gafem: 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, prob = 0.05, block = NULL, 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.

prob

The error probability. Defaults to 0.05.

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.

verbose

Logical argument. If verbose = FALSE the code are run silently.

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.

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: $Y_{i j} = m + g_{i} + r_{j} + e_{i j}$ where $Y_{i j}$ is the response variable of the ith genotype in the jth block; m is the grand mean (fixed); $g_{i}$ is the effect of the ith genotype; $r_{j}$ is the effect of the jth replicate; and $e_{i j}$ is the random error.

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

$Y_{i j k} = m + g_{i} + r_{j} + b_{j k} + e_{i j k}$ where where $y_{i j k}$ is the response variable of the ith genotype in the kth block of the jth replicate; m is the intercept, $t_{i}$ is the effect for the ith genotype $r_{j}$ is the effect of the jth replicate, $b_{j k}$ is the effect of the kth incomplete block of the jth replicate, and $e_{i j k}$ is the plot error effect corresponding to $y_{i j k}$ . All effects, except the random error are assumed to be fixed.

References

Patterson, H.D., and E.R. Williams. 1976. A new class of resolvable incomplete block designs. Biometrika 63:83-92. doi:10.1093/biomet/63.1.83

Examples

Run this code

# NOT RUN {
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)

# }
# NOT RUN {
# }

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