reproducibility instructions added

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: retel
 Type: Package
 Title: Regularized Exponentially Tilted Empirical Likelihood
-Version: 0.1.0.9002
+Version: 0.1.0.9003
 Authors@R: c(
     person("Eunseop", "Kim", email = "markean@pm.me", 
             role = c("aut", "cph", "cre")),
@@ -25,7 +25,7 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Imports: 
     checkmate,
     Matrix,

README.Rmd

@@ -31,7 +31,7 @@ The following functions enable users to set estimating functions by providing da
 * `retel()` computes regularized exponentially tilted empirical likelihood with regularization parameters.
 
 This repository accompanies the research paper titled 'Regularized Exponentially Tilted Empirical Likelihood for Bayesian Inference,' available on [arXiv](https://arxiv.org/abs/2312.17015).
-The `retel-paper` folder contains code and additional resources related to the paper.
+The `retel-paper/` folder contains code and outputs from the paper.
 This work was supported by the U.S. National Science Foundation under Grants No. [SES-1921523](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1921523) and [DMS-2015552](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2015552).
 
 

README.md

@@ -29,9 +29,8 @@ providing data and parameters:
 This repository accompanies the research paper titled ‘Regularized
 Exponentially Tilted Empirical Likelihood for Bayesian Inference,’
 available on [arXiv](https://arxiv.org/abs/2312.17015). The
-`retel-paper` folder contains code and additional resources related to
-the paper. This work was supported by the U.S. National Science
-Foundation under Grants
+`retel-paper/` folder contains code and outputs from the paper. This
+work was supported by the U.S. National Science Foundation under Grants
 No. [SES-1921523](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1921523)
 and
 [DMS-2015552](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2015552).

retel-paper/README.Rmd

@@ -16,15 +16,16 @@ knitr::opts_chunk$set(
 # retel-paper
 
 Reproducible code for generating figures and outputs from simulations and the application presented in the paper 'Regularized Exponentially Tilted Empirical Likelihood for Bayesian Inference,' accessible on [arXiv](https://arxiv.org/abs/2312.17015).
-The following sections outline the directory structure and provide detailed instructions for replicating the results.
+
+The following sections outline the directory structure and provide instructions for replicating the results.
 
 ## Directory Structure
 
 ```
 .
 ├── application/        <- 📂 Application outputs
 ├── code/               <- 📂 All code for reproducibility
-│   ├── application/        <- 📂 Code for application in Section 5
+│   ├── application/        <- 📂 Code for application in Section 5 and Table 4
 │   ├── figures/            <- 📂 Code for figures 
 │   │   ├── supplement/         <- 📂 Supplement figures  
 │   ├── simulations/        <- 📂 Code for simulations
@@ -61,4 +62,33 @@ The following sections outline the directory structure and provide detailed inst
 ├── retel-paper.Rproj   <- 🖥️ R Project file for RStudio 
 ```
 
-## Instructions for Reproducibility
+## Instructions for Reproducibility
+
+Please ensure Git, R (version 4.1.0 or higher), and preferably RStudio (for interactive script execution on a personal computer) are installed.
+
+1. Clone this repository.
+
+2. Set the working directory to the `retel-paper/` folder or open the `retel-paper.Rproj` project file in RStudio.
+
+3. Restore the project library by executing the following command in R:
+
+```{r, eval = FALSE}
+# install.packages("renv")
+renv::restore()
+```
+
+This command will automatically install all the required packages, including 'retel.'
+To maintain reproducibility and prevent potential issues, it is strongly advised not to manually install the packages.
+
+4. Run the R scripts in the `code/` folder. 
+Each script is designed to run independently, with script names corresponding to specific methods, configuration settings, or outputs from the paper. 
+No edits or modifications are needed.
+
+For example:
+
+- `code/application/retel_f.R` reproduces the RETEL_f results for Table 4.
+- `code/figures/figure1.R` reproduces Figure 1.
+- `code/simulations/cr/l0/n5s05.R` reproduces the results for Table 2 when n = 5 and s = 0.5.
+
+Note: The simulations and application code were run in a high-performance computing (HPC) environment.
+The total run time for sequentially executing all scripts in the `code/` folder can vary, potentially extending to many hours, depending on the machine or hardware specifications.

retel-paper/README.md

@@ -6,16 +6,17 @@
 Reproducible code for generating figures and outputs from simulations
 and the application presented in the paper ‘Regularized Exponentially
 Tilted Empirical Likelihood for Bayesian Inference,’ accessible on
-[arXiv](https://arxiv.org/abs/2312.17015). The following sections
-outline the directory structure and provide detailed instructions for
-replicating the results.
+[arXiv](https://arxiv.org/abs/2312.17015).
+
+The following sections outline the directory structure and provide
+instructions for replicating the results.
 
 ## Directory Structure
 
     .
     ├── application/        <- 📂 Application outputs
     ├── code/               <- 📂 All code for reproducibility
-    │   ├── application/        <- 📂 Code for application in Section 5
+    │   ├── application/        <- 📂 Code for application in Section 5 and Table 4
     │   ├── figures/            <- 📂 Code for figures 
     │   │   ├── supplement/         <- 📂 Supplement figures  
     │   ├── simulations/        <- 📂 Code for simulations
@@ -52,3 +53,41 @@ replicating the results.
     ├── retel-paper.Rproj   <- 🖥️ R Project file for RStudio 
 
 ## Instructions for Reproducibility
+
+Please ensure Git, R (version 4.1.0 or higher), and preferably RStudio
+(for interactive script execution on a personal computer) are installed.
+
+1.  Clone this repository.
+
+2.  Set the working directory to the `retel-paper/` folder or open the
+    `retel-paper.Rproj` project file in RStudio.
+
+3.  Restore the project library by executing the following command in R:
+
+``` r
+# install.packages("renv")
+renv::restore()
+```
+
+This command will automatically install all the required packages,
+including ‘retel.’ To maintain reproducibility and prevent potential
+issues, it is strongly advised not to manually install the packages.
+
+4.  Run the R scripts in the `code/` folder. Each script is designed to
+    run independently, with script names corresponding to specific
+    methods, configuration settings, or outputs from the paper. No edits
+    or modifications are needed.
+
+For example:
+
+- `code/application/retel_f.R` reproduces the RETEL_f results for Table
+  4.
+- `code/figures/figure1.R` reproduces Figure 1.
+- `code/simulations/cr/l0/n5s05.R` reproduces the results for Table 2
+  when n = 5 and s = 0.5.
+
+Note: The simulations and application code were run in a
+high-performance computing (HPC) environment. The total run time for
+sequentially executing all scripts in the `code/` folder can vary,
+potentially extending to many hours, depending on the machine or
+hardware specifications.

retel-paper/renv.lock

@@ -1236,21 +1236,16 @@
     "retel": {
       "Package": "retel",
       "Version": "0.1.0",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteUsername": "markean",
-      "RemoteRepo": "retel",
-      "RemoteRef": "HEAD",
-      "RemoteSha": "df36eeba74543a30850940129694a06dd976dd03",
-      "RemoteHost": "api.github.com",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "Matrix",
         "R",
         "checkmate",
         "matrixcalc",
         "nloptr"
       ],
-      "Hash": "6e15addb6ddddfc7c8ef20dc027a212e"
+      "Hash": "ebab6ad44ec41ef703a3f43cb73e87c2"
     },
     "rlang": {
       "Package": "rlang",