{"id":947,"date":"2014-04-04T20:54:18","date_gmt":"2014-04-04T20:54:18","guid":{"rendered":"http:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=947"},"modified":"2014-04-04T20:54:18","modified_gmt":"2014-04-04T20:54:18","slug":"sismid-2013-mathematical-modeling-of-infectious-disease","status":"publish","type":"page","link":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=947","title":{"rendered":"SISMID 2013: Mathematical Modeling of Infectious Disease"},"content":{"rendered":"<p><strong>Program:<\/strong> 5th Annual Summer Institute in Statistical Modeling of Infectious Diseases<br \/>\n<strong>Location:<\/strong> University of Washington<br \/>\n<strong>Date:<\/strong> July 8-10, 2013<br \/>\n<strong>Instructors:<\/strong> Pejman Rohani (<a href=\"mailto:rohani@umich.edu\">rohani@umich.edu<\/a>)\u00a0&amp; John M. Drake (<a href=\"mailto:jdrake@uga.edu\">jdrake@uga.edu<\/a>)<br \/>\n<a href=\"SISMID13-list-of-exercises.pdf\" target=\"_blank\">Objectives<\/a><\/p>\n<table style=\"text-align: left; width: 100%;\" border=\"1\" cellspacing=\"2\" cellpadding=\"2\">\n<tbody>\n<tr>\n<th style=\"vertical-align: top; text-align: center; width: 209px;\">Monday<br \/>\nMorning<\/th>\n<th style=\"vertical-align: top; text-align: center; width: 224px;\">Monday<br \/>\nAfternoon<\/th>\n<th style=\"vertical-align: top; text-align: center; width: 232px;\">Tuesday<br \/>\nMorning<\/th>\n<th style=\"vertical-align: top; text-align: center; width: 238px;\">Tuesday<br \/>\nAfternoon<\/th>\n<th style=\"vertical-align: top; text-align: center; width: 215px;\">Wednesday<br \/>\nMorning<\/th>\n<\/tr>\n<tr>\n<td style=\"vertical-align: top; width: 209px;\">Lecture notes<a href=\"Lecture1_Intro.pdf\"><br \/>\n<\/a><\/p>\n<ul>\n<li><a href=\"Lecture1_Intro.pdf\">Mathematical models of infectious diseases<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 224px;\">Lecture notes<a href=\"Lecture2_Stability.pdf\"><br \/>\n<\/a><\/p>\n<ul>\n<li><a href=\"Lecture2_Stability.pdf\">Anatomy of an epidemic<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 232px;\">Lecture notes<\/p>\n<ul>\n<li><a href=\"Lecture3_Stochasticity.pdf\" target=\"_blank\">Stochastic models<br \/>\n<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 238px;\">Lecture notes<\/p>\n<ul>\n<li><a href=\"Lecture4_Estimation.pdf\" target=\"_blank\">Parameter estimation<br \/>\n<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 215px;\">Lecture notes<\/td>\n<\/tr>\n<tr>\n<td style=\"vertical-align: top; width: 209px;\">Files for computer lab<\/p>\n<ul>\n<li><a href=\"SISMID13-intro.pdf\" target=\"_blank\">Intro to R<br \/>\n(Handout)<\/a><\/li>\n<li><a href=\"SISMID13-intro.R\" target=\"_blank\">Intro to R (Code)<\/a><\/li>\n<li><a href=\"Introduction-R-slides.pdf\" target=\"_blank\">Intro to R (Slides)<\/a><\/li>\n<li><a href=\"SISMID12-intro-solutions.pdf\">Intro to R (Solutions)<\/a><\/li>\n<li><a href=\"data.RData\">Data<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 224px;\">Files for computer lab<\/p>\n<ul>\n<li><a href=\"SISMID13-deterministic-models.pdf\" target=\"_blank\">Deterministic models (Handout)<\/a><\/li>\n<li><a href=\"SISMID13-deterministic-models.R\" target=\"_blank\">Deterministic models (Code)<\/a><\/li>\n<li><a href=\"CompartmentalModelsPresentation.pdf\" target=\"_blank\">Deterministic models (Slides)<\/a><\/li>\n<li><a href=\"SISMID12-deterministic-models-solutions.pdf\" target=\"_blank\">Deterministic models (Solutions)<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 232px;\">Files for computer lab<span style=\"font-style: italic;\"><br \/>\nStochastic models<\/span><\/p>\n<ul>\n<li><a href=\"SISMID13-stochastic-simulation.pdf\" target=\"_blank\">Stochastic models (Handout)<\/a><\/li>\n<li><a href=\"SISMID13-stochastic-simulation.R\" target=\"_blank\">Stochastic models (Code)<\/a><\/li>\n<li><a href=\"stochastic-simulation.pdf\" target=\"_blank\">Stochastic models (Slides)<\/a><\/li>\n<li><a href=\"SISMID12-stochastic-models-solutions.pdf\">Stochastic models (Solutions)<\/a><\/li>\n<\/ul>\n<p><span style=\"font-style: italic;\">R<\/span><sub style=\"font-style: italic;\">0<\/sub><span style=\"font-style: italic;\"> and parameter estimation<\/span><a href=\"ParameterEstimationPresentation.pdf\" target=\"_blank\"><br \/>\n<\/a><\/p>\n<ul>\n<li><a href=\"estimation-slides.pdf\" target=\"_blank\">Estimation (Slides)<\/a><\/li>\n<li><a href=\"SISMID13-estimating-R0.pdf\" target=\"_blank\">Estimating <span style=\"font-style: italic;\">R<\/span><sub style=\"font-style: italic;\">0<\/sub> (Handout)<\/a><\/li>\n<li><a href=\"SISMID13-estimating-R0.R\" target=\"_blank\">Estimating <span style=\"font-style: italic;\">R<\/span><sub style=\"font-style: italic;\">0<\/sub> (Code)<\/a><\/li>\n<li><a href=\"SISMID12-R0-solutions.pdf\">Estimating <span style=\"font-style: italic;\">R<\/span><sub style=\"font-style: italic;\">0<\/sub><\/a> (Solutions)<\/li>\n<li><a href=\"SISMID13-estimating-parameters-least-squares.pdf\" target=\"_blank\">Least squares estimation (Handout)<\/a><\/li>\n<li><a href=\"SISMID13-estimating-parameters-least-squares.R\" target=\"_blank\">Least squares estimation (Code)<\/a><\/li>\n<li><a href=\"SISMID12-least-squares-estimation-solutions.pdf\">Least squares estimation (Solutions)<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 238px;\">Files for computer lab<\/p>\n<ul>\n<li><a href=\"SISMID13-structured-models.pdf\" target=\"_blank\">Age-structured models (Handout)<\/a><\/li>\n<li><a href=\"SISMID13-structured-models.R\" target=\"_blank\">Age-structured models (Code)<\/a><\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top; width: 215px;\">Files for computer lab<br \/>\n<span style=\"font-style: italic;\">Sensitivity analysis<\/span><br style=\"font-style: italic;\" \/><\/p>\n<ul>\n<li><a href=\"SISMID13-lhs.pdf\">Sensitivity analysis through latin hypercube sampling (Handout)<\/a><\/li>\n<li><a href=\"SISMID13-lhs.R\">Sensitivity analysis through latin hypercube sampling (Code)<\/a><\/li>\n<li><a href=\"lhs-slides.pdf\">Sensitivity analysis through latin hypercube sampling (Slides)<\/a><a href=\"LHSSolutions.pdf\" target=\"_blank\"><br \/>\n<\/a><\/li>\n<li>Sensitivity analysis through latin hypercube sampling (Solutions)<\/li>\n<\/ul>\n<p><span style=\"font-style: italic;\">Seasonality<\/span><\/p>\n<ul>\n<li><a href=\"SISMID13-seasonality.pdf\">Seasonality (Handout)<\/a><\/li>\n<li><a href=\"SISMID13-seasonality.R\">Seasonality (Code)<\/a><\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><big>Further exercises:<\/big><\/p>\n<ul>\n<li><a href=\"SISMID13-immune-escape.pdf\">Estimating model parameters through maximum likelihood<\/a> (<a href=\"equine.RData\">Data<\/a>)<\/li>\n<li><a href=\"SISMID13-immune-escape.pdf\" target=\"_blank\">The distribution of outbreak sizes: Immune escape and transmission of equine influenza<\/a><\/li>\n<\/ul>\n<p><big>Suggested reading (case studies):<\/big><\/p>\n<ul>\n<li>Anonymous. 1978. Influenza in a boarding school. <span style=\"font-style: italic;\">British Medical Journal <\/span>1:587.<\/li>\n<li>Blower, S.M., H. B. Gershengorn, R.M.. 2000. A tale of two futures: HIV and antiretroviral therapy in San Francisco. <span style=\"font-style: italic;\">Science <\/span>287:650-654.<\/li>\n<li>Grais, R.F., M.J. Ferrari, C. Dubray, O.N. Bjornstad, B.T. Grenfell, A. Djibo, F. Fermon, P.J. Guerin. 2006.\u00a0 Estimating transmission intensity for a measles epidemic in Niamey, Niger: Lessons for intervention. <span style=\"font-style: italic;\">Transactions of the Royal Society of Tropical Medicine and Hygiene<\/span> 100:867-873.<\/li>\n<li>Park, A.W., J.M. Daly, N.S. Lewis, D.J. Smith, J.L.N. Wood, B.T. Grenfell. 2009. Quantifying the impact of immune escape on transmission dynamics of influenza. <span style=\"font-style: italic;\">Science <\/span>326:726-728.<\/li>\n<\/ul>\n<p><big>Suggested reading (modeling infectious diseases):<\/big><\/p>\n<ul>\n<li>Keeling, M.J. &amp; P. Rohani. 2007.\u00a0 <span style=\"font-style: italic;\">Modeling infectious diseases in humans and animals.<\/span> Princeton University Press.<\/li>\n<li>Vynnyky, E., &amp; R. White. 2010. <span style=\"font-style: italic;\">An introduction to infectious disease modelling.<\/span> Oxford University Press.<\/li>\n<\/ul>\n<p><big>Suggested reading (programming in R):<\/big><\/p>\n<ul>\n<li>Crawley, M.J. 2007. <span style=\"font-style: italic;\">The R book.<\/span> Wiley.<\/li>\n<li>Matloff, N. 2011. <a style=\"font-style: italic;\" href=\"http:\/\/heather.cs.ucdavis.edu\/%7Ematloff\/132\/NSPpart.pdf\" target=\"_blank\">The Art of R Programming<\/a>. No Starch Press.<\/li>\n<li>Venables, W.N., &amp; B.D Ripley. 2002.<span style=\"font-style: italic;\"> Modern Applied Statistics with S.<\/span> 4th edition. Springer.<\/li>\n<li>Jones, O., R. Maillardet, &amp; A. Robinson. 2009. <span style=\"font-style: italic;\">Introduction to scientific programming and simulation with R.<\/span> Chapman &amp; Hall.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Program: 5th Annual Summer Institute in Statistical Modeling of Infectious Diseases Location: University of Washington Date: July 8-10, 2013 Instructors: Pejman Rohani (rohani@umich.edu)\u00a0&amp; John M&#8230;.<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":941,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-template-fullwidth.php","meta":{"footnotes":""},"class_list":["post-947","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/947","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=947"}],"version-history":[{"count":8,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/947\/revisions"}],"predecessor-version":[{"id":955,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/947\/revisions\/955"}],"up":[{"embeddable":true,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/941"}],"wp:attachment":[{"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=947"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}