Analysis of variance for a mixeff LMM — anova.mm

With no extra models, anova() returns a term-level F-test table for object shaped like lmerTest's: a data frame of class "anova" with columns Sum Sq, Mean Sq, NumDF, DenDF, F value and Pr(>F) (rows named by term; Mean Sq = F * sigma^2 and Sum Sq = NumDF * Mean Sq, as in lmerTest). With further fitted models in ..., it returns lme4's likelihood-ratio table (npar, AIC, BIC, logLik, -2*log(L), Chisq, Df, Pr(>Chisq), rows named after the arguments; lme4 before 2.0 called the -2*log(L) column deviance), computed by compare() (REML fits are refit by ML, as in lme4).

Usage

# S3 method for class 'mm_lmm'
anova(
  object,
  ...,
  type = c("III", "II", "I", "block"),
  method = c("auto", "satterthwaite", "kenward_roger", "bootstrap", "asymptotic", "none"),
  refit_for_comparison = c("auto", "error", "ml"),
  ddf = NULL
)

Arguments

object: A fitted mm_lmm.
...: Optional additional fitted models; triggers compare().
type: Term-hypothesis type. "III" (default) tests marginal Type III hypotheses: a term's own contrast columns plus the equally-weighted average over the levels of every term that contains it, which makes the test invariant to which factor level is the reference and matches SAS / car / lmerTest Type III. "II" respects marginality (each term adjusted for all terms that do not contain it). "I" is sequential in terms() order (main effects, then two-way interactions, and so on). "block" tests the raw coefficient block for each term — under treatment coding that is the simple effect at the other factors' reference levels, which is a legitimate quantity but is not Type III on unbalanced designs; it is the hypothesis mixeff computed for "III" before engine 1f3f689. lmerTest's spellings 3, 2, 1 (numeric or character) are accepted.
method: Degrees-of-freedom / test method.
refit_for_comparison: Passed to compare() when ... is used.
ddf: lmerTest's spelling of the method: "Satterthwaite" (method = "satterthwaite"), "Kenward-Roger" (method = "kenward_roger"), or "lme4", which returns lme4's own single-model table (sequential npar, Sum Sq, Mean Sq, F value, no denominator df or p-values). Supply ddf or method, not both.

Value

A data frame of class c("mm_anova", "anova", "data.frame") for one model, or c("mm_anova_comparison", "mm_model_comparison", "anova", "data.frame") for several.

Details

mixeff's provenance stays on the result: x$table is the full term-level (or compare()) table with method, status, reliability and reason columns, and x$type / x$requested_method record the request. Rows the engine could not certify keep NA statistics and their reason is printed under the table.