anova.lm.rrpp: ANOVA for lm.rrpp model fits

In RRPP: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

ANOVA for lm.rrpp model fits

Description

Computes an analysis of variance (ANOVA) table using distributions of random statistics from lm.rrpp. ANOVA can be performed on one model or multiple models. If the latter, the first model is considered a null model for comparison to other models. The ANOVA is functionally similar to a non-parametric likelihood ratio test for all null-full model comparisons Residuals from the null model will be used to generate random pseudo-values via RRPP for evaluation of subsequent models. The permutation schedule from the null model will be used for random permutations. This function does not correct for improper null models. One must assure that the null model is nested within the other models. Illogical results can be generated if this is not the case.

Usage

## S3 method for class 'lm.rrpp'
anova(
  object,
  ...,
  effect.type = c("F", "cohenf", "SS", "MS", "Rsq"),
  error = NULL,
  print.progress = TRUE
)

Arguments

object	Object from lm.rrpp
...	Additional lm.rrpp model fits or other arguments passed to anova.
effect.type	One of "F", "cohenf", "SS", "MS", "Rsq" to choose from which distribution of statistics to calculate effect sizes (Z). See lm.rrpp.
error	An optional character string to define MS error term for calculation of F values. See lm.rrpp for examples.
print.progress	A logical argument if multiple models are used and one wishes to view progress for sums of squares (SS) calculations.

Author(s)

Michael Collyer

Examples

## Not run: 
# See examples for lm.rrpp to see how anova.lm.rrpp works in conjunction
# with other functions

data(Pupfish)
names(Pupfish)
Pupfish$logSize <- log(Pupfish$CS) # better to not have functions in formulas

# Single-Model ANOVA

fit <- lm.rrpp(coords ~ logSize + Sex*Pop, SS.type = "I", 
data = Pupfish, print.progress = FALSE, iter = 999) 
anova(fit)
anova(fit, effect.type = "MS")
anova(fit, effect.type = "Rsq")
anova(fit, effect.type = "cohenf")

# Multi-Model ANOVA (like a Likelihood Ratio Test)
fit.size <- lm.rrpp(coords ~ logSize, SS.type = "I", data = Pupfish, 
print.progress = FALSE, iter = 999) 
fit.sex <- lm.rrpp(coords ~ logSize + Sex, SS.type = "I", data = Pupfish, 
print.progress = FALSE, iter = 999) 
fit.pop <- lm.rrpp(coords ~ logSize + Pop, SS.type = "I", data = Pupfish, 
print.progress = FALSE, iter = 999) 
anova(fit.size, fit.sex, fit.pop, 
print.progress = FALSE) # compares two models to the first

# see lm.rrpp examples for mixed model ANOVA example and how to vary SS type

## End(Not run)

RRPP documentation built on June 22, 2024, 6:45 p.m.