Variance-covariance matrices for designed experiments

Compute variance-covariance and correlation matrices using data from a designed (RCBD or CRD) experiment.

Usage

covcor_design(.data, gen, rep, resp, design = "RCBD", by = NULL, type = NULL)

Arguments

.data: The data to be analyzed. It can be a data frame, possible with grouped data passed from dplyr::group_by().
gen: The name of the column that contains the levels of the genotypes.
rep: The name of the column that contains the levels of the replications/blocks.
resp: The response variables. For example resp = c(var1, var2, var3).
design: The experimental design. Must be RCBD or CRD.
by: One variable (factor) to compute the function by. It is a shortcut to dplyr::group_by(). To compute the statistics by more than one grouping variable use that function.
type: What the matrices should return? Set to NULL, i.e., a list of matrices is returned. The argument type allow the following values 'pcor', 'gcor', 'rcor', (which will return the phenotypic, genotypic and residual correlation matrices, respectively) or 'pcov', 'gcov', 'rcov' (which will return the phenotypic, genotypic and residual variance-covariance matrices, respectively). Alternatively, it is possible to get a matrix with the means of each genotype in each trait, by using type = 'means'.

Value

An object of class covcor_design containing the following items:

geno_cov The genotypic covariance.
phen_cov The phenotypic covariance.
resi_cov The residual covariance.
geno_cor The phenotypic correlation.
phen_cor The phenotypic correlation.
resi_cor The residual correlation.

If .data is a grouped data passed from dplyr::group_by() then the results will be returned into a list-column of data frames.

Author

Tiago Olivoto tiagoolivoto@gmail.com

Examples

# \donttest{
library(metan)
# List of matrices
data <- subset(data_ge2, ENV == 'A1')
matrices <- covcor_design(data,
                          gen = GEN,
                          rep = REP,
                          resp = c(PH, EH, NKE, TKW))

# Genetic correlations
gcor <- covcor_design(data,
                      gen = GEN,
                      rep = REP,
                      resp = c(PH, EH, NKE, TKW),
                      type = 'gcor')

# Residual (co)variance matrix for each environment
rcov <- covcor_design(data_ge2,
                      gen = GEN,
                      rep = REP,
                      resp = c(PH, EH, CD, CL),
                      by = ENV,
                      type = "rcov")
#> Warning: There were 4 warnings in `mutate()`.
#> The first warning was:
#> ℹ In argument: `data = purrr::map(.data$data, .fun, ...)`.
#> Caused by warning in `sqrt()`:
#> ! NaNs produced
#> ℹ Run dplyr::last_dplyr_warnings() to see the 3 remaining warnings.
# }