Chapter 1 Preface

1.1 Book overview

This book includes a series of hands-on practical introductory guides to analysis of bio-medical data using R. It will provide learners with applied statistical knowledge, practical data analysis skill, basic statistical programming skill in R. The knowledge and skills from this series are also useful and applicable for those who use other statistical software.

1.2 About this Book

Data analysis is an essential part of bio-medical research. R is a free open source statistical analysis software which has been extensively used for analysis of bio-medical data. Being able to use R for data analysis is a handy skill for bio-medical researchers. During COVID-19 restriction in 2020, Nhan Thi Ho MD, PhD from Vinmec Healthcare System, Vietnam developed and together with other lecturers: Hien Nguyen PhD from Penn State University US, Phuong Thi Minh Chu Msc from Vietnam Academy of Sciences, Thuy Tien Bui from A*STAR Singapore delivered an online course organized by Vinmec Healthcare System: “Bio-Medical Data Analysis with R: Intro Series”. This course included a series of hands-on practical lectures conducted in English. It attracted hundreds of participants from Vietnam and other countries around the world and was highly evaluated by course participants.
This book is an edited collection of the lectures of the aforementioned course with the aim to sustain and deliver the course values to larger number of students and researchers worldwide.

1.3 Table of contents

Chapter Title Author
Chapter 1 Preface Nhan Thi Ho MD, PhD
Chapter 2 Introduction to R Nhan Thi Ho MD, PhD
Chapter 3 Data visualization with R Tien Thuy Bui Msc, Nhan Thi Ho MD, PhD
Chapter 4 R Programming Tien Thuy Bui Msc, Nhan Thi Ho MD, PhD
Chapter 5 Basic statistics with R Hien Nguyen PhD
Chapter 6 Linear regression with R Nhan Thi Ho MD, PhD
Chapter 7 Logistic regression with R Phuong Thi Minh Chu MScs & Nhan Thi Ho MD, PhD
Chapter 8 Survival data analysis with R Nhan Thi Ho MD, PhD
Chapter 9 Longitudinal data analysis with R Nhan Thi Ho MD, PhD
Chapter 10 Special topic: Clinical trial data analysis with R Nhan Thi Ho MD, PhD
Chapter 11 Special topic: Analysis and Meta-analysis of Microbiome Data with “metamicrobiomeR” package Nhan Thi Ho MD, PhD

1.4 About authors

Editor and primary author: Nhan Thi Ho MD, PhD

Ho Thi Nhan, MD, PhD is Head of Biomedical Data Sciences & Research Methodology at Vinmec Healthcare System, Hanoi, Vietnam. Beforehand, she was a Pediatrician trained by Hochiminh City University of Medical Sciences and Paris V University, France before getting her PhD degree in (quantitative) Epidemiology at Michigan State University, US. Since then, she was a Researcher & Biostatistician at Oxford University Clinical Research Unit, Visiting Scholar in mathematical modeling at Princeton University, US and Fellow in Epidemiology at Columbia University Medical Center (CUMC), US before joining Vinmec. She is the author and creator of the R package “metamicrobiomeR” for the analysis and meta-analysis of microbiome data. She is experienced in Biostatistics for various types of data and is experienced with various statistical software such as R, SAS, and Stata.

Nguyen Hien, PhD is an Assistant Professor in Computer Science & Mathematics at Pennsylvania State University at Harrisburg, US. He got his Bachelor Degree in Computer Engineering from Ho Chi Minh City University of Technology, Vietnam, his Master Degree in Software Engineering from University of Wisconsin – La Crosse, US and his PhD Degree in Computer Science from New Mexico State University, US. He is skilled with statistics, bioinformatics, machine learning and is experienced with various programming languages.

Chu Thi Minh Phuong, Msc is a Data Scientist at Institute of Biotechnology, Vietnam Academy of Science and Technology, Vietnam. She got her Bachelor Degree in Biology from Belgorod State National Research University, Russia; and two Master Degrees: Comparative Vertebrate Morphology and Genomics Informatics, Mathematics for Health and Environment in Europe. She is skilled in biostatistics and bioinformatics.

Bui Thuy Tien, Msc is a software engineer. Beforehand, she got her Bachelor in Bioengineering from Nanyang Technological University, Singapore and was a researcher at Institute of Food and Biotechnology Innovation, and Institute of Bioengineering and Nanotechnology - A*STAR, Singapore. She is experienced with various programming languages.

1.5 Acknowledgements

We would like to thank Vinmec Healthcare System for their support during the organization of the course “Bio-Medical Data Analysis with R: Intro Series” and during the preparation and publication of this book.