save_lm_diagnostic_plots: Plot model diagnostics

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

Plot model diagnostics for lm or lmer models fit separately for each feature. One page of plots is saved per feature. Uses autoplot function from ggfortify

Usage

save_lm_diagnostic_plots(object, formula_char, model_type = c("lm",
  "lmer"), file, all_features = FALSE, width = 12, height = 18, ...)

Arguments

object	a MetaboSet object
formula_char	character, the formula to be used in the linear model (see Details)
model_type	the type of model, either "lm" or "lmer"
file	the file where the plots will be saved
all_features	should all features be included?
width, height	the dimension of the plot
...	other parameters passed to lm/lmer and/or autoplot function from the ggfortify package

Examples

## Not run: 
save_lm_diagnostic_plots(example_set, formula_char = "Feature ~ Group", model_type = "lm", file = "test.pdf")

# Add colouring by time point (don't mind the warnings)
save_lm_diagnostic_plots(example_set, formula_char = "Feature ~ Group",
                         model_type = "lm", file = "test.pdf", colour = "Group")

# Linear mixed model
save_lm_diagnostic_plots(example_set, formula_char = "Feature ~ Group + (1|Subject_ID)",
                         model_type = "lmer", file = "test.pdf")

## End(Not run)

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.