compare_groups: Compare groups from fitted models and return confidence...
In wfforrest/maeve: Modeling Accessories Enabling Visualization of Experiments

Description Usage Arguments Value Author(s) References Examples

Compare groups from fitted models and return confidence intervals & figures

compare_groups(
  model_list,
  xmin = NULL,
  xmax = NULL,
  custom_contrast = NULL,
  subtract_starting_value = TRUE,
  conf_level = 0.95,
  adjustment_method = c("single-step", "Shaffer", "Westfall", "free", "holm",
    "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"),
  extended_output = FALSE,
  draw_figures = TRUE,
  facet_wrap_scales = c("fixed", "free_y", "free_x", "free"),
  study_ID_value = "",
  reference_Dunnett = maeve_options("reference_Dunnett"),
  modeling_data_frame = maeve_options("modeling_data_frame"),
  metric = maeve_options("metric"),
  break_points = maeve_options("break_points"),
  poly_degree = maeve_options("poly_degree"),
  progress = maeve_options("progress"),
  contrast = maeve_options("contrast"),
  xrange_norm_method = maeve_options("xrange_norm_method"),
  N_integration_grid = maeve_options("N_integration_grid"),
  truncated_group_levels = maeve_options("truncated_group_levels"),
  geom_na_rm = maeve_options("geom_na_rm"),
  axis_text_x_size = maeve_options("axis_text_x_size"),
  axis_text_x_angle = maeve_options("axis_text_x_angle"),
  axis_text_x_hjust = maeve_options("axis_text_x_hjust"),
  axis_text_x_vjust = maeve_options("axis_text_x_vjust"),
  axis_text_y_size = maeve_options("axis_text_y_size"),
  strip_text_size = maeve_options("strip_text_size"),
  legend_text_size = maeve_options("legend_text_size"),
  legend_position_char = maeve_options("legend_position_char")
)

`model_list`	R list with model objects from maeve::model_study().
`xmin`	numeric lower bound of definite integral
`xmax`	numeric upper bound of definite integral
`custom_contrast`	numeric matrix of contrasts with number of columns equal to number of treatment groups and number of rows equal to desired number of contrasts. Column names must equal treatment group names.
`subtract_starting_value`	logical: Subtract from all computed AUCs the spline fit at xmin for that group.
`conf_level`	numeric value in (0,1) to determine the level of confidence intervals returned.
`adjustment_method`	character string specifying a method for p-value adjustment. Setting to 'none' will return unadjusted p-values and confidence intervals. Setting to anything else (the default is 'single_step') will implement a particular p-value adjustment from multcomp. Although the p-value adjustment method varies for different options of this parameter, all the options other than 'none' will return the same FWER- or FDR-adjusted confidence intervals implemented via setting "calpha = multcomp:::adjusted_calpha()" in "multcomp:::confint.glht()". Setting adjustment_method = 'none' will return confidence intervals with "calpha = multcomp:::univariate_calpha()" in "multcomp:::confint.glht()".
`extended_output`	logical determining whether to compute extra output to return to a DIVOS summary table.
`draw_figures`	logical determining whether to draw figures. If FALSE, then NULL is returned for each figure.
`facet_wrap_scales`	character string passed to "ggplot::facet_wrap( ..., scales = ...)" giving scales parameter. Usually 'fixed' or 'free_y' here.
`study_ID_value`	character string with five digit DIVOS study ID, OR a DivoStudy object.
`reference_Dunnett`	character. See ?maeve_options() for documentation.
`modeling_data_frame`	data.frame. See ?maeve_options().
`metric`	character. See ?maeve_options() for documentation.
`break_points`	numeric vector. See ?maeve_options().
`poly_degree`	numeric. See ?maeve_options().
`progress`	logical. See ?maeve_options() for documentation.
`contrast`	character. See ?maeve_options() for documentation.
`xrange_norm_method`	character. See ?maeve_options() for documentation.
`N_integration_grid`	numeric. See ?maeve_options() for documentation.
`truncated_group_levels`	character. See ?maeve_options() for documentation.
`geom_na_rm`	logical. See ?maeve_options() for documentation.
`axis_text_x_size`	numeric. See ?maeve_options() for documentation.
`axis_text_x_angle`	numeric. See ?maeve_options() for documentation.
`axis_text_x_hjust`	numeric. See ?maeve_options() for documentation.
`axis_text_x_vjust`	numeric. See ?maeve_options() for documentation.
`axis_text_y_size`	numeric. See ?maeve_options() for documentation.
`strip_text_size`	numeric. See ?maeve_options() for documentation.
`legend_text_size`	numeric. See ?maeve_options() for documentation.
`legend_position_char`	character. See ?maeve_options() for documentation.

An R list with named output.

Bill Forrest <forrest@gene.com>

Bill Forrest forrest@gene.com

www.r-project.org

 ### cat('Currently no running example for compare_groups(). See "\dontrun()" text.')
 ## Not run: 
  data( vismodegib )
  vismo21 <- dplyr::filter( vismodegib, DAY_OF_STUDY <= 21 )
  cg_out  <- vismo21 %>% maeve::model_study() %>% maeve::compare_groups()

## End(Not run)