Create coordinated plots, tables and text from supplied effect estimates and confidence intervals, with the requested multiplicity adjustment. Model-scale estimates and sensitivity quantities remain separate from reported unit conversions.
Usage
margot_plot(
.data,
type = c("RD", "RR"),
order = c("alphabetical", "magnitude_desc", "magnitude_asc", "evaluebound_desc",
"evaluebound_asc", "custom", "default"),
custom_order = NULL,
title_binary = NULL,
include_coefficients = TRUE,
standardize_label = c("NZ", "US", "none"),
e_val_bound_threshold = 1.2,
adjust = c("none", "bonferroni", "holm", "BH"),
alpha = 0.05,
...,
options = list(),
label_mapping = NULL,
save_output = FALSE,
use_timestamp = FALSE,
base_filename = "margot_plot_output",
prefix = NULL,
save_path = here::here("push_mods"),
original_df = NULL,
bold_rows = FALSE,
rename_cols = FALSE,
col_renames = list(`E-Value` = "E_Value", `E-Value bound` = "E_Val_bound"),
rename_ate = FALSE,
rename_evalue = FALSE,
scale_info = NULL
)Arguments
- .data
data frame containing causal effect estimates with columns for effect sizes, confidence intervals, E-values and E-value bounds
- type
character. type of effect estimate: "RD" (risk difference) or "RR" (risk ratio)
- order
Outcome ordering rule; the table and text follow the graph from top to bottom.
- custom_order
Outcome labels in the requested custom factor order.
- title_binary
Retained compatibility argument.
- include_coefficients
Whether to print numerical coefficients on the plot.
- standardize_label
Axis-label convention: New Zealand, US, or no standardisation label.
- e_val_bound_threshold
E-value lower-bound threshold for colouring and prose selection.
- adjust
character. multiplicity correction method: "none", "bonferroni"
- alpha
numeric. significance level for corrections
- ...
other parameters as in original function
- options
Plotting options; explicit arguments override corresponding option entries.
- label_mapping
Optional mapping from source outcome names to display labels.
- save_output
Whether to save the complete reporting list.
- use_timestamp
Whether to append a timestamp to saved filenames.
- base_filename
Base name for the saved reporting object.
- prefix
Optional saved-filename prefix.
- save_path
Directory for saved output.
- original_df
Legacy unstandardised source data for inferred scale metadata. Explicit saved metadata is preferred.
- bold_rows
Whether table row labels above the reporting threshold receive Markdown emphasis.
- rename_cols
Whether to apply the requested table column-name mapping.
- col_renames
Named mapping from new table column names to existing names.
- rename_ate
Whether to rename the estimate column, or a supplied replacement name.
- rename_evalue
Whether to use display names for E-value columns.
- scale_info
Optional data frame keyed by the original outcome name, with transformation (`identity`, `log`, or `log1p`), saved `center` and positive `scale`, `orientation` (1 or -1), `unit`, and positive `unit_multiplier`. Constants describe the model outcome as orientation * (g(Y) - center) / scale. Explicit metadata overrides inference from `original_df`.