analyses lmer4 and lm models created using help function `strategy_lm` or `strategy_lmer`

used in project p2901

model_analyse(
  pepIntensity,
  model_strategy,
  subject_Id = "protein_Id",
  modelName = "Model"
)

See also

Other modelling: Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, build_model(), 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(), merge_contrasts_results(), model_summary(), moderated_p_limma(), moderated_p_limma_long(), my_contest(), my_contrast(), my_contrast_V1(), my_contrast_V2(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_peptide_predictions(), sim_build_models_lm(), sim_build_models_lmer(), sim_make_model_lm(), sim_make_model_lmer(), strategy_lmer(), summary_ROPECA_median_p.scaled()

Examples

x <- sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
formula_randomPeptide <-
  strategy_lmer("abundance  ~ group_ + (1 | peptide_Id)")
mr <- model_analyse( x$data,
 formula_randomPeptide,
 subject_Id = x$config$table$hierarchy_keys_depth())
#> Warning: There were 4 warnings in `dplyr::mutate()`.
#> The first warning was:
#> ℹ In argument: `linear_model = purrr::map(data, model_strategy$model_fun, pb =
#>   pb)`.
#> ℹ In group 2: `protein_Id = "7cbcrd~5725"`.
#> Caused by warning in `value[[3L]]()`:
#> ! WARN :Error: grouping factors must have > 1 sampled level
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
#> Joining with `by = join_by(protein_Id)`
stopifnot(nrow(get_complete_model_fit(mr$modelProtein)) == 6)