fullfact (version 1.0)

resampLmer3: Bootstrap components for normal data 3

Description

Extracts additive genetic, non-additive genetic, and maternal variance components from a linear mixed-effect model using the lmer function of the lme4 package. Model random effects are dam, sire, dam by sire, and any additional fixed and/or random effects.

Usage

resampLmer3(resamp, dam, sire, response, start, end, remain, ml = F)

Arguments

resamp

Data frame of bootstrap resampled data.

dam

Column name containing dam(female) parent identity information.

sire

Column name containing sire(male) parent identity information.

response

Column name containing the offspring (response) phenotype values.

start

Starting model number.

end

Ending model number.

remain

Remaining formula using lme4 package format with # sign (see column names), e.g. fixed# + (1|random#).

ml

Default is FALSE for restricted maximum likelihood. Change to TRUE for maximum likelihood.

Value

A data frame with columns containing the raw variance components for dam, sire, dam by sire, residual, total, additive genetic, non-additive genetic, and maternal. Also columns containing the raw variance components for remaining formula components. The number of rows in the data frame matches the number of iterations in the resampled data set and each row represents a model number.

Details

Used for bootstrap resampled data set produced using resampRepli or resampFamily. Extracts the dam, sire, dam, dam by sire, and residual variance components. Extracts any additional fixed effect and random effect variance components. The fixed-effect variance component is as a single group using the method described by Nakagawa and Schielzeth (2013). Calculates the total variance component. Calculates the additive genetic, non-additive genetic, and maternal variance components (see Lynch and Walsh 1998, p. 603).

References

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. 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

See Also

resampLmer, resampLmer2

Examples

data(chinook_resampL)

#length_rcomp3<- resampLmer3(resamp=length_datR,dam="dam",sire="sire",response="length",
#start=1,end=1000,remain="egg_size# + (1|tray#)")
length_rcomp3<- resampLmer3(resamp=chinook_resampL,dam="dam",sire="sire",response="length",
start=1,end=5,remain="egg_size# + (1|tray#)")