Usage
env_stratification(
.data,
env,
gen,
resp,
use = "complete.obs",
mineval = 1,
verbose = TRUE
)
Arguments
- .data
The dataset containing the columns related to Environments, Genotypes, replication/block and response variable(s)
- env
The name of the column that contains the levels of the environments.
- gen
The name of the column that contains the levels of the genotypes.
- resp
The response variable(s). To analyze multiple variables in a single procedure use, for example,
resp = c(var1, var2, var3)
.- use
The method for computing covariances in the presence of missing values. Defaults to
complete.obs
, i.e., missing values are handled by casewise deletion.- mineval
The minimum value so that an eigenvector is retained in the factor analysis.
- verbose
Logical argument. If
verbose = FALSE
the code will run silently.
Value
An object of class env_stratification
which is a list with one
element per analyzed trait. For each trait, the following values are given.
data
The genotype-environment means.cormat
: The correlation matrix among the environments.PCA
: The eigenvalues and explained variance.FA
: The factor analysis.env_strat
: The environmental stratification.mega_env_code
: The environments within each mega-environment.mega_env_stat
: The statistics for each mega-environment.KMO
: The result for the Kaiser-Meyer-Olkin test.MSA
: The measure of sampling adequacy for individual variable.communalities_mean
: The communalities' mean.initial_loadings
: The initial loadings.
References
Murakami, D.M.D., and C.D.C. Cruz. 2004. Proposal of methodologies for environment stratification and analysis of genotype adaptability. Crop Breed. Appl. Biotechnol. 4:7-11.
Author
Tiago Olivoto, tiagoolivoto@gmail.com
Examples
# \donttest{
library(metan)
model <-
env_stratification(data_ge,
env = ENV,
gen = GEN,
resp = everything())
gmd(model)
#> Class of the model: env_stratification
#> Variable extracted: env_strat
#> # A tibble: 28 × 7
#> TRAIT ENV MEGA_ENV MEAN MIN MAX CV
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 GY E1 ME1 2.52 1.97 2.90 13.3
#> 2 GY E10 ME1 2.18 1.54 2.57 14.4
#> 3 GY E11 ME1 1.37 0.899 1.68 16.4
#> 4 GY E12 ME1 1.61 1.02 2 20.3
#> 5 GY E13 ME1 2.91 1.83 3.52 16.8
#> 6 GY E5 ME1 3.91 3.37 4.81 10.7
#> 7 GY E3 ME2 4.06 3.43 4.57 8.22
#> 8 GY E6 ME2 2.66 2.34 2.98 7.95
#> 9 GY E14 ME3 1.78 1.43 2.06 11.7
#> 10 GY E8 ME3 2.54 2.05 2.88 10.5
#> # … with 18 more rows
# }