Helper that assembles a concise Markdown interpretation of the results. By default it lists every outcome whose confidence interval excludes the null, in plot order from top to bottom, with its E-value bound and E-value flag, and states the correction and confidence level. When `include_adjust_note = FALSE` (the default for a single-outcome call from `margot_plot()`), the correction is not mentioned; the confidence level is still stated.
Usage
margot_interpret_marginal(
df,
type = c("RD", "RR"),
order = c("alphabetical", "magnitude_desc", "magnitude_asc", "evaluebound_desc",
"evaluebound_asc", "custom", "default"),
original_df = NULL,
e_val_bound_threshold = 1,
adjust = c("none", "bonferroni", "holm", "BH"),
alpha = 0.05,
include_adjust_note = TRUE,
effect_type = "ATE",
scale_info = NULL,
custom_order = NULL,
category_rule = c("interval", "interval_and_evalue"),
e_val_bound_comparison = c(">", ">="),
order_direction = c("top_to_bottom", "bottom_to_top"),
effect_label = NULL,
listed_in_plot_order = FALSE
)Arguments
- df
Estimate table accepted by [margot_plot()], already corrected for multiplicity when `adjust` is not `"none"`.
- type
character. type of effect estimate: "RD" (risk difference) or "RR" (risk ratio)
- order
Outcome ordering rule. The first outcome in the ordering is drawn at the top of the plot (see `order_direction`), and the table and text follow the graph from top to bottom. `"magnitude_desc"` puts the largest absolute effect at the top; `"magnitude_asc"` the smallest; `"evaluebound_desc"` the largest E-value bound; `"alphabetical"` runs A to Z down the plot; `"custom"` follows `custom_order` from the top.
- original_df
Legacy unstandardised source data for inferred scale metadata. Explicit saved metadata is preferred.
- e_val_bound_threshold
Reporting threshold for the E-value bound. By default it sets only the E-value flag reported beside each estimate (table column and prose); it does not change the plotted category. Under `category_rule = "interval_and_evalue"` it also gates the category, as in earlier versions.
- adjust
character. multiplicity correction method: "none", "bonferroni", "holm" or "BH". With `"none"`, the supplied intervals and E-values are used unchanged. `"holm"` and `"BH"` stop under the default interval rule: margot builds their intervals at coverage 1 - adjusted p, so the intervals exclude the null whatever the adjusted p-value and cannot carry an interval decision. `category_rule = "interval_and_evalue"` still runs them, with a warning, to reproduce earlier output; it carries the same limitation.
- alpha
numeric. significance level for corrections
- include_adjust_note
logical; if `FALSE`, any reference to adjustment methods is omitted. default `TRUE`.
- effect_type
Label identifying ATE, ATT, ATC, ATO or an association.
- 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`.
- custom_order
Outcome display labels in the requested order, first at the top of the plot (with the default `order_direction`).
- category_rule
How estimates are classified for colour, legend, table and prose. `"interval"` (default) uses the (adjusted) confidence interval alone: above the null, below the null, or including the null. `"interval_and_evalue"` reproduces margot 1.3.2 and earlier, for reproducing earlier results only: an estimate is "positive" or "negative" only when its interval excludes the null and its E-value bound passes the threshold, and is otherwise labelled "not reliable"; the prose then lists only estimates whose bound passes the threshold.
- e_val_bound_comparison
Comparison between the E-value bound and `e_val_bound_threshold`: `">"` (default) flags a bound that exceeds the threshold; `">="` reproduces margot 1.3.2 and earlier, which also flagged a bound equal to it. The comparison uses full precision.
- order_direction
Where the ordering starts. `"top_to_bottom"` (default) draws the first outcome of `order` at the top. `"bottom_to_top"` reproduces margot 1.3.2 and earlier, for reproducing earlier results only: the first outcome was drawn at the bottom, so `"magnitude_desc"` put the largest effect at the bottom. The table and prose follow the plot from top to bottom under either value.
- effect_label
Name for the model-scale estimate in each bullet, for example `"ATE (standardised)"`; `NULL` uses the effect type.
- listed_in_plot_order
logical; `TRUE` when the prose accompanies a plot, so that it says the outcomes are listed in plot order.