the types of selection pressure acting on individual genes of VWMPCPLIRMat, MSV-VW and MSV-MatA, we used the random effects likelihood (REL), fixed effects likelihood (FEL), internal fixed effects likelihood (IFEL), and single-likelihood ancestor counting (SLAC) methods implemented in the web-server Datamonkey (http: http://www.datamonkey.org) [ 57, 58].

These models were single likelihood ancestor counting (SLAC) and fixed effects likelihood (FEL) [18].

To identify site-specific selection we used a single likelihood ancestral counting (SLAC), fixed effects likelihood (FEL) and random effects likelihood (REL) model implemented in the HyPhy (www.hyphy.org) software package [44] and Datamonkey web-interface [45].

Datamonkey includes three methods for detecting sites under selection: single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL) and random effects likelihood (REL).

We made separate analyses with the fixed effects likelihood methods (FEL and iFEL) and with the random effect likelihood method (REL) (Pond and Frost 2005).

To identify codon sites under positive (adaptive) or negative (purifying) selection, we used the single-likelihood ancestor counting, the fixed effects likelihood and the random effects likelihood methods.

A codon-based site-by-site fixed effect likelihood (FEL) analysis comparing selective pressures between the two species along internal branches and leaves of the phylogenetic tree was also performed (ComparesSelectivePressure.bf in HYPHY) [75].

The dN/dS ratio among codons was calculated using the maximum likelihood method with the codeml program in PAML 4.5 [ 35, 36], as well as the fixed effect likelihood (FEL) method implemented in HyPhy (version 0.99b) [ 37].

We estimated parameters with random effects (one intercept by plot 1|plot) and fixed effects using maximum likelihood by maximizing the joint density of the parameters and the random component.

In the GLMM, the Wald statistics are recommended to test the null hypothesis of fixed effects because the likelihood ratio tests are unreliable for small to moderate sample sizes [ 8- 10].

Kenward, M. G. & Roger, J. H. Small sample inference for fixed effects from restricted maximum likelihood.