From 01a6857946617236eacd8540337e27fcad1c5fb7 Mon Sep 17 00:00:00 2001
From: Kris Sankaran <sankaran.kris@gmail.com>
Date: Wed, 28 Aug 2024 18:09:32 -0500
Subject: [PATCH] update manual

---
 man/mediation_models.Rd     | 1 +
 man/mindfulness.Rd          | 3 +++
 man/outcome_models.Rd       | 1 +
 man/plot_sensitivity.Rd     | 6 +++---
 man/sensitivity.Rd          | 5 +++--
 man/sensitivity_pathwise.Rd | 2 +-
 6 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/man/mediation_models.Rd b/man/mediation_models.Rd
index f7490ff..f1126da 100644
--- a/man/mediation_models.Rd
+++ b/man/mediation_models.Rd
@@ -17,6 +17,7 @@ A list containing all the fitted mediation models.
 Accessor for Outcome Models
 }
 \examples{
+data(mindfulness)
 exper <- mediation_data(
     mindfulness,
     phyloseq::taxa_names(mindfulness),
diff --git a/man/mindfulness.Rd b/man/mindfulness.Rd
index 7db1531..357f475 100644
--- a/man/mindfulness.Rd
+++ b/man/mindfulness.Rd
@@ -18,4 +18,7 @@ stored as a phyloseq object. Measurements are from 50 subjects before and
 after a real and active control mindfulness intervention. We are interested
 in changes in subject-level metadata, stored in the sample_data slot
 }
+\examples{
+data(mindfulness)
+}
 \keyword{data}
diff --git a/man/outcome_models.Rd b/man/outcome_models.Rd
index b59dc6e..1877ac2 100644
--- a/man/outcome_models.Rd
+++ b/man/outcome_models.Rd
@@ -17,6 +17,7 @@ A list containing all the fitted outcome models.
 Accessor for Outcome Models
 }
 \examples{
+data(mindfulness)
 exper <- mediation_data(
     mindfulness,
     phyloseq::taxa_names(mindfulness),
diff --git a/man/plot_sensitivity.Rd b/man/plot_sensitivity.Rd
index 92a02cd..0b9c002 100644
--- a/man/plot_sensitivity.Rd
+++ b/man/plot_sensitivity.Rd
@@ -8,9 +8,9 @@ plot_sensitivity(sensitivity_curve, x_var = "rho", y_var = "indirect_effect")
 }
 \arguments{
 \item{sensitivity_curve}{The output of a call to sensitivity or
-sensitivity_perturb. A data.frame whose columns are: outcome, {x_var},
-{y_var}, and {y_var}_standard_error, where x_var and y_var are defined in
-the two arguments below.}
+sensitivity_perturb. A data.frame whose columns are: outcome, \{x_var\},
+\{y_var\}, and \{y_var\}_standard_error, where x_var and y_var are defined
+in the two arguments below.}
 
 \item{x_var}{The type of perturbation variable to plot along the x-axis.
 Defaults to "rho", following the sensitivity approach implemented in
diff --git a/man/sensitivity.Rd b/man/sensitivity.Rd
index 82c605a..c512021 100644
--- a/man/sensitivity.Rd
+++ b/man/sensitivity.Rd
@@ -31,7 +31,7 @@ so enforcing independence between mediators and outcomes)}
 
 \item{rho_seq}{We will evaluate correlations Cor(e', e) between mediation and
 outcome model errors ranging along this grid. Defaults to NULL, which
-internally sets the sequence to rho = \link{-0.9, -0.7 ..., 0.7, 0.9}.}
+internally sets the sequence to rho = (-0.9, -0.7 ..., 0.7, 0.9).}
 
 \item{n_bootstrap}{The number of bootstrap resamples used to build confidence
 bands around the sensitivity curves. Defaults to 100.}
@@ -63,5 +63,6 @@ model <- multimedia(
 ) |>
     estimate(exper)
 rho_seq <- c(-0.2, 0, 0.2)
-sensitivity(model, exper, subset_indices, rho_seq, n_bootstrap = 2)
+confound_ix <- expand.grid(mediator = 1, outcome = 1:2)
+sensitivity(model, exper, confound_ix, rho_seq, n_bootstrap = 2)
 }
diff --git a/man/sensitivity_pathwise.Rd b/man/sensitivity_pathwise.Rd
index 5fafff0..af90d99 100644
--- a/man/sensitivity_pathwise.Rd
+++ b/man/sensitivity_pathwise.Rd
@@ -31,7 +31,7 @@ so enforcing independence between mediators and outcomes)}
 
 \item{rho_seq}{We will evaluate correlations Cor(e', e) between mediation and
 outcome model errors ranging along this grid. Defaults to NULL, which
-internally sets the sequence to rho = \link{-0.9, -0.7 ..., 0.7, 0.9}.}
+internally sets the sequence to rho = (-0.9, -0.7 ..., 0.7, 0.9).}
 
 \item{n_bootstrap}{The number of bootstrap resamples used to build confidence
 bands around the sensitivity curves. Defaults to 100.}