Introduction to Statistical Analysis using R Workshop

Introduction to Statistical Analysis using R Workshop


African Centre of Excellence in Population
Health & Policy Conference Room

Aminu Kano Teaching Hospital, Kano, Nigeria

March 1 – 5, 2021
 

Theme: Introduction to R programming


 

Course Overview

This five-day hands-on course is designed for physician scientists at Aminu Kano Teaching Hospital/ Bayero University, Kano, Nigeria who are interested in learning the various fundamental statistical tests that are commonly used in clinical research settings and to use the R statistical software. Course participants will learn how to develop research questions, select the most appropriate statistical test to answer those questions, and operationalize these statistical methods using R software. Participants do not need previous statistical experience to take this course as the course will cover basic concepts using illustrative examples that are grounded in clinically relevant topics and are easily understood.

Workshop Objectives

Completion of all the 5 (five) modules will empower the course participant to:

  1. understand statistical jargon used in clinical research;
  2. demonstrate improvement in course participant’s level of statistical literacy as applied to clinical research;
  3. improve the course participant’s understanding and skills in using R statistical software.

Specific Statistical Tests Covered:

  • One Sample t-test
  • Two Sample t-test
  • Paired sample t-test
  • One-way ANOVA
  • Correlation
  • Simple Linear Regression
  • Logistic Regression
  • Chi-square test
  • Fisher’s Exact test
  • McNemar’s test

The Nigerian Medical Association (NMA) will award 10 CME points to all attendees who complete this course.

  •  

    aliyu   Muktar Aliyu, MBBS, DrPH, Professor of Health Policy & Medicine, Associate Director for Research, Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA. V-BRCH Multiple Principal Investigator
         
    musa   Baba Musa, MBBS, MPH, Associate Professor of Medicine, Bayero University, Nigeria. Consultant Physician, Aminu Kano Teaching Hospital, Nigeria. V-BRCH Investigator.
         
    salihu   Hamisu M. Salihu, MBBS, PhD, Professor of Family and Community Medicine, Baylor College of Medicine, Houston, Texas, USA. V-BRCH Consultant
         
    sani   Mahmoud Sani, MBBS, PhD, Professor of Medicine and Dean of Clinical Sciences, Bayero University, Nigeria. Consultant Cardiologist, Aminu Kano Teaching Hospital, Nigeria. V-BRCH Multiple Principal Investigator
         
    fatimah ahmed   Fatimah Tsiga-Ahmed, MBBS, MSc, Assistant Professor of Community Medicine & Director, MS Public Health Program, Aminu Kano Teaching Hospital, Nigeria. V-BRCH Investigator
         
  •  

    Day

    Module

    Learning Objectives

    Day 1
    9:00am

    9:00am - 4:00pm

    Welcome Address by the Chief Medical Director, AKTN

    Module 1: Study Design

          –
     

    • Levels of evidence
    • Case-control and cross-sectional studies
    • Cohort study designs
    • Experimental study designs
    • Validity in epidemiologic studies: bias, confounding and effect modification
    • span style="font-size:11pt"> Dimensions of Data Quality Screening Tests

    Day 2

    9:00am - 4:00pm

    Module 2: Statistical Concepts

    • Basic Statistical Concepts
    • Confidence Intervals and Normal Distribution
    • Hypothesis Testing

     

    R training: Discuss R interface, Learn how to upload datasets, save programs, run libname statements

    Day 3

    9:00am - 4:00pm

    Module 3: T-tests

    • One Sample t-test
    • Two Sample t-test
    • Paired sample t-test

    R training: run all t-tests in R, interpret results, and complete end of the data t-tests class activity

    Day 4

    9:00am - 4:00pm

    Module 4: ANOVA, Correlation and Regression

    • One-way ANOVA
    • Correlation
    • Simple Linear Regression
    • Logistic Regression

    R training: run One-Way ANOVA, Correlation, and Simple Linear Regression, Logistic Regression in R and interpret results

    Day 5

    9:00am - 4:00pm

     

     

     

     

    4:00pm-4:30pm

    4:30pm

    Module 5: Chi-square, Fisher’s exact, and McNemar’s test

     

     

     

     

    Presentation of Certificates by VIGH and ACEPHAP Directors

    Group Pictures and Adjourn

     

    • Chi-square test
    • Fisher’s Exact test
    • McNemar’s test

    R training: run Chi-square test, Fisher’s Exact test, and McNemar’s test in R and interpret results.

     



    *Comprehensive assignment: At the end of the lecture, participants will receive a comprehensive list of research questions in which they will be expected to select the appropriate statistical test, operationalize the test in R, and interpret results.

  • Detailed list of topics covered in Module 1

    • Introduce basic epidemiologic study design concepts and terms
    • Discuss the various types of study designs commonly used in clinical epidemiology
    • Differentiate between bias, confounding and effect modification
    • Describe the levels of evidence assigned to studies based on their methodological quality/rigor, validity, and applicability to clinical decision-making
    • Discuss examples of clinical practice recommendations developed using levels of evidence
    • Discuss dimensions of data quality
    • Describe screening test characteristics 

    Detailed list of topics covered in Module 2

    • Introduce basic statistical concepts and terms
    • Discuss the various types of variables commonly used in statistics
    • Differentiate between selection bias and random sampling error
    • Define confidence intervals and interpret their significance and utility
    • Describe the characteristics of a normal distribution
    • Compare and relate confidence interval, standard deviation, and standard error
    • Recognize components of a hypothesis statement
    • Differentiate between the null and alternative hypothesis
    • Learn about the purpose of p-values in clinical research methods, and how to
    • interpret them
    • Describe and distinguish between type I and type II error
      • Detect when they occur and interpret them using the null hypothesis
    • Describe and identify one-tailed and two-tailed hypothesis testing

    Detailed list of topics covered in Module 3

    • Introduce one-sample t-test and recognize clinical situations in which it can be appropriately used
    • Create an R dataset and operationalize a one-sample t-test for the clinical example presented in class
    • Interpret output from a one-sample t-test
    • Introduce a two-sample t-test
    • Identify clinical situations amenable to a two-sample t-test
    • Generate a dataset and perform a two-sample t-test
    • Interpret output from a two-sample t-test
    • Introduce the paired sample t-test
    • Identify clinical situations amenable to a paired sample t-test
    • Generate a dataset and perform analysis paired sample t-test
    • Interpret output from a paired sample t-test

    Detailed list of topics covered in Module 4

    • Introduce one-way ANOVA
    • Identify clinical situations amenable to an ANOVA procedure
    • Understand terms related to ANOVA
    • Investigate a research question in which the ANOVA procedure is appropriate
    • Create dataset and perform an ANOVA statistical analysis
    • Interpret output from the ANOVA analysis
    • Identify clinical situations where the use of a correlation analysis is appropriate
    • Understand terms used in correlation analysis
    • Generate a dataset and perform correlation analysis on it
    • Interpret output from a correlation analysis
    • Identify clinical situations where the use of simple linear regression is appropriate
    • Understand terms used in simple linear regression (e.g., Sums of squares, least squares regression, R-squared, coefficients, etc.)
    • Generate a dataset and perform simple linear regression procedure on it
    • Interpret output from a simple linear regression procedure
    • Generate a dataset, perform a logistic regression procedure, and interpret the results

    Detailed list of topics covered in Module 5

    • Introduce chi-square test
    • Identify clinical situations where the use of a chi-square test is appropriate
    • Generate a dataset and perform a chi-square test
    • Interpret output from a chi-square test
    • Introduce Fisher’s exact test
    • Identify clinical situations where the use of Fisher’s exact test is appropriate
    • Generate a dataset and perform a Fisher’s exact test
    • Interpret output from a Fisher’s exact test
    • Introduce McNemar’s test
    • Identify clinical situations where the use of McNemar’s test is appropriate
    • Generate a dataset and perform a McNemar’s test
    • Interpret output from a McNemar’s test
  •  

    Adamu Halima Adamu, MBBS, FCMPaed
    Halima Adamu is a female indigen of Kano state who completed her academic training in Kano from primary school through tertiary education and obtained a MBBS in 2006 from BUK. She completed postgraduate training at AKTH and became a fellow with NPMCN in Paediatrics (FMCPaed) in 2018, with special interest in paediatric neurology. She is currently developing her career in this field under the mentorship of certified neurologists. Her training has exposed her to many courses in leadership and management, research, training, and capacity building, in addition to clinical expertise. She participates in multiple research studies with both local and international collaborators and has published and presented in conferences and has held positions in medical and non-medical associations.  
     
    Adeyemo Yewande Adeyemo, BDS, FWACS
    Yewande Adeyemo is a Lecturer and Sub-Dean (Academics) and Consultant Paediatric Dentist, Faculty of Dentistry at Bayero University, Kano and Aminu Kano Teaching Hospital, Kano State. She is contributing her quota, step by step, to improving oral health-related quality of life in the paediatric age group one smile at a time, which she feels is a strongly motivating factor.  
     
    Ahmad Jameel Ismail Ahmad, MBBS, FWACS, MBA/FWACP
    Jameel Ismail Ahmad is a resilient Cardiovascular and Thoracic Surgeon who is keen on making sure interventional cardiovascular services are available locally. Being an Assistant Professor in Surgery has given him the opportunity to teach and mentor undergraduate and postgraduate students and trainees. He believes in using technology and media to attain universal health coverage. He currently chairs a group that has developed and is soon to implement a digital health solution and is working with artists to produce a movie series on heart diseases. He believes in teamwork and altruism to achieve favorable healthcare indices in developing countries.  
     
    Ahmad Abdullahi Ahmad, MBBS, FMCPath/FWACP
    Abdullahi Ahmad is a junior faculty member at Bayero University and an Honorary Consultant Pathologist with Aminu Kano Teaching Hospital. He completed his medical degree at University of Maiduguri, and thereafter proceeded to do a residency in Anatomic Pathology. His research interests are in the field of cancer epidemiology.  
     
    Ahmed Mustapha Ahmed Yusuf, MBBS, MSc, PhD
    I am a lecturer and trained medical entomologist with expertise in biotherapy in the Department of Medical Microbiology and Parasitology, College of Health Sciences, Faculty of Clinical Sciences, Bayero University, Kano and a Honourary Consultant overseeing the Maggot Debridement Therapy Unit in the Department of Microbiology Aminu Kano Teaching Hospital, Kano. I am a young researcher with a medical background (MBBS, MSc, PhD), and I have cumulative experience in the academics, laboratory, and biotherapy. I have been teaching students at both undergraduate and postgraduate levels, and I also supervise these students in the handling and analysis of data.

     
    ali Usman Ali, MBBS
    I am a native of Durbunde town, Takai LGA, of Kano State. I graduated with a Bachelor of Medicine, Bachelor of Surgery degree from Bayero University Kano in 2010. I am currently a hospital consultant in the Department of Chemical Pathology at Aminu Kano Teaching Hospital.  

    bello-manga
    Halima Bello-Manga, MBBS, MPH
    I am a board certified Hematologist and Senior Lecturer working at Barau Dikko Teaching Hospital/Kaduna State University. I have devoted my clinical and research career to the care of children and adults with hematologic conditions, with emphasis on sickle cell disease (SCD). I am an alumni of the Vanderbilt Institute of Research Development and Ethics (2017 and 2019) and the American Society of Hematology’s Clinical research Institute (2019). I am currently working my NIH/FIC/NINDS-funded K43 award on scaling up stroke prevention in children with sickle cell anemia in a community hospital in Kaduna State using implementation science.  
     
    Ibrahim Hafsat Ibrahim, MBBS
    Hafsat Ibrahim is a young paediatrician with a strong back ground in general paediatrics and infectious diseases, practicing in the most populous country in sub-Saharan Africa, where communicable and non-communicable diseases abound. Infectious diseases account for up to 80% of all admissions, driving her zeal and enthusiasm for knowledge and research in these areas to build and strengthen her passion for improving care and increasing the knowledge base. She is also currently involved in research in these areas, with multiple publications.  
     
    Ibrahim Zainab Ibrahim, MBBS, FWACP
    Zainab Ibrahim is a lecturer and consultant chemical pathologist at Kano, Nigeria. Nigeria is one of the world’s most HIV-burdened countries, being home to the second largest population of persons living with the virus. Realizing this huge public health problem kindled my interest in HIV research, and I have since been involved in evaluation of endocrine/metabolic disorders in HIV patients. I specialize in development, validation, quality assessment of biochemical assays, and interpretative commenting of routine and specialized investigations, including dynamic function tests. For the duration of her career, she has mentored a number of medical students and resident doctors.  
     
    Idris Ibrahim Idris, MBBS, MPH
    I am a board-certified hematologist with Aminu Kano Teaching Hospital, as well as an alumnus of VECD-Fogarty Global Health program, the American Society of Hematology Clinical Research Training Institute, and the Vanderbilt Institute for Research Development and Ethics (VIRDE). I have a Master of Public Health in Epidemiology. My research interests cover some of the devastating complications of sickle cell disease (SCD), such as reproductive and sexual health challenges of male patients, neurological injuries, and SCD as an accelerated aging syndrome. Over the past three years, I have focused on understanding the clinical epidemiology and treatment strategies for recurrent ischemic priapism in men with SCD.  
     
    Ismail Anas Ismail, MBBS, FMCR
    Anas Ismail graduated from Bayero University Kano (BUK) in 2004, completed residency training in Radiology and a fellowship of the National Postgraduate Medical College of Nigeria (FMCR) in 2011, and completed additional training in vascular radiology and image-guided interventions at Medical University of Graz, Austria in 2012. He joined the BUK department of Radiology in 2012 and is currently an Associate Professor. Since joining BUK, and as an honorary consultant at Aminu Kano Teaching Hospital, he has been active in teaching undergraduate and post-graduate students in the aspects of vascular and image-guided interventions. He has passion for research in vascular ultrasound and non-communicable diseases (especially sickle cell disease, diabetes, arterial disease and cancers) and has published a number of collaborative scientific papers.  
     
    kibir Halima Kabir, MBBS
    Halima Kabir graduated from Ahmadu Bello University (MBBS, 2002) and completed a fellowship in paediatrics by The National Postgraduate Medical College of Nigeria. She currently teaches undergraduates, postgraduates and Paediatric residents. Her research interests include emergency and critical paediatrics and paediatric nutrition, including reducing morbidity and mortality among critically ill children presenting to emergency units in resource-poor settings and improving knowledge and skills of health care providers in these units, particularly in triage and airway management. Over the last five years, she has helped lead a successful training workshop in collaboration with Paediatric Universal Life Saving Effort (PULSE), New York, USA to train health care workers from resource-poor settings on the immediate management of critically ill children, particularly those with sepsis and septic shock. She is currently a co-investigator for the Sepsis Incidence, Determinants and Outcome in Kano (SIDOK) study. In addition to her academic and research responsibilities, she heads the AKTH Emergency Paediatric Unit, a position she has held since 2014.
     
    Kana Shehu Kana, MBBS, FWACP
    Shehu Abubakar Kana is currently a consultant cardiologist at Aminu Kano Teaching Hospital, Kano, Nigeria. His goals and aspirations are to be a world-class research fellow, be a a good leader worthy of emulation by younger colleagues, and to impact positively on the lives of my patients, around whom my world revolves. His most relevant achievements are the award of fellowship of the West African College of Physicians and having participated in some international trials and registries. He has special interest in conducting clinical research and training younger colleagues.  
     
    Nalado Aishatu Nalado, PhD
    Aishatu Nalado is a consultant physician and the first trained female nephrologist in Kano, Nigeria. Her areas of research interest are in prevalent disease conditions associated with end stage renal disease and developing effective options of managing renal disease in the tropics, including kidney transplant and dialysis. She provides clinical care at the renal disease clinic at Aminu Kano Teaching Hospital, where she teaches medical residents and provides clinical leadership and technical guidance in the management of patients with renal disease.  
     
    Ramalan Mansur Ramalan, MBBS, MSc, FMCP
    Mansur Ramalan is a Consultant Physician/Endocrinologist at the Aminu Kano Teaching Hospital, Kano, Nigeria. He is a fellow of the National Postgraduate Medical College of Nigeria in Internal Medicine with subspecialty in endocrinology, diabetes and metabolism. He is currently undertaking a VECD fellowship focusing integration of care for adrenal insufficiency in patients with HIV infection under the mentorship of Muktar Aliyu, MBBS, DrPH, Zubairu Iliyasu, MBBS, MPH, PhD and Ibrahim Gezawa MD. Dr. Ramalan's research work has been on the epidemiology of diabetes mellitus and endocrine disorders in resource poor settings.  
     
    Sabo Umar Abba Sabo, MBBS, MSc, MPH
    I am a child neurologist and a lecturer at the department of Paediatrics, at Aminu Kano Teaching Hospital (AKTH) and Bayero University Kano (BUK). I graduated from BUK and did my paediatric residency at AKTH. I obtained an MPH from Manchester Metropolitan University. I went University of Witwatersrand, Johannesburg for my MSc Medicine in Paediatrics. While in Johannesburg I did my fellowship in Paediatric neurology at Charlotte Maxeke and Chris Hani Baragwanath academic hospitals. I completed my Fogarty mentored Research fellowship in 2019. I am a VIRDE alumnus. My research interests are childhood epilepsy, child neurology and global health.  
     
    Suleiman Abdullahi Kabir Suleiman, MBBS, MHEcon
    Abdullahi Kabir Suleiman is a Family Physician working with the Department of Family Medicine at Aminu Kano Teaching Hospital, Kano, Nigeria. He holds an MBBS and a Masters degree in Health Economics from Bayero University, Kano. He is a Fellow of the National Postgraduate College of Nigeria in Family Medicine. He hopes to become a foremost physician and researcher in his field. He was a Kano site investigator for the Comparison of Dual Therapies for Lowering Blood Pressure in Black Africans Study.  
     
    sulaiman Ibrahim Suleiman, MBBS, FWACS
    I am currently employed with Bayero University Kano as a Senior Lecturer and with Aminu Kano Teaching Hospital as a Consultant General Surgeon (since June 2015). I am also a laparoscopic surgeon and gastrointestinal endoscopist. I graduated from Ahmadu Bello University Zaria in 2002, served a 1 year internship with Ahmadu Bello University Teaching Hospital, and proceeded to National Service at Lobia Cottage hospital, Bayesla State. I did my residency in General Surgery at the University of Maiduguri Teaching Hospital from 2006 to 2012 and worked as a Consultant Surgeon at Federal Medical Centre Nguru Yobe State from 2012 to 2015.  
     
    Tijjani Hasiya Tijjani Ismael, MBBS
    Hasiya Tijjani Ismail received her MBBS in 2006 from Bayero University Kano and completed a fellowship in Internal Medicine and Neurology (FWACP) and a Masters in Health Economics in 2019. She is the first student from the Bayero University MPH program to be selected as a V-BRCH trainee. She has completed multiple training workshops and courses in Nigeria and in international settings.  
     
    Usman Fatima Usman, MBBS, FWACP, MSc
    Fatima Usman is a neonatologist and lecturer at Aminu Kano Teaching Hospital/Bayero University Kano, Nigeria. She has a West African College of Physician’s fellowship (2016), a postgraduate qualification in pediatric nutrition with Boston University (2017) and master’s in advanced pediatrics from King’s College London (2019). She received numerous awards of excellence throughout her training and career.She is the MSc thematic lead in pediatrics for Maternal Child Health and Population Policy, a trainer for Nigerian Society of Neonatal Medicine and a member of the International Academy of Perinatal Medicine’s young scientists.She loves teaching and research, with interest in preventable newborn neurologic disorders.  
     
    Yusuf Aminu Abba Yusuf, MBBS, MSc, FMCPath
    Dr. Yusuf is a board-certified Hematologist and a Consultant at the Aminu Kano Teaching Hospital, Kano, Nigeria. He also holds master of science degree in Molecular Medicine from Cranfield University, UK and is a faculty member at Bayero University Kano, Nigeria. Dr. Yusuf is also a VECD-Fogarty alumnus (2018/2019 cohort) and a Fogary-IeDEA West Africa trainee (2019/2020 cohort). His main area of research interest is in genomics of non-communicable diseases prevalent in sub-Saharan Africa, including HIV-associated kidney disease and sickle cell disease. His main career aspiration is to become a leading clinician-scientist in Genomics of Non-communicable Diseases in Africa.