make interaction model for examples
sim_make_model_lm(
model = c("parallel2", "parallel3", "factors", "interaction")
)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_analyse(),
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_lmer(),
strategy_lmer(),
summary_ROPECA_median_p.scaled()
m <- sim_make_model_lm()
#> creating sampleName from fileName column
#> completing cases
#> Joining with `by = join_by(protein_Id)`
mi <- sim_make_model_lm("interaction")
#> creating sampleName from fileName column
#> completing cases
#> Joining with `by = join_by(protein_Id)`
stopifnot(length(coefficients(summary(mi))[,"Estimate"]) == 4)
mf <- sim_make_model_lmer("factors")
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> Warning: There were 4 warnings in `dplyr::mutate()`.
#> The first warning was:
#> ℹ In argument: `linear_model = purrr::map(data, model_strategy$model_fun, pb =
#> pb)`.
#> ℹ In group 2: `protein_Id = "7cbcrd~5725"`.
#> Caused by warning in `value[[3L]]()`:
#> ! WARN :Error: grouping factors must have > 1 sampled level
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
#> Joining with `by = join_by(protein_Id)`
m2 <- sim_make_model_lmer("parallel2")
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> Warning: There were 4 warnings in `dplyr::mutate()`.
#> The first warning was:
#> ℹ In argument: `linear_model = purrr::map(data, model_strategy$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)`
m3 <- sim_make_model_lmer("parallel3")
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> 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)`