inbreedR (version 0.1.0)

r2_Wf: Expected r2 between inbreeding level (f) and fitness (W)

Description

Expected r2 between inbreeding level (f) and fitness (W)

Usage

r2_Wf(genotypes, trait, family = "gaussian", type = c("msats", "snps"))

Arguments

genotypes

data.frame with individuals in rows and loci in columns, containing genotypes coded as 0 (homozygote), 1 (heterozygote) and NA (missing)

trait

vector of any type which can be specified in R's glm() function

family

distribution of the trait. Default is gaussian. For other distributions, just naming the distribution (e.g. binomial) will use the default link function (see ?family). Specifying another link function can be done in the same way as in the glm() function

type

specifies g2 formula to take. Type "snps" for large datasets and "msats" for smaller datasets.

Value

• call
  function call.
• exp_r2_full
  expected r2 between inbreeding and sMLH for the full dataset
• nobs
  number of observations
• nloc
  number of markers

References

Slate, J., David, P., Dodds, K. G., Veenvliet, B. A., Glass, B. C., Broad, T. E., & McEwan, J. C. (2004). Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data. Heredity, 93(3), 255-265. Szulkin, M., Bierne, N., & David, P. (2010). HETEROZYGOSITY-FITNESS CORRELATIONS: A TIME FOR REAPPRAISAL. Evolution, 64(5), 1202-1217.

Examples

data(mouse_msats)
data(bodyweight)
genotypes <- convert_raw(mouse_msats)

(out <- r2_Wf(genotypes, bodyweight, family = "gaussian", type = "msats"))