gafem: Genotype analysis by fixed-effect models

In TiagoOlivoto/metan: Multi Environment Trials Analysis

Genotype analysis by fixed-effect models

Description

One-way analysis of variance of genotypes conducted in both randomized complete block and alpha-lattice designs.

Usage

gafem(
  .data,
  gen,
  rep,
  resp,
  block = NULL,
  by = NULL,
  prob = 0.05,
  verbose = TRUE
)

Arguments

.data	The dataset containing the columns related to, Genotypes, replication/block and response variable(s).
gen	The name of the column that contains the levels of the genotypes, that will be treated as random effect.
rep	The name of the column that contains the levels of the replications (assumed to be fixed).
resp	The response variable(s). To analyze multiple variables in a single procedure a vector of variables may be used. For example resp = c(var1, var2, var3). Select helpers are also allowed.
block	Defaults to NULL. In this case, a randomized complete block design is considered. If block is informed, then a resolvable alpha-lattice design (Patterson and Williams, 1976) is employed. All effects, except the error, are assumed to be fixed. Use the function gamem() to analyze a one-way trial with mixed-effect models.
by	One variable (factor) to compute the function by. It is a shortcut to dplyr::group_by().This is especially useful, for example, when the researcher want to fit a fixed-effect model for each environment. In this case, an object of class gafem_grouped is returned. mgidi() can then be used to compute the mgidi index within each environment.
prob	The error probability. Defaults to 0.05.
verbose	Logical argument. If verbose = FALSE the code are run silently.

Details

gafem analyses data from a one-way genotype testing experiment. By default, a randomized complete block design is used according to the following model: \loadmathjax \mjsdeqnY_ij = m + g_i + r_j + e_ij where \mjseqnY_ij is the response variable of the ith genotype in the jth block; m is the grand mean (fixed); \mjseqng_i is the effect of the ith genotype; \mjseqnr_j is the effect of the jth replicate; and \mjseqne_ij is the random error.

When block is informed, then a resolvable alpha design is implemented, according to the following model:

\mjsdeqn

Y_ijk = m + g_i + r_j + b_jk + e_ijk where where \mjseqny_ijk is the response variable of the ith genotype in the kth block of the jth replicate; m is the intercept, \mjseqnt_i is the effect for the ith genotype \mjseqnr_j is the effect of the jth replicate, \mjseqnb_jk is the effect of the kth incomplete block of the jth replicate, and \mjseqne_ijk is the plot error effect corresponding to \mjseqny_ijk. All effects, except the random error are assumed to be fixed.

Value

A list where each element is the result for one variable containing the following objects:

• anova: The one-way ANOVA table.

• model: The model with of lm.

• augment: Information about each observation in the dataset. This includes predicted values in the fitted column, residuals in the resid column, standardized residuals in the stdres column, the diagonal of the 'hat' matrix in the hat, and standard errors for the fitted values in the se.fit column.

• hsd: The Tukey's 'Honest Significant Difference' for genotype effect.

• details: A tibble with the following data: Ngen, the number of genotypes; OVmean, the grand mean; Min, the minimum observed (returning the genotype and replication/block); Max the maximum observed, MinGEN the loser winner genotype, MaxGEN, the winner genotype.

Author(s)

Tiago Olivoto [e-mail]

References

Patterson, H.D., and E.R. Williams. 1976. A new class of resolvable incomplete block designs. Biometrika 63:83-92.

See Also

get_model_data() gamem()

Examples

library(metan)
# RCBD
rcbd <- gafem(data_g,
             gen = GEN,
             rep = REP,
             resp = c(PH, ED, EL, CL, CW))

# Fitted values
get_model_data(rcbd)

# ALPHA-LATTICE DESIGN
alpha <- gafem(data_alpha,
              gen = GEN,
              rep = REP,
              block = BLOCK,
              resp = YIELD)

# Fitted values
get_model_data(alpha)

TiagoOlivoto/metan documentation built on March 27, 2024, 2:35 a.m.