From b76a9b60e9723f77c564971d7d0ded59ace68ade Mon Sep 17 00:00:00 2001
From: Kris Sankaran <sankaran.kris@gmail.com>
Date: Mon, 2 Sep 2024 19:09:16 -0500
Subject: [PATCH] create default and rebuild docs

---
 R/estimators.R           | 2 +-
 man/bootstrap.Rd         | 4 +++-
 man/glmnet_model.Rd      | 5 ++++-
 man/indirect_pathwise.Rd | 4 +++-
 man/lm_model.Rd          | 6 +++++-
 man/parallelize.Rd       | 4 +++-
 man/rf_model.Rd          | 5 ++++-
 7 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/R/estimators.R b/R/estimators.R
index ccfc9f3..13f68fc 100644
--- a/R/estimators.R
+++ b/R/estimators.R
@@ -327,7 +327,7 @@ glmnet_model_params <- function(...) {
 #' multimedia(exper, glmnet_model(lambda = 0.1)) |>
 #'     estimate(exper)
 #' @export
-glmnet_model <- function(progress, ...) {
+glmnet_model <- function(progress = TRUE, ...) {
     check_if_installed(
         c("glmnet", "glmnetUtils"),
         "to use a glmnet regression model for multimedia estimation."
diff --git a/man/bootstrap.Rd b/man/bootstrap.Rd
index 02106d2..f8b6c8d 100644
--- a/man/bootstrap.Rd
+++ b/man/bootstrap.Rd
@@ -4,7 +4,7 @@
 \alias{bootstrap}
 \title{Bootstrap Distribution for Estimators}
 \usage{
-bootstrap(model, exper, fs = NULL, B = 1000)
+bootstrap(model, exper, fs = NULL, B = 1000, progress = TRUE)
 }
 \arguments{
 \item{model}{An object of class multimedia with specified mediation and
@@ -18,6 +18,8 @@ are assumed to be a vector of functions (for example, direct_effect or
 indirect_effect), and they will each be applied to each bootstrap resample.}
 
 \item{B}{The number of bootstrap samples. Defaults to 1000.}
+
+\item{progress}{A logical indicating whether to show a progress bar.}
 }
 \value{
 stats A list of length B containing the results of the fs applied on
diff --git a/man/glmnet_model.Rd b/man/glmnet_model.Rd
index 7763b40..c458193 100644
--- a/man/glmnet_model.Rd
+++ b/man/glmnet_model.Rd
@@ -4,9 +4,12 @@
 \alias{glmnet_model}
 \title{Regularized Glmnet Model across Responses}
 \usage{
-glmnet_model(...)
+glmnet_model(progress = TRUE, ...)
 }
 \arguments{
+\item{progress}{A logical indicating whether to show a progress bar during
+estimation.}
+
 \item{...}{Keyword parameters passed to glmnet.}
 }
 \value{
diff --git a/man/indirect_pathwise.Rd b/man/indirect_pathwise.Rd
index fb6de53..f2d7e5a 100644
--- a/man/indirect_pathwise.Rd
+++ b/man/indirect_pathwise.Rd
@@ -4,7 +4,7 @@
 \alias{indirect_pathwise}
 \title{Indirect Effects via Single Mediation Paths}
 \usage{
-indirect_pathwise(model, exper = NULL, t1 = 1, t2 = 2)
+indirect_pathwise(model, exper = NULL, t1 = 1, t2 = 2, progress = TRUE)
 }
 \arguments{
 \item{model}{An object of class multimedia containing the estimated mediation
@@ -19,6 +19,8 @@ outcome data from which the direct effects are to be estimated.}
 
 \item{t2}{The alternative level of the treatment to be used when computing
 the (pathwise) indirect effect.}
+
+\item{progress}{A logical indicating whether to show a progress bar.}
 }
 \value{
 A data.frame summarizing the pathwise (per-mediator) indirect effects
diff --git a/man/lm_model.Rd b/man/lm_model.Rd
index 4b1eb9a..c7f09ae 100644
--- a/man/lm_model.Rd
+++ b/man/lm_model.Rd
@@ -4,7 +4,11 @@
 \alias{lm_model}
 \title{Linear Model across Responses}
 \usage{
-lm_model()
+lm_model(progress = TRUE)
+}
+\arguments{
+\item{progress}{A logical indicating whether to show a progress bar during
+estimation.}
 }
 \value{
 model An object of class \code{model} with estimator, predictor, and
diff --git a/man/parallelize.Rd b/man/parallelize.Rd
index ce93e30..08551c1 100644
--- a/man/parallelize.Rd
+++ b/man/parallelize.Rd
@@ -4,12 +4,14 @@
 \alias{parallelize}
 \title{Parallelize Estimation across Responses}
 \usage{
-parallelize(f)
+parallelize(f, progress = TRUE)
 }
 \arguments{
 \item{f}{A function for estimating a single response model given a formula
 and input dataset. This is the model that we would like to parallelize
 across responses.}
+
+\item{progress}{A logical indicating whether to show a progress bar.}
 }
 \value{
 f_multi A function that takes a formula and dataset and applies f to
diff --git a/man/rf_model.Rd b/man/rf_model.Rd
index 41c7778..e1cdc13 100644
--- a/man/rf_model.Rd
+++ b/man/rf_model.Rd
@@ -4,9 +4,12 @@
 \alias{rf_model}
 \title{Random Forest Model}
 \usage{
-rf_model(...)
+rf_model(progress = TRUE, ...)
 }
 \arguments{
+\item{progress}{A logical indicating whether to show a progress bar during
+estimation.}
+
 \item{...}{Keyword parameters passed to ranger.}
 }
 \value{