SACEMA

Introduction to R: Management, Exploration and Communication
2022-08-15 09:00 - 2022-08-19 17:00 (Africa/Johannesburg) | STIAS, Marais Rd, Mostertsdrift, Stellenbosch, Western Cape, 7600, South Africa
Applications are closed. Enquiries may be directed to the SACEMA Training Coordinator, Faikah Bruce faikah@sun.ac.za
Applications for the short course on Introduction to R: Management, Exploration and Communication of Data are closed.
Course fee
The course fee is R9 495,00 for early bird registration (by 15 July 2022) and R10 550,00 for late registration.
Please note that full payment must be processed prior to start of the course.
Enquiries may be directed to the SACEMA Training Coordinator, Faikah Bruce (faikah@sun.ac.za) or the SACEMA Deputy Director: Operations, Lynnemore Scheepers (scheepersl@sun.ac.za).
Course Overview
R is an open-source, statistical software platform that is growing in popularity due to its rapidly expanding amount of libraries containing cutting-edge statistical functions, as well as the user-friendly, built-in communication tools in RStudio. Course participants will not only be introduced to the basics of programming in R, but they will also learn how import and clean data in addition to visualising and reporting results. Specific topics that will be covered include: importing data; reshaping/tidying data; merging/joining datasets; handling dates, transforming numeric and categorical variables and summarizing data with plots and tables.
Course Outline
Participants will learn the basics of:

Base R programming and coding style
Data importation into and exportation out of RStudio
Data cleaning/tidying into a format suitable for analysis (using tidyverse packages like dplyr and tidyr)
Data analysis using basic descriptive statistics
Data exploration and visualization using ggplot 2 and a combination of R packages for plotting and summarising data and a sneak peek into creating reproducible, dynamic reports using RMarkdown

The course is suitable for graduate students or professionals who are familiar with statistical analysis and have managed or interacted with datasets using other software platforms.
Applications are closed.
Intro to R Course 2022
Presenters
Dr James Azam
Dr James Azam is currently a Junior Researcher at SACEMA. He recently completed a PhD in Applied Mathematics from Stellenbosch University (through SACEMA) with a project that involved a systematic review of outbreak response models of human vaccine-preventable diseases and foot-and-mouth disease, and modelling analyses of outbreak response strategies for responding to a measles outbreak using outside cold chain strategies and a hypothetical disease that faces the risk of variant emergence. His PhD project was supervised by Prof. Juliet Pulliam (SACEMA director) and Prof. Matt Ferrari (Penn State University). James holds a master’s degree in Mathematics from Stellenbosch University (through SACEMA), a Structured Master’s degree from the African Institute for Mathematical Sciences in Senegal, and a bachelor’s degree in Actuarial Science from the Kwame Nkrumah University of Science and Technology (KNUST) in Ghana. He has tutored courses at SACEMA, and the Mathematics Departments of Stellenbosch University and KNUST. He has research interests in outbreak response modelling and analytics, health data science/analytics, science policy and communication. As a Junior Researcher, he will contribute to an ongoing project involving the development of a routine surveillance pipeline for monitoring and flagging changes in COVID-19 severity in South Africa, participating in SACEMA’s Modelling and Analytics Response Team (SMART), contributing to some short courses and training activities, and publishing previous work from his PhD.
Dr. Larisse Bolton
Dr Larisse Bolton holds a BSc in Chemistry and a PhD in Applied Mathematics from the University of the Free State in Bloemfontein, South Africa. Her postgraduate research focused on the application of mathematical modelling in oncology using different approaches – model adaptation and model construction. She was a postdoctoral research fellow at the DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA) in Stellenbosch from 2018-2021 and now holds the position of Researcher at SACEMA. Her current research focuses on blood systems analysis. She has been assessing blood product usage and demand in South Africa and is developing a predictive model for red blood cell product usage. The model will be used to investigate various scenarios of health system structuring.

Seminar, Dr David Niyukuri
2022-08-12 15:00 - 16:00 | Online (MS Teams)
Malaria diagnosis in Burundi: use of RDTs for Plasmodium falciparum infections in a high transmission setting
Speaker: Dr David Niyukuri

Seminar, Reshma Kassanjee
2022-08-05 15:00 - 16:00 | Online (MS Teams)
Addressing COVID-19 knowledge gaps using observational individual-level data on the Western Cape population
Speaker: Dr Reshma Kassanjee

Seminar, Glyn Vale
2022-06-24 15:00 - 16:00 | Online (MS Teams)
Biological aspects of modelling the ecology, behaviour and control of disease vectors.
Speaker: Glyn Vale

SMART Retreat
2022-05-18 09:00 - 2022-05-19 16:00 | STIAS, Marais Rd, Mostertsdrift, Stellenbosch, Western Cape, 7600, South Africa
The SMART team will apply lessons from the SMART program to their own research projects.

Seminar, Sam Abbott
2022-05-06 15:00 - 16:00 | Online (MS Teams)
Hierarchical nowcasting of right censored epidemiological counts with an application to COVID-19 hospitalisations in Germany
Speaker: Sam Abbott

Seminar, Jonathan Dushoff
2022-04-22 15:00 - 16:00 | Online (MS Teams)
Transmission intervals and COVID control
Speaker: Jonathan Dushoff

Staff Meeting
2022-04-05 09:00 - 10:00 | STIAS, Marais Rd, Mostertsdrift, Stellenbosch, Western Cape, 7600, South Africa
SACEMA Staff Meeting

Introduction to Epidemiology and Research
2022-04-05 06:00 - 2022-06-30 18:00 | Online (MS Teams)
Applications are now closed. Enquiries can be directed to SACEMA Training Coordinator, Faikah Bruce faikah@sun.ac.za.
Speaker: Dr. Jo Barnes

Seminar, Abigail de Villiers
2022-03-18 15:00 - 16:00 | Online (MS Teams)
Spatially-targeted digital chest radiography-based screening to reduce tuberculosis in high-burden settings: simulation of an adaptive decision-making approach and cost-effectiveness analysis
Speaker: Abigail de Villiers

SACEMA Team Building
2022-03-11 09:00 - 15:00 | SACEMA, 19 Jonkershoek Road, Stellenbosch, Western Cape, 7800, South Africa
SACEMA Team Building tour to Cape Point

Seminar, James Azam
2022-01-25 15:30 - 16:30 | Online (MS Teams)
Modelling outbreak response intervention strategies for decision-making
Speaker: James Azam

DAIDD 2021
2021-12-12 09:00 - 2021-12-18 18:00 | Online (MS Teams)
Applications are now closed. Enquiries can be directed to SACEMA Training Coordinator, Faikah Bruce faikah@sun.ac.za
Clinic on Dynamical Approaches to Infectious Disease Data: 12-18 December 2021
Application Deadline: 4 November 2021
The International Clinics on Infectious Disease Dynamics and Data (ICI3D) Program invites applications for the 10th annual Clinic on Dynamical Approaches to Infectious Disease Data (DAIDD), which will be held 12-18 December 2021. The Clinic will be held virtually via Microsoft Teams.
The Clinic is open to public health professionals (including researchers, students, and clinicians) and population biologists studying infectious diseases. Participants should have limited (or no) prior modelling experience, and should want to learn about dynamic models as tools to inform data collection, analysis, and interpretation. The Clinic is particularly appropriate for those in the process of developing new research projects related to infectious disease epidemiology.
The course fee is ZAR 3,000 or US $215. A small number of scholarships are available for Clinic . All participants must have access to high-speed internet for the duration of the Clinic.
For more information, please see the full Request for Applications attached (pdf document).
The deadline for receipt of applications is 4 November 2021 at 23:59 SAST (17:59 Eastern).
Incomplete applications will not be considered.
Apply

End of year function
2021-12-10 12:45 - 17:00 | Warwick Wine Estate, Warwick Wine Estate, R44, Stellenbosch, Western Cape, 7607, South Africa

SACEMA Year End Function
2021-12-10 12:45 - 17:00 | Warwick Wine Estate, Warwick Wine Estate, R44, Stellenbosch, Western Cape, 7607, South Africa

Staff Meeting
2021-12-10 09:30 - 11:30 | STIAS, Marais Rd, Mostertsdrift, Stellenbosch, Western Cape, 7600, South Africa

Seminar, Dr. Keletso Makofane
2021-11-26 15:00 - 16:00 | Online (MS Teams)
Networked Resources, Causal Inference, and Health: Evidence from population-based studies in South Africa
Speaker: Dr. Keletso Makofane

Seminar, Sarah Davies
2021-11-12 15:00 - 16:00 | Online (MS Teams)
Opening the floor for discussion: Science and policy-making in South Africa
Speaker: Sarah Davies

Steering Committee Meeting
2021-11-05 10:00 - 12:30 | Admin B, Rectorate Room

Defence, Dylan Geldenhuys
2021-10-27 11:00 - 12:00 | Online (MS Teams)
A Deep Learning Approach to Landmark Detection in Tsetse Fly Wing Images
Speaker: Dylan Geldenhuys

Research Days 2021
2021-09-20 09:00 - 2021-09-22 17:00 | Online (MS Teams)
SACEMA’s annual Research Days meeting will take place online 20-22 September 2021.

SACEMA 2021 Biomath Honours Roadshow
2021-08-17 15:00 - 16:00 | SACEMA, 19 Jonkershoek Road, Stellenbosch, Western Cape, 7800, South Africa
2021 Biomath Honours Roadshow: SACEMA Funding Opportunity
See Details (pdf)

Seminar, Dr Eleanor Gouws
2021-07-23 15:00 - 16:00 | Online (MS Teams)
The role of cities in ending the AIDS epidemic
Speaker: Eleanor Gouws

Seminar, Dr. Muhammad Osman
2021-06-18 15:00 - 16:00 | Online (MS Teams)
TB associated mortality in South Africa: Longitudinal trends and the impact of health system interventions
Speaker: Dr.Muhammad Osman

Seminar, Dr. Reza Yaesoubi
2021-06-11 15:00 - 16:00 | Online (MS Teams)
Adaptive Policies to Balance Health Benefits and Economic Costs of Physical Distancing Interventions
during COVID19
Speaker: Dr. Reza Yaesoubi

SSJC
2021-04-21 15:00 - 16:00 | SACEMA, 19 Jonkershoek Road, Stellenbosch, Western Cape, 7800, South Africa
SACEMA student journal club 21/04/21

MSc Expression of interest presentation
2021-04-16 09:00 - 10:00 | SACEMA, 19 Jonkershoek Road, Stellenbosch, Western Cape, 7800, South Africa
Presentation – Expression of Interest SACEMA Masters Degree Programme 2022
See details (pdf)

SSJC
2021-04-14 15:00 - 16:00 | SACEMA, 19 Jonkershoek Road, Stellenbosch, Western Cape, 7800, South Africa
SACEMA student journal club 14/04/21

SSJC
2021-04-07 15:00 - 16:00 | SACEMA, 19 Jonkershoek Road, Stellenbosch, Western Cape, 7800, South Africa
SACEMA student journal club 07/04/21

SSJC
2021-03-31 15:00 - 16:00 | SACEMA, 19 Jonkershoek Road, Stellenbosch, Western Cape, 7800, South Africa
SACEMA student journal club 31/03/21
