Extracts the power values of dam, sire, and dam by sire variance components from a generalized linear mixed-effect model using the glmer function of the lme4 package. Options to include one random position and/or one random block effect(s).
powerGlmer2(varcomp, nval, fam_link, alpha = 0.05, nsim = 100, position = NULL,
block = NULL, poisLog = NULL)Prints a data frame with the sample sizes, variance component inputs, variance component outputs, and power values.
Vector of known dam, sire, dam by sire, and position and/or block variance components, i.e. c(dam, sire, dam x sire, position/block). If there is a position and a block c(..., dam x sire, position, block).
Vector of known dam, sire, offspring per family, and offspring per position or number of blocks sample sizes, i.e. c(dam, sire, offspring, position/block). If there is a position and a block c(..., offspring, position, block).
The family and link in family(link) format. Supported options are binomial(link="logit"), binomial(link="probit"), poisson(link="log"), and poisson(link="sqrt").
Statistical significance value. Default is 0.05.
Number of simulations. Default is 100.
Optional number of positions.
Optional vector of dams and sires per block, e.g. c(2,2).
The residual variance component value if using poisson(link="log").
Extracts the dam, sire, dam, dam by sire, and position and/or block power values. The residual variance component for the fam_links are described by Nakagawa and Schielzeth (2010, 2013). Power values are calculated by stochastically simulation data and then calculating the proportion of significance values less than alpha for each component (Bolker 2008). Significance values for the random effects are determined using likelihood ratio tests (Bolker et al. 2009).
Bolker BM. 2008. Ecological models and data in R. Princeton University Press, New Jersey.
Bolker BM, Brooks ME, Clark CJ, Geange SW, Poulsen JR, Stevens MHH, White J-SS. 2009. Generalized linear mixed models: a practical guide for ecology and evolution. Trends in Ecology and Evolution 24(3): 127-135. DOI: 10.1016/j.tree.2008.10.008
Lynch M, Walsh B. 1998. Genetics and Analysis of Quantitative Traits. Sinauer Associates, Massachusetts.
Nakagawa S, Schielzeth H. 2010. Repeatability for Gaussian and non-Gaussian data: a practical guide for biologists. Biological Reviews 85(4): 935-956. DOI: 10.1111/j.1469-185X.2010.00141.x
Nakagawa S, Schielzeth H. 2013. A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods in Ecology and Evolution 4(2): 133-142. DOI: 10.1111/j.2041-210x.2012.00261.x
powerGlmer, powerGlmer3
#100 simulations
if (FALSE) powerGlmer2(varcomp=c(0.7880,0.1667,0.1671,0.0037),nval=c(11,11,300,3300),
position=11,fam_link=binomial(link="logit"))
Run the code above in your browser using DataLab