jekyll-theme-ici3d 0.1.0

data/_data/team/sempa.yml

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+---
+name: Joseph Sempa, PhD
+type: i3d_toNA
+role: I3D Research Exchange Scholar
+home: Uganda
+former: Researcher at Infectious Diseases Institute, Uganda (IDI)
+position: SACEMA Postdoctoral Fellow
+affiliation: South African Centre for Epidemiological Modelling and Analysis
+img: scholars/sempa.jpg
+year: 2014
+host: University of Texas at Austin
+mentor: Dr. Steve Bellan
+project: evaluating cumulative viral load as a predictor of opportunistic infection and mortality in HIV patients
+outputs:
+  - title: Reevaluating cumulative HIV-1 viral load as a prognostic predictor - predicting opportunistic infection incidence and mortality in a Ugandan cohort
+    authors: <em>Sempa, JB</em>, <b>J Dushoff</b>, MJ Daniels, M Nieuwoudt, and <b>SE Bellan</b>
+    link: http://dx.doi.org/10.1093/aje/kwv303
+    journal: American Journal of Epidemiology
+    year: 2016
+degrees:
+  - degree: PhD
+    discipline: Clinical epidemiology
+    institution: Stellenbosch University
+    year: 2017
+papers:
+  - title: Reevaluating cumulative HIV-1 viral load as a prognostic predictor - predicting opportunistic infection incidence and mortality in a Ugandan cohort
+    authors: <em>Sempa, JB</em>, <b>J Dushoff</b>, MJ Daniels, M Nieuwoudt, and <b>SE Bellan</b>
+    link: http://dx.doi.org/10.1093/aje/kwv303
+    journal: American Journal of Epidemiology
+    year: 2016
+bio: Joseph is currently a postdoctoral fellow at SACEMA, working on the repurposing of HIV diagnostic assays for HIV management and is supervised by Prof Alex Welte. Previously, he was funded by SACEMA to do a PhD in Epidemiology, focusing on the effects of longitudinal HIV viral load on treatment outcomes in people on ART in sub-Saharan Africa, under the supervision of Prof Martin Nieuwoudt. He attended MMED in 2013 after which he received an I3D scholarship under the supervision of Prof Steve Bellan. Joseph is interested in the analysis and interpretation of dynamic range of HIV diagnostic assays, for post-diagnosis patient management.
+---

data/_data/team/sikhondze.yml

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+---
+name: Welile Sikhondze
+type: i3d_toNA
+role: I3D Research Exchange Scholar
+home: Swaziland
+former: PhD student at University of Cape Town
+position: Clinician Scientist
+affiliation: ‎National TB Control Program (NTCP), Ministry of Health, Swaziland
+img: transmission.png
+year: 2015
+host: University of California – San Francisco (UCSF)
+mentor: Prof. Travis Porco
+project: modeling the impact of novel diagnostic methods on TB incidence
+---

data/_data/team/template.yml

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+---
+name:
+type: director/core/workshop/former/founding/inactive
+role:
+involvement:
+position:
+affiliation:
+img:
+summary:
+github:
+orcid:
+linkedin:
+gscholar:
+twitter:
+impactstory:
+website:
+cv:
+---

data/_data/team/ujeneza.yml

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+---
+name: Eva Ujeneza, MSc
+type: inactive
+role: Faculty Member, DAIDD 2016, MMED 2018
+involvement: Faculty Member, MMED and DAIDD clinics
+position: PhD candidate, Stellenbosch University and
+affiliation: South African Centre for Epidemiological Modelling and Analysis
+img: team/ujeneza.jpg
+summary: Eva is a PhD candidate in the Department of Mathematics at Stellenbosch University. She was an MMED participant in 2014, served as an MMED mentor in 2015-2016, and joined the Workshop Faculty in 2016.
+github: EvaLiliane
+orcid:
+linkedin:
+gscholar: 5P1vkeMAAAAJ
+twitter: EvaUje
+impactstory:
+website:
+cv:
+degrees:
+  - degree: MSc
+    discipline: Environmental and Geographical Sciences
+    institution: University of Cape Town
+    year: 2014
+  - degree: Postgraduate Diploma
+    discipline: Mathematical Sciences
+    institution: African Institute for Mathematical Sciences
+    year: 2011
+  - degree: BSc
+    discipline: Applied Mathematics
+    institution: National University of Rwanda
+    year: 2009
+bio: Eva completed an undergraduate (Honours) degree in Applied Mathematics, at the National University of Rwanda. She then attended the African Institute for Mathematical Sciences (AIMS) in South Africa and obtained a postgraduate diploma in Mathematical Sciences. In June 2014, she obtained a Master of Science in Environmental and Geographical Sciences (Climate Modeling) from the University of Cape Town, after which she joined the South African Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA) as a PhD student. Eva is registered in the Department of Mathematics at Stellenbosch University, and her research focuses on how to use mathematical models to describe the reconstitution of the immune system in HIV-infected patients that are on highly active antiretroviral therapy. She was an MMED participant in 2014, served as an MMED mentor in 2015-2016, and joined the Workshop Faculty in 2016.
+papers:
+  - title: Impact of Age and Sex on CD4+ Cell Count Trajectories following Treatment Initiation - An Analysis of the Tanzanian HIV Treatment Database
+    authors: Means, Risher, <b>Ujeneza</b>, I Maposa, J Nondi, <b>Bellan</b>
+    link: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0164148
+    journal: PLOS ONE
+    year: 2016
+---

data/_data/team/vanschalkwyk.yml

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+---
+name: Cari van Schalkwyk, PhD
+type: workshop
+role: Faculty Member, DAIDD 2016-2019, MMED 2017, 2019, 2021
+involvement: Faculty Member, MMED and DAIDD clinics
+position: Senior Researcher
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, South Africa
+img: team/vanschalkwyk.jpg
+summary: Cari holds a PhD in Epidemiology and Biostatistics from the University of Cape Town and is a Senior Researcher at SACEMA. She was an MMED participant in 2012 and a DAIDD participant in 2013. Cari served as an MMED mentor in 2014 and 2016 and joined the Workshop Faculty in 2016.
+github: carivs
+orcid: 0000-0001-5154-1390
+linkedin: cari-van-schalkwyk-b618b851
+gscholar: WLoOeH4AAAAJ
+twitter:
+impactstory:
+website:
+cv:
+degrees:
+  - degree: PhD 
+    discipline: Epidemiology and Biostatistics
+    institution: University of Cape Town
+    year: 2021
+  - degree: MComm
+    discipline: Mathematical Statistics
+    institution: University of Stellenbosch
+    year: 2009
+  - degree: BComm
+    discipline: Actuarial Science
+    institution: University of Stellenbosch
+    year: 2006
+bio: Cari holds a PhD in Epidemiology and Biostatistics from the University of Cape Town and is a Senior Researcher at SACEMA. She was an MMED participant in 2012 and a DAIDD participant in 2013. Cari served as an MMED mentor in 2014 and 2016 and joined the Workshop Faculty in 2016. Cari became involved with SACEMA through a Masters project relating to HIV incidence estimation. In recent years her research has focused on the epidemiology of HIV, human papillomavirus (HPV), the synergies between these two viruses, the progression of HPV to cervical cancer and the impact of prevention of these diseases in South Africa. She has also done work on other infections of national priority in South Africa, such as COVID and TB.
+---

data/_data/team/welte.yml

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+---
+name: Alex Welte, PhD
+type: founding
+role: Faculty Member, MMED and DAIDD clinics
+involvement: Faculty Member, MMED and DAIDD clinics
+position: Research Professor
+affiliation: South African Centre for Epidemiological Modelling and Analysis<br>Stellenbosch University, Stellenbosch, Western Cape, South Africa
+img: team/welte.jpg
+summary: Alex is a Research Professor at the South African Centre for Epidemiological Modelling and Analysis (SACEMA) and Stellenbosch University. He served as the Director of SACEMA from 2010-2016 and the ICI3D Program Director for Africa from 2012-2016. Alex has been a member of the ICI3D Faculty since the program started in 2012.
+github: alexwelte
+orcid:
+linkedin:
+gscholar:
+twitter:
+impactstory:
+website:
+cv:
+---

data/_data/team/williams.yml

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+---
+name: Brian Williams, PhD
+type: founding
+role: Faculty Member, MMED and DAIDD clinics
+involvement:
+position: Research Fellow
+affiliation: South African Centre for Epidemiological Modelling and Analysis
+img: team/williams.jpg
+summary: Brian is a Visiting Senior Research Fellow at the South African Centre for Epidemiological Modelling and Analysis (SACEMA) and retired from the TB program at the World Health Organization (WHO). He has been on the ICI3D Core Faculty since the program started in 2012.
+github: BrianGerardWilliams
+papers:
+  - title: Progress and prospects for the control of HIV and tuberculosis in South Africa - a dynamical modelling study
+    authors: <b>Williams</b>, Gupta, Wollmers, Granich
+    link: http://dx.doi.org/10.1016/S2468-2667(17)30066-X
+    journal: The Lancet Public Health
+    year: 2017
+  - title: Epidemiological trends for HIV in southern Africa - implications for reaching the elimination targets
+    authors: <b>Williams</b>, Gouws, Somse, Mmelesi, Lwamba, Chikoko, Fazito, Turay, Kiwango, Chikukwa, Damisoni, Gboun
+    link: https://www.dropbox.com/s/jrlui80bg3ij0bi/CHAR%202015%20Williams.pdf?dl=0
+    journal: Current HIV/AIDS Research
+    year: 2015
+  - title: Universal voluntary HIV testing with immediate antiretroviral therapy as a strategy for elimination of HIV transmission - a mathematical model
+    authors: Granich, Gilks, Dye, de Cock, <b>Williams</b>
+    link: http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(08)61697-9/fulltext
+    journal: Epidemics
+    year: 2017
+bio: Brian retired from the TB program in the World Health Organization (WHO). Having originally studied Physics, first at the University of Natal and then at Cambridge University, he has carried out research in solid-state physics, ecology, and epidemiology. Before joining the WHO in 2001 he was the Director of the Epidemiological Research Unit in Johannesburg where he led research into occupational diseases of mine-workers, especially TB and silicosis. In 1994, as the epidemic of HIV/AIDS became apparent in South Africa, he set up the Mothusimpilo Project in Carletonville, South Africa, the biggest gold-mining complex in the world. There he worked with mine-workers, sex-workers, and adolescents to understand and to find ways to manage the epidemic of HIV. More recently, he has been closely involved with developing and promoting the use of treatment-as-prevention to stop the epidemic of HIV. He conceived the idea of a center for the application of mathematics to biological systems in South Africa,  which led to the founding of SACEMA in 2006. Dr. Williams has contributed to the MMED clinics and precursor programs since 2009, inspiring participants to tackle the challenge of learning to do meaningful modeling that will have real-world public health impacts.
+---

data/_data/team/ying.yml

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+---
+name: Roger Ying
+type: i3d_toAfrica
+role: I3D Research Exchange Scholar
+home: USA
+former: Medical student at Cornell University
+position: Medical student
+affiliation: Cornell University
+img: scholars/ying.jpg
+year: 2015
+host: South African Centre for Epidemiological Modelling and Analysis
+mentor: Dr. Brian Williams
+project: developing improved modeling tools for use by public health officials to inform decision-making for HIV-related policies
+outputs:
+  - title: CD4 cell count - Declining value for antiretroviral therapy eligibility
+    authors: <em>Ying, R</em>, RM Granich, S Gupta, and <b>BG Williams</b>
+    link: http://cid.oxfordjournals.org/content/early/2016/01/28/cid.civ1224.full
+    journal: Clinical Infectious Diseases
+    year: 2016
+bio: Roger received his Bachelors of Science degree in Bioengineering from the University of Washington in 2012. He worked for two years with Dr. Ruanne Barnabas at the University of Washington on modeling the cost-effectiveness of pre-exposure prophylaxis for HIV prevention in Uganda and community-based HIV testing and counseling in South Africa. He first became involved with the ICI3D program in 2013 at the MMED workshop, and then as an I3D exchange scholar in 2015. He also spent one year at the UNAIDS in Geneva working with Drs. Reuben Granich and Brian Williams on antiretroviral treatment guideline policy. Roger is now a fourth year medical student at Weill Cornell Medical College in New York City.
+---

data/_includes/MedPH/assignments.md

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+<div markdown="1">
+
+### Major Assignments
+
+There will be two major assignments for this course, a short oral presentation and a final written project (due July 15).
+
+### Academic Integrity and Plagiarism
+
+All sources for information, figures, and wording must be properly cited. Before submitting any assignments for this class, please **review the following**:
+
+- [Stellenbosch guidelines on academic integrity](https://www.sun.ac.za/english/research-innovation/Research-Development/Documents/Policies%20and%20Guidelines/ENGLISH/SU%20Plagiarism%20Policy_2016.pdf)
+- Examples of plagiarism versus acceptable paraphrasing and summarizing
+    - [From the Academic Integrity Office at MIT](https://integrity.mit.edu/handbook/academic-writing/avoiding-plagiarism-paraphrasing)
+    - [From The Writing Center at University of Wisconsin – Madison](http://writing.wisc.edu/Handbook/QPA_paraphrase.html)
+
+### Oral presentations (project proposals)
+
+At the end of the second week (24 June), you will have to give a short "Research Pitch" to a small group of recent MedPH students and instructors. We will help you develop your presentation throughout Weeks 1-2 of MedPH.
+
+- Prepare a short oral presentation summarizing your research (10 minutes max, using the slide template that will be provided)
+    - You should focus on a project idea that's of interest to you and would be feasible to conduct with available resources (e.g. existing data sets).
+    - The presentation should include enough background information to motivate the proposed research and should clearly state the research question. You should also briefly summarize the proposed approach to the research question.
+    - We recommend selecting a few visual aids (eg, figures or diagrams) that will help you explain key aspects of the proposed research. Please keep the text on your slides to a minimum.
+    - You will be kept to time.
+
+### Final written project
+
+- [Project instructions]({{page.repo}}/blob/master/Project_guidelines.pdf)
+- Your final project should be based on your project proposal but can be modified based on feedback you receive from the faculty and others. You will have three weeks to develop and write up your project (due 15 July), and we encourage you to seek feedback as you're working on it. The instructors will be available for online meetings during the week of 27 June and will be in Muizenberg and available for in-person meetings the week of 4 July.
+- [Example written project]({{page.repo}}/blob/master/assignments/LourensTrachoma2013.pdf?raw=true)
+
+### Other assignments
+
+- Your marks for the course will also depend on your participation during the first two weeks of the course and your submitted responses to the benchmark questions for the required R tutorials. See the schedule tab for details of the additional assignments and when they are due.
+
+Readings
+========
+
+- [Panum's Investigation of the 1846 Measles Outbreak on the Faroe Islands](./panum.html)
+- [Hampson *et al*. 2009]({{page.repo}}/blob/master/readings/Hampson2009.pdf?raw=true)
+
+</div>

data/_includes/MedPH/assignmentsStandard.md

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+<div markdown="1">
+
+### Major Assignments
+
+There will be two major assignments for this course, a short oral presentation (given during the MMED Clinic) and a final written project (due July 12).
+
+### Academic Integrity and Plagiarism
+
+All sources for information, figures, and wording must be properly cited. Before submitting any assignments for this class, please **review the following**:
+
+- [Stellenbosch guidelines on academic integrity](https://www.sun.ac.za/english/research-innovation/Research-Development/Documents/Policies%20and%20Guidelines/ENGLISH/SU%20Plagiarism%20Policy_2016.pdf)
+- Examples of plagiarism versus acceptable paraphrasing and summarizing
+    - [From the Academic Integrity Office at MIT](https://integrity.mit.edu/handbook/academic-writing/avoiding-plagiarism-paraphrasing)
+    - [From The Writing Center at University of Wisconsin – Madison](http://writing.wisc.edu/Handbook/QPA_paraphrase.html)
+
+### Oral presentations (project proposals)
+
+During the first week of MMED, you will have to give a short "Research Pitch" in one of the evening sessions. We will help you develop your presentation throughout Week 1 of MedPH.
+
+- Prepare a short oral presentation summarizing your research (2 minutes max, 1 slide in PDF format)
+    - You should focus on a project idea that's of interest to you and would be feasible to conduct with available resources (e.g. existing data sets).
+    - The presentation should include enough background information to motivate the proposed research and should clearly state the research question. You should also briefly summarize the proposed approach to the research question.
+    - We recommend selecting 1-2 visual aids (eg, figures or diagrams) that will help you explain key aspects of the proposed research. Please keep the text on your slide to a minimum.
+    - You will be kept to time.
+
+### Final written project
+
+- [Project instructions]({{page.repo}}/blob/master/Project_guidelines.pdf)
+- Your final project can be based on your project proposal or your MMED group project. You will have lot of free time during the last week of MMED to write this.
+- A list of suggested topics for MMED group projects will be made available at [on this page]({{ site.url }}/projects).
+- [Example written project]({{page.repo}}/blob/master/assignments/LourensTrachoma2013.pdf?raw=true)
+
+### For Wednesday
+
+- Finish Tutorial 1
+    - **Submit answers to Tutorial 1 BMQs by email to Zinhle at zinhle@aims.ac.za**
+- Read Hampson _et al_. 2009 ([Rabies]({{page.repo}}/blob/master/readings/Hampson2009.pdf?raw=true)) – due Wed AM
+- Consider possible topics for projects (browse the information available under the references tab for ideas)
+    - Come prepared to discuss at least one disease and at least one question that interest you - due Wed PM
+- Review the material on Academic Integrity and Plagiarism above
+
+### For Thursday
+
+- Complete Tutorial 2
+    - **Submit answers to Tutorial 2 BMQs 3 and 4 by email to Zinhle at zinhle@aims.ac.za**
+- Progress on project proposal – due Thurs AM
+    - Decide on a topic and research question
+    - Read at least one relevant article
+    - Identify potential data source/s
+    - Take careful notes on relevant background information (making sure you keep track of sources and any direct quotes)
+
+### For Friday
+
+- Complete Tutorial lab 3
+    - **Submit answer to Tutorial 3, Question 3 by email to Zinhle** – due Friday AM
+- Continue proposal development
+- Draft of presentation for practice - due Friday PM
+
+### For Sunday
+
+- Finalize presentations, as needed (submit slides by Sun PM)
+- Complete the remaining items for [MMED preparation](http://www.ici3d.org/MMED/preparation/)
+    - Software installation
+    - Introduciton to Git
+    - Readings (recommended but not required)
+- Rest up for the weeks ahead!
+
+Readings
+========
+
+- [Panum's Investigation of the 1846 Measles Outbreak on the Faroe Islands](./panum.html)
+- [Hampson *et al*. 2009]({{page.repo}}/blob/master/readings/Hampson2009.pdf?raw=true)
+
+</div>

data/_includes/MedPH/computerlabs.md

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+
+<div markdown="1">
+
+### R and R studio
+
+- First, you should get comfortable using R in your computing environemnt. We encourage you to use R through the [R Studio](http://rstudio.org) interface, because it allows you to run scripts line by line or region by region which will help you move through the tutorials. R Studio is already installed on the AIMS computers and should be accessible through the Applications tab.
+- Introduction to R Studio: [Tutorial](https://raw.githubusercontent.com/ICI3D/RTutorials/master/introRstudio.R)
+
+### Introduction to R
+
+**Note that the Benchmark Questions you are asked to complete for Tutorials 2 and 3 are different from those for the MMED clinic.**
+
+- Introduction to R, Tutorial 1: [Introduction to R and its quirks](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_1.R)
+- Introduction to R, Tutorial 2: [More on Vectors, Data Frames, and Functions](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_2.R)
+    - [**Benchmark questions**]({{page.repo}}/blob/master/assignments/tutorials/Tutorial2_questions.pdf?raw=true): Answer these questions **instead of** the questions that are included in the Tutorial.
+	- Question 4 Tip: **answer should look like the following**
+	  ei.star <- function(population.size, R0) {
+
+	  ouptut <- ????
+
+	  return(output)
+
+	  }
+    - **Assignment**: Submit your solutions to Benchmark Questions 3 and 4 to Zinhle by email.
+    - Supplementary file: **[seir\_2012.R]({{page.repo}}/blob/master/assignments/tutorials/seir_2012.R?raw=true)**
+- [Binomial distribution tutorial](https://raw.githubusercontent.com/ICI3D/RTutorials/master/binomialDistribution.R)
+- Introduction to R, Tutorial 3: [Probability Distributions and Control Structures](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_3.R)
+    - **Assignment**: **In addition to** completing the benchmark questions at the end of the Tutorial, download the supplementary assignment file linked below. Work through the example of a chain binomial SIR model, then complete and submit the assignment as described in the file.
+    - Supplementary file: **[cb\_2012.R]({{page.repo}}/blob/master/assignments/tutorials/cb_2012.R?raw=true)**
+
+### Other modeling tutorials
+
+- [Visualizing Infectious Disease Data in R](https://raw.githubusercontent.com/ICI3D/RTutorials/master/visualizeData.R)
+- [Gillespie algorithm](././tutorials/gillespie)
+- [spillover SIR implemented with Gillespie algorithm](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_spillover_introductions.R)
+- [ODE Models in R](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab1_ODEmodels.R) and steps for constructing a [seasonal SEIR model](https://raw.githubusercontent.com/ICI3D/RTutorials/master/seir.w.seasonal.R) from the model in the ODE lab
+
+</div>

data/_includes/MedPH/computerlabsStandard.md

@@ -0,0 +1,38 @@
+
+<div markdown="1">
+
+### R and R studio
+
+- First, you should get comfortable using R in your computing environemnt. We encourage you to use R through the [R Studio](http://rstudio.org) interface, because it allows you to run scripts line by line or region by region which will help you move through the tutorials. R Studio is already installed on the AIMS computers and should be accessible through the Applications tab.
+- Introduction to R Studio: [Tutorial](https://raw.githubusercontent.com/ICI3D/RTutorials/master/introRstudio.R)
+
+### Introduction to R
+
+**Note that the Benchmark Questions you are asked to complete for Tutorials 2 and 3 are different from those for the MMED clinic.**
+
+- Introduction to R, Tutorial 1: [Introduction to R and its quirks](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_1.R)
+- Introduction to R, Tutorial 2: [More on Vectors, Data Frames, and Functions](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_2.R)
+    - [ **Benchmark questions**]({{page.repo}}/blob/master/assignments/tutorials/Tutorial2_questions.pdf?raw=true): Answer these questions **instead of** the questions that are included in the Tutorial.
+	- Question 4 Tip: **answer should look like the following**
+	  ei.star <- function(population.size, R0) {
+
+	  ouptut <- ????
+
+	  return(output)
+
+	  }
+    - **Assignment** (*due by Wednesday evening*): Submit your solutions to Benchmark Questions 3 and 4 to Zinhle by email.
+    - Supplementary file: **[seir\_2012.R]({{page.repo}}/blob/master/assignments/tutorials/seir_2012.R?raw=true)**
+- [Binomial distribution tutorial](https://raw.githubusercontent.com/ICI3D/RTutorials/master/binomialDistribution.R)
+- Introduction to R, Tutorial 3: [Probability Distributions and Control Structures](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_RTutorial_3.R)
+    - **Assignment** (*due by Sunday evening*): **In addition to** completing the benchmark questions at the end of the Tutorial, download the supplementary assignment file linked below. Work through the example of a chain binomial SIR model, then complete and submit the assignment as described in the file.
+    - Supplementary file: **[cb\_2012.R]({{page.repo}}/blob/master/assignments/tutorials/cb_2012.R?raw=true)**
+
+### Other modeling tutorials
+
+- [Visualizing Infectious Disease Data in R](https://raw.githubusercontent.com/ICI3D/RTutorials/master/visualizeData.R)
+- [Gillespie algorithm](././tutorials/gillespie)
+- [spillover SIR implemented with Gillespie algorithm](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_spillover_introductions.R)
+- [ODE Models in R](https://raw.githubusercontent.com/ICI3D/RTutorials/master/ICI3D_Lab1_ODEmodels.R) and steps for constructing a [seasonal SEIR model](https://raw.githubusercontent.com/ICI3D/RTutorials/master/seir.w.seasonal.R) from the model in the ODE lab
+
+</div>

data/_includes/MedPH/lectures.md

@@ -0,0 +1,12 @@
+<ul>
+  <li> <a href="{{page.repo}}/raw/master/lectures/Intro_PH_Epi_ID.pdf">Introduction to Public Health, Epidemiology, and Infectious Diseases</a> </li>
+  <li> <a href="{{page.repo}}/raw/master/lectures/Intro_ID_Dynamics_I.pdf">Introduction to Infectious Disease Dynamics I</a> </li>
+  <li> <a href="{{page.repo}}/raw/master/lectures/Intro_ID_Dynamics_II.pdf">Introduction to Infectious Disease Dynamics II</a> </li>
+  <li> <a href="{{page.repo}}/raw/master/lectures/Intro_ID_Dynamics_III.pdf">Introduction to Infectious Disease Dynamics III</a> </li>
+  <li> <a href="{{page.repo}}/raw/master/lectures/How_to_read_exRabies.pdf">How to read a scientific paper</a> </li>
+  <li> <a href="{{page.repo}}/raw/master/lectures/FinitePopModels.pdf">Transmission in finite populations</a> </li>
+  <li> <a href="{{page.repo}}/raw/master/lectures/Dynamics_VB_Pathogens.pdf">Dynamics of Vector-borne Pathogens</a> </li>
+    <ul>
+      <li> For information on the method used to calculate $R_0$, see <a href="{{page.repo}}/raw/master/references/Van_den_DreisscheWatmough_2002.pdf">van den Dreissche & Watmough 2002 Mathematical Biosciences</a>.
+      </ul>
+  </ul>

data/_includes/MedPH/references.md

@@ -0,0 +1,71 @@
+<div markdown="1">
+
+You can visit these pages to find general information on many diseases and specific information about recent outbreaks:
+
+- [US Centers for Disease Control and Prevention](http://www.cdc.gov/DiseasesConditions)
+- [ProMED mail](http://www.promedmail.org) - a list serve about disease outbreaks
+- [WHO disease outbreak site](http://www.who.int/csr/don/en/index.html)
+- [Research and Policy for Infectious Disease Dynamics (RAPIDD program)](http://scholar.google.com/citations?hl=en&user=ngDeGF8AAAAJ) - publications on the dynamics of infectious diseases, with a emphasis on data-driven modeling methods
+- [Project Tycho](http://www.tycho.pitt.edu/) - long-term data sets on many infectious diseases in the US
+
+### For groups working on Measles
+
+Measles data to be used in the projects are made available courtesy of **Professor David Earn, Department of Mathematics, McMaster University**. The data files are available online from the International Infectious Disease Data Archive (IIDDA, <http://iidda.mcmaster.ca>). **Note that use of these data is only permitted for the purposes of this course, and any outside use must receive prior approval from Prof. Earn.** These data were originally analyzed in the following two publications:
+
+- [D. J. D. Earn; P. Rohani; B. M. Bolker; B. T. Grenfell (2000) A simple model for complex dynamical transitions in epidemics Science 287(5453): 667-670.]({{page.repo}}/blob/master/references/Earn2000.pdf?raw=true)
+- [C. T. Bauch and D. J. D. Earn (2003) Transients and Attractors in Epidemics. Proceedings of the Royal Society of London Series B 270:1573-1578.]({{page.repo}}/blob/master/references/Bauch2003.pdf?raw=true)
+
+### For groups working on London data
+
+- All available data from London ([download]({{page.repo}}/blob/master/projectData/dataLondon_all.Rdata?raw=true))
+
+### For groups working on US data
+
+This paper gives a nice explanation of the relationship between infectious disease population parameters and the periodicity of the expected limit cycle:
+
+- [Dushoff, J, Plotkin, JB, Levin, SA, & Earn, DJD (2004). Dynamical resonance can account for seasonality of influenza epidemics. _Proceedings of the National Academy of Sciences of the United States of America_, 101(48), 16915–6. <doi:10.1073/pnas.0407293101>]({{page.repo}}/blob/master/references/Dushoff2004.pdf?raw=true)
+
+- All available data from the US ([download]({{page.repo}}/blob/master/projectData/dataUS_all.Rdata?raw=true))
+
+### For groups working on Ebola
+
+- WHO Ebola Response Team. [Ebola Virus Disease in West Africa - The First 9 Months of the Epidemic and Forward Projections]({{page.repo}}/blob/master/references/EbolaFirst9Months.pdf?raw=true). N Engl J Med 2014.
+- Chowell G, Hengartner NW, Castillo-Chavez C, Fenimore PW, Hyman JM. [The basic reproductive number of Ebola and the effects of public health measures: The cases of Congo and Uganda]({{page.repo}}/blob/master/references/ChowellEbola2004.pdf?raw=true). J Theor Biol 2004; 229: 119–26.
+- Bellan SE, Pulliam JRC, Dushoff J, Meyers LA. [Ebola control: effect of asymptomatic infection and acquired immunity]({{page.repo}}/blob/master/references/BellanAsymptomaticEbola2014.pdf?raw=true). Lancet 2014. (accompanying [SEIR model code](http://ebola.ici3d.org/Lancet/ebolaSEIR.R))
+- [Kucharski et al. (2015). Measuring the impact of Ebola control measures in Sierra Leone. PNAS.]({{page.repo}}/blob/master/references/KucharskiPNAS2015.pdf)
+
+### Data Sets
+
+#### Ebola in West Africa
+
+- **Liberia 2014-2016 Ebola Epidemic<sup>1</sup>** ([download figures]({{page.repo}}/blob/master/projectData/LiberiaEVD.pdf?raw=true), [download data]({{page.repo}}/blob/master/projectData/WAevddat.Rdata?raw=true))
+- **Sierra Leone 2014-2016 Ebola Epidemic<sup>1</sup>** ([download figures]({{page.repo}}/blob/master/projectData/SLEVD.pdf?raw=true), [download data]({{page.repo}}/blob/master/projectData/WAevddat.Rdata?raw=true))
+- **Guinea 2014-2016 Ebola Epidemic<sup>1</sup>** ([download figures]({{page.repo}}/blob/master/projectData/GuineaEVD.pdf?raw=true), [download data]({{page.repo}}/blob/master/projectData/WAevddat.Rdata?raw=true))
+
+<sup>1</sup> Data from the [Humanitarian Data Exchange](https://data.humdata.org/dataset/rowca-ebola-cases) and cleaned by Steve Bellan.
+
+#### Other data sets
+
+- **London<sup>1</sup>:** ([download figures]({{page.repo}}/blob/master/projectData/figsLondon.pdf?raw=true), [download data]({{page.repo}}/blob/master/projectData/dataLondon.Rdata?raw=true))
+- **Zaire 1976 Ebola Epidemic<sup>2</sup>:** ([download figures]({{page.repo}}/blob/master/projectData/figsZaireEbola.pdf?raw=true), [download data]({{page.repo}}/blob/master/projectData/dataZaireEbola.Rdata?raw=true))
+- **Nigeria Lassa Fever Epidemic<sup>3</sup>:** ([download figures]({{page.repo}}/blob/master/projectData/figsNigeriaLF.pdf?raw=true), [download data]({{page.repo}}/blob/master/projectData/dataNigeriaLF.Rdata?raw=true))
+- **Democratic Republic of Congo Ebola Epidemic<sup>4</sup>:** ([download figures]({{page.repo}}/blob/master/projectData/figsDRC_Ebola.pdf?raw=true), [download data]({{page.repo}}/blob/master/projectData/dataDRC_Ebola.Rdata?raw=true))
+
+<sup>1</sup> Data made available courtesy of **Prof. David Earn, Dept. of Mathematics, McMaster University**. The data files are available online from the International Infectious Disease Data Archive (IIDDA, <http://iidda.mcmaster.ca>) and were first published in either *D. J. D. Earn; P. Rohani; B. M. Bolker; B. T. Grenfell (2000) A simple model for complex dynamical transitions in epidemics Science 287(5453): 667-670.* or *C. T. Bauch and D. J. D. Earn (2003) Transients and Attractors in Epidemics. Proceedings of the Royal Society of London Series B 270:1573-1578.* **Note that use of these data is only permitted for the purposes of this course, and any outside use must receive prior approval from Prof. Earn.**
+
+<sup>2</sup> Data from [Camacho a., Kucharski a. J, Funk S, Breman J, Piot P, Edmunds WJ. Potential for large outbreaks of Ebola virus disease. Epidemics 2014](http://linkinghub.elsevier.com/retrieve/pii/S1755436514000528) supplementary material and cleaned by Becky.
+
+<sup>3</sup> Data made available courtesy of **Dr. Caitlin Rivers, Johns Hopkins Center for Health Security** (https://github.com/cmrivers/ebola_drc) GitHub repository and cleaned by Becky. The original data files are available online from the WHO Disease Outbreak Network ( <http://www.who.int/csr/don/en/>), WHO situation reports (<http://www.who.int/ebola/situation-reports/drc-2018/en/>), and the DRC Ministry of Health mailing list.
+
+<sup>4</sup> Data made available courtesy of **Dr. Simon Frost, Dept of Veterinary Medicine, University of Cambridge** (https://github.com/sdwfrost/nigeria-lassa-data) GitHub repository and cleaned by Becky.
+
+### Code that groups might find useful
+
+- [Example ODE weekly incidence code ](https://raw.githubusercontent.com/ICI3D/RTutorials/master/seir_cumInc.R)
+
+### Poster examples from previous years
+
+- [2014 Example]({{page.repo}}/blob/master/projectData/KathleenKagisoPoster.pdf?raw=true)
+- [2015 Example]({{page.repo}}/blob/master/projectData/WhoopingCoughOntario2.pdf?raw=true)
+
+</div>

data/_includes/MedPH/schedule.md

@@ -0,0 +1,85 @@
+<div markdown="1">
+
+### Monday, 13 June
+
+-  13:30 – 13:50 Introductions, Overview of course (structure and expectations)
+-  13:50 – 14:30 [Introduction to public health, epidemiology, and infectious diseases]({{page.repo}}/raw/master/lectures/Intro_PH_Epi_ID.pdf) (Juliet)
+-  14:35 – 15:30 [Introduction to infectious disease dynamics, Part I]({{page.repo}}/raw/master/lectures/Intro_ID_Dynamics_I.pdf) (Zinhle)
+
+Assignments
+
+- Install R and R Studio (if not already installed)
+    - R - a statistical programming language (download links for [Windows](http://cran.r-project.org/bin/windows/base/), [Linux](http://cran.r-project.org/bin/linux/), and [MacOS](http://cran.r-project.org/bin/macosx/))
+        - If you already have R, please check that you have a recent version, or else update. Versions starting with 3.5 or 3.6 should be OK.
+    - R Studio - a user interface for R that will be needed for computer exercises ([download link](http://www.rstudio.com/products/rstudio/download/))
+- Complete Introduction to R Studio tutorial
+- Complete [Tutorial I](#computerlabs) – due Tues AM **email to Zinhle at zinhle@aims.ac.za**
+- Review material on Academic Integrity and Plagiarism (see Assignments tab for more details)
+
+### Tuesday, 14 June
+
+-  13:30 – 13:45 [Introduction to projects]({{page.repo}}/raw/master/Project_guidelines.pdf) (Juliet)
+- 13:45 - 14:00 Discussion of BMQs from Tutorial 1 (Juliet)
+-  14:00 – 14:45 Contemporary example (Rabies): [Background lecture and how to read a scientific paper]({{page.repo}}/raw/master/lectures/How_to_read_exRabies.pdf) (Zinhle)
+- 14:45 - 15:30 [Introduction to infectious disease dynamics, Part II]({{page.repo}}/raw/master/lectures/Intro_ID_Dynamics_II.pdf) (Zinhle)
+
+Assignments
+
+- Read [Hampson et al. 2009]({{page.repo}}/raw/master/readings/Hampson2009.pdf) (Rabies) – due Wed
+- Start thinking about possible projects (see Assignments tab for more details)
+
+### Wednesday, 15 June
+
+-  13:30 – 14:15 Contemporary example (Rabies): Discussion session (Zinhle)
+-  14:15 – 14:35 Project discussion and development (Juliet)
+-  14:35 – 15:30 [Dynamics of directly transmitted pathogens]({{page.repo}}/raw/master/lectures/Intro_ID_Dynamics_III.pdf) (Juliet)
+
+Assignments
+
+- Complete [Tutorial II & benchmark questions](#computerlabs)
+    - **turn in figure (and code) from Tutorial II,  Questions 3 and 4 by email to Zinhle at zinhle@aims.ac.za**
+- Progress on projects – due Monday (see Assignments tab for more details)
+
+### Monday, 20 June
+
+-  13:30 - 13:50  Discussion of BMQs from Tutorial 2 (Zinhle)
+-  13:50 – 14:15 Project discussion and development
+    - One-on-one meetings
+-  14:15 - 15:30 [Transmission in Finite Populations]({{page.repo}}/raw/master/lectures/FinitePopModels.pdf) (Juliet)
+
+Assignments
+
+- Complete [Binomial Distribution Tutorial](#computerlabs)
+- Continue proposal/project development
+- Draft of presentations for practice – due Wednesday
+- Complete [Tutorial III: simple stochastic models of epidemics](#computerlabs) – due Tues AM
+    - **turn in figures and code from Tutorial III Questions by email to Zinhle**
+
+### Wednesday, 22 June
+
+- 13:30 – 14:30 [Dynamics of vector-borne pathogens]({{page.repo}}/raw/master/lectures/Dynamics_VB_Pathogens.pdf) (Zinhle)
+- 14:30 – 15:00  Discussion of BMQs from Tutorial 3 (Juliet)
+- 15:00 – 15:30 Practice presentations and feedback (Moderator: Juliet)
+
+Assignments
+
+- Finalize presentations, as needed (submit final slides by Thurs AM)
+
+### Thursday, 23 June
+
+- 13:30 - 14:00 Research pitches
+- 14:00 - 15:15 Dynamical Fever Tutorial
+- 15:15 - 15:30 Wrap-up and preparation for next week (Zinhle)
+
+Assignments
+
+- Complete the remaining items for [MMED preparation](http://www.ici3d.org/MMED/preparation/)
+    - Software installation
+    - Readings (recommended but not required)
+- Complete final project (due 22 July)
+
+### Monday, 27 June through Friday, 8 July
+
+To be modified from [MMED schedule](http://www.ici3d.org/MMED/schedule)
+
+</div>