tw_complex {peramo}

Permutation Test for Two-Way Layout with Extra Factors

Description

tw_complex performs the permutation test for ANOVA of two-factor experiments with complex design.

Usage

tw_complex(df, res, mains, nested, nuis, seed = 1, rand = 1999, emm = FALSE)

Arguments

df

a data frame with at least three columns.

res

a character string, name of response variable.

mains

two character strings, names of two main factors.

nested

(optional) a character string, name of the nested factor.

nuis

(optional) a character string, name of the nuisance factor.

seed

an integer, the seed for random number generation. Setting a seed ensures the reproducibility of the result. See set.seed for more details.

rand

an integer, the number of randomization samples. The default value is 1999.

emm

a logical, whether to compute estimated marginal means.

Details

res, mains, nested, and nuis refer to column names in df. While nuis column must be a numeric vector, mains and nested columns must be factors. res can be a numeric or logical vector.

tw_complex currently support linear models with only mains, generalized linear mixed-effects models with mains and nested, and linear mixed-effects models with mains, nested, and nuis.

Value

tw_complex returns a list with 3 main components:

lm, glmer, or lmer

model results.

anova

anova table.

perm

permutation test results with F-statistics, p-values, and strength of evidence.

References

Manly, B. F. J. (2007). Randomization, bootstrap, and Monte Carlo methods in biology (3rd ed). Chapman & Hall/ CRC.

Ernst, M. D. (2004). Permutation Methods: A Basis for Exact Inference. Statistical Science, 19(4), 676–685. doi:10.1214/088342304000000396.

Anderson, M., & Braak, C. T. (2003). Permutation tests for multi-factorial analysis of variance. Journal of Statistical Computation and Simulation, 73(2), 85–113. doi:10.1080/00949650215733.

See Also

lm, glmer, and lmer.

Examples

tw_complex(df = subset(ctm_Cu, run == "Jan",
select = c("copper", "temp", "sediment")),
res = "sediment",
mains = c("copper", "temp"))


#might take more than 5s in some machines