my_contest: applies contrast computation using lmerTest::contest function

In wolski/prolfqua: Proteomics Label Free Quantification

applies contrast computation using lmerTest::contest function

Description

applies contrast computation using lmerTest::contest function

Usage

my_contest(model, linfct, ddf = c("Satterthwaite", "Kenward-Roger"))

Arguments

linfct	linear function
ddf	method to determine denominator degrees of freedom
m	mixed effects model

See Also

Other modelling: Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, build_model(), build_models(), contrasts_fisher_exact(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), isSingular_lm(), linfct_all_possible_contrasts(), linfct_factors_contrasts(), linfct_from_model(), linfct_matrix_contrasts(), make_model(), merge_contrasts_results(), model_analyse(), model_summary(), moderated_p_limma(), moderated_p_limma_long(), my_contrast(), my_contrast_V1(), my_contrast_V2(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_model_and_data(), plot_lmer_peptide_noRandom(), plot_lmer_peptide_predictions(), plot_lmer_predicted_interactions(), strategy_lmer(), summary_ROPECA_median_p.scaled()

Examples

mb <- prolfqua_data('data_basicModel_p1807')
summary(mb)

linfct <- linfct_from_model(mb)
names(linfct)
my_contest(mb, linfct$linfct_factors)
my_contest(mb, linfct$linfct_interactions)

# my_glht(mb, linfct$linfct_factors)
# my_glht(mb, linfct$linfct_interactions)
lmerTest::contest(mb, c( 0 ,1 , 0 , 0),joint = FALSE)
summary(mb)


#library(pbkrtest)
#(fm1 <- lme4::lmer(Reaction ~ Days + (Days | Subject), sleepstudy))
#class(fm1)
#pbkrtest::get_ddf_Lb.lmerMod(fm1)

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.