ADD-SIS for Interval-Valued Response

Install Packages:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("Icens")

install.packages("interval")

install.packages("energy")

Case Study Folder:

Folder Code Description:

File Name	Description
CaseStudyCode_Final.Rmd	The Rmd file for the case study

Folder Data Description:

File Name	Description
REAL_DATA.csv	The original text data
Words.csv	The 1043 words generated from the original text data
Words_Filter.csv	The 677 words generated from the original text data by filtering out the words whose frequencies are less than 5
WordMatrix_Filter.csv	The big design matrix (X) table consists of 0,1
SelectedWord	The several top words based on ADD-SIS associated with the English translation

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Note: since the data contain Chinese characters, so we need to encode the CSV file as UTF-8. To display these CSV files in the correct way, go to Data > From Text to launch a Text Import Wizard. Now select the file origin to pick ¡°65001: Unicode (UTF-8)¡±, this will turn the CSV files into something that is legible, then choose New Sheet to display the CSV files in the correct way.

Simulation Folder

Example1-3 Description:

File Name	Description
Code/COX_FullVersion.R	The original code to run the simulation under Cox Model setup
Code/GLM_FullVersion.R	The original code to run the simulation under Generalized Linear Model setup
Code/LM_FullVersion.R	The original code to run the simulation under Linear Model setup
Code/ResultsAnalysis.Rmd	Analyze the intermediate results and generate Table 1 in paper
Folder Intermediate	Store all the intermediate data for simulations

Example 4 Description:

File Name	Description
Code/Robustness.R	The original code to run the simulation
Code/ResultsAnalysis.Rmd	Analyze the intermediate results and generate Table 2 in paper
Folder Intermediate	Store all the intermediate data for simulations.
Code/ResultsAnalysis.Rmd	Analyze the intermediate results and generate Table 1 in paper
Folder Intermediate	Store all the intermediate data for simulations

Instructions:

The following steps give the instruction on how to reproduce the analytical results:

Step 1: Install the corresponding packages:

Step 2: Load the following R- packages with the specified versions:

Package	Version
Icens version	1.58.0
Interval version	1.1-0.1
MASS version	7.3-51.6
dplyr version	0.8.5
energy version	1.7-7
readr version	1.3.1

Step 3: Simulation Example1-3:

Use the “”Simulation/Example1-3” folder

(1) Run the “Code/COX_FullVersion.R”, “Code/GLM_ FullVersion.R” and “Code/LM_ FullVersion.R” code.
(2) We store the intermediate results for simulation in “Intermediate” folder.
(3) Use ‘Code/ResultsAnalysis.Rmd’ to generate performance evaluation for simulation.

Step 4: Simulation Exampe 4:

Use the “”Simulation/Example4” folder

(1) Run the “Code/Robustness.R”. It might take 10 hours to run this file.
(2) We store the intermediate results for simulation in “Intermediate” folder.
(3) Use ‘Code/ResultsAnalysis.Rmd to generate performance evaluation for simulation.

Step 5: Case Study Part:

Use the “”CaseStudy” folder

(1) Use ‘CaseStudy/Code/CaseStudyCode_Final.Rmd’ file to generate the results.

Step 6: Supplementary Part:

Use the ‘”SUPP” folder

(1) ‘TableS.1/TableS.1.Rmd’ reproduces the results in Table S.1.
(2) For reproducing the results TableS.2, file ‘TableS.2/Code/DistanceComparison.Rmd’ runs the simulation examples and we store the intermediate results in ‘TableS.2/Intermediate’ folder. File ‘TableS.2/Code/ResultsAnalysis.Rmd’ analyzes the intermediate results.
(3) For Table S.3, ‘TableS.3/Overlap.Rmd’ reproduces the results.
(4) For Table S.4 and TableS.5, the utilized data is in ‘TableS.4&5/Data’ folder, and ‘TableS.4&5/Code/CaseStudy-Web.Rmd’ runs the corrosponding analysis.
(5) For Table S.6-S.8, use the code within ‘TableS.6-8’ folder.