From 320606b8ede0f7cb2cdaafa55804d49e43632f11 Mon Sep 17 00:00:00 2001
From: Sima Najafzadehkhoei <u1418987@umail.utah.edu>
Date: Tue, 10 Dec 2024 14:48:07 -0700
Subject: [PATCH] updates

---
 .github/.gitignore            |  1 +
 NAMESPACE                     |  1 +
 man/prepare_data.Rd           | 19 +++++++++++++++++++
 man/run_simulations.Rd        |  2 +-
 man/simulate_calibrate_sir.Rd |  2 +-
 man/train_model.Rd            |  2 +-
 tests/testthat.R              |  4 ++--
 vignettes/calibrate.Rmd       | 12 ++++++++----
 8 files changed, 34 insertions(+), 9 deletions(-)
 create mode 100644 .github/.gitignore
 create mode 100644 man/prepare_data.Rd

diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/NAMESPACE b/NAMESPACE
index b566a6e..f62ea7c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(filter_non_null)
 export(filter_non_null_infected)
 export(generate_theta)
 export(plot_results)
+export(prepare_data)
 export(prepare_data_for_tensorflow)
 export(prepare_data_infected)
 export(preprocessing_data)
diff --git a/man/prepare_data.Rd b/man/prepare_data.Rd
new file mode 100644
index 0000000..b623611
--- /dev/null
+++ b/man/prepare_data.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dataprep.R
+\name{prepare_data}
+\alias{prepare_data}
+\title{Prepare Data for TensorFlow Model: General SIR Data Preparation}
+\usage{
+prepare_data(m, max_days = max_days)
+}
+\arguments{
+\item{m}{An \code{epiworldR} model object.}
+
+\item{max_days}{The maximum number of days to consider for data preparation. Defaults to 50.}
+}
+\value{
+A reshaped array of processed data suitable for TensorFlow models. If an error occurs, it returns the error object.
+}
+\description{
+Prepare Data for TensorFlow Model: General SIR Data Preparation
+}
diff --git a/man/run_simulations.Rd b/man/run_simulations.Rd
index c6a3816..5d7572d 100644
--- a/man/run_simulations.Rd
+++ b/man/run_simulations.Rd
@@ -4,7 +4,7 @@
 \alias{run_simulations}
 \title{Run SIR Model Simulations}
 \usage{
-run_simulations(N, n, ndays, ncores, theta, seeds, path)
+run_simulations(N, n, ndays, ncores, theta, seeds)
 }
 \arguments{
 \item{N}{Integer. The number of simulations to run.}
diff --git a/man/simulate_calibrate_sir.Rd b/man/simulate_calibrate_sir.Rd
index cc833eb..18d43c8 100644
--- a/man/simulate_calibrate_sir.Rd
+++ b/man/simulate_calibrate_sir.Rd
@@ -4,7 +4,7 @@
 \alias{simulate_calibrate_sir}
 \title{simulate calibrate sir Function}
 \usage{
-simulate_calibrate_sir(N, n, ndays, ncores)
+simulate_calibrate_sir(N, n, ndays, ncores, epochs, verbose)
 }
 \arguments{
 \item{N}{Integer. The number of simulations to run.}
diff --git a/man/train_model.Rd b/man/train_model.Rd
index d891d28..c2a80c5 100644
--- a/man/train_model.Rd
+++ b/man/train_model.Rd
@@ -4,7 +4,7 @@
 \alias{train_model}
 \title{Train the CNN Model}
 \usage{
-train_model(model, train_data, epochs = 100)
+train_model(model, train_data, epochs = epochs, verbose = verbose)
 }
 \arguments{
 \item{model}{Keras model. The compiled model to be trained.}
diff --git a/tests/testthat.R b/tests/testthat.R
index 268608c..3342db3 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -7,6 +7,6 @@
 # * https://testthat.r-lib.org/articles/special-files.html
 
 library(testthat)
-library(myfirst.package)
+library(epiworldRcalibrate)
 
-test_check("myfirst.package")
+test_check("epiworldRcalibrate")
diff --git a/vignettes/calibrate.Rmd b/vignettes/calibrate.Rmd
index 04eda40..5c7660f 100644
--- a/vignettes/calibrate.Rmd
+++ b/vignettes/calibrate.Rmd
@@ -18,19 +18,23 @@ The vignette guides you through the different stages of the function, including
 ## Prerequisites
 
 Ensure that the following libraries are installed and loaded:
-
-```{r}
-library(epiworldRcalibrate)
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  eval = FALSE, # Globally disables evaluation of all chunks
+  echo = TRUE   # Shows code in the vignette but does not run it
+)
 ```
 
+
+
 ```{r}
 library(epiworldR)
-library(epiworldRcalibrate)
 library(keras3)
 library(data.table)
 library(tensorflow)
 library(reticulate)
 reticulate::import("numpy")
+library(epiworldRcalibrate)
 ```
 
 # Function Overview