{"id":2710,"date":"2021-12-31T15:09:38","date_gmt":"2021-12-31T15:09:38","guid":{"rendered":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=2710"},"modified":"2022-03-17T11:22:42","modified_gmt":"2022-03-17T11:22:42","slug":"csels-2021","status":"publish","type":"page","link":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=2710","title":{"rendered":"CSELS (2022)"},"content":{"rendered":"\n<p><strong>Location:<\/strong>&nbsp;Online<br><strong>Date:<\/strong>&nbsp;January-March, 2022<br><strong>Instructors:<\/strong>&nbsp;John M. Drake (<a rel=\"noreferrer noopener\" href=\"mailto:jdrake@uga.edu\" target=\"_blank\">jdrake@uga.edu<\/a>) &amp; Pej Rohani (<a href=\"mailto:rohani@uga.edu\">rohani@uga.edu<\/a>)<br><strong>Data for exercises:<\/strong> <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/data.zip\">data.zip<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Syllabus<\/h2>\n\n\n\n<p><a href=\"https:\/\/docs.google.com\/document\/d\/1mTAVYTlTJatlHQq5XwwbjnRPlGMTDxJo\">Syllabus<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Project<\/h2>\n\n\n\n<p><a href=\"https:\/\/docs.google.com\/document\/d\/1F_kgzO2BLwCW-hMTplpo_egTprKi0sarKBFLaSmbVdc\/edit?usp=sharing\">Assignment<\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Schedule<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Day 1 (January 4, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Introductions and <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/12\/Overview.html\">course overview<\/a><\/li><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/12\/The-art-of-modeling.html\">The art of modeling<\/a><\/li><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/12\/Modeling-pragmatics.html\">Modeling pragmatics and practicalities<\/a><\/li><\/ul>\n\n\n\n<p>Assigned reading: <a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1007679\">Brett et al. 2020. Detecting critical slowing down in high-dimensional epidemiological systems. PLOS Computational Biology 16:e1007679.<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Day 2 (January 11, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/Deterministic-models.html#\/\">Deterministic compartmental models<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/deterministic-models.pdf\">Numerical solution of deterministic epidemiological models<\/a> <\/li><\/ul>\n\n\n\n<p>Assigned reading: <a href=\"https:\/\/www.science.org\/doi\/10.1126\/science.abd7343\">Saad-Roy, C.M. et al. 2020. Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years. Science 370:811-818.<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Day 3 (January 18, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/www.dropbox.com\/s\/q7tq2rbmv02s836\/Stability&amp;NGM.key.pdf?dl=0\">Stability analysis and next generation method<\/a><\/li><\/ul>\n\n\n\n<p>Assigned reading: <a href=\"https:\/\/royalsocietypublishing.org\/doi\/full\/10.1098\/rspb.2020.3074\">Drake, J.M. et al. 2021. Five approaches to the suppression of SARS-CoV-2 without intensive social distancing. <em>Proceedings of the Royal Society, Series B<\/em> 288:20203074.<\/a> <a href=\"https:\/\/royalsocietypublishing.org\/doi\/suppl\/10.1098\/rspb.2020.3074\">Supplement<\/a> (please read at least the first three pages of the supplement).<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Day 4 (February 1, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/01\/Stochastic-models.html\">Stochastic compartmental models<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/stochastic-simulation.pdf\">Numerical solution of stochastic epidemiological models<\/a><\/li><\/ul>\n\n\n\n<p><a href=\"https:\/\/royalsocietypublishing.org\/doi\/10.1098\/rsif.2017.0115\">Assigned reading: Brett, T.S., J.M. Drake, &amp; P. Rohani. 2017. Anticipating the emergence of infectious diseases. <em>Journal of the Royal Society Interface<\/em> 14:20170115.<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Day 5 (February 8, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/02\/Lecture5_Control.pdf\">Modeling interventions<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/02\/pulsed-vaccination.pdf\">Pulsed vaccination<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 6 (February 15, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/02\/Lecture6Inference2.key.pdf\">Model calibration I: ad hoc estimation<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/estimation.pdf\">Estimation<\/a> (<a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/02\/estimation-solutions.pdf\">Solutions<\/a>)<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 7 (February 22, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/02\/maximum-likelihood.html\">Model calibration II: estimation by maximum likelihood<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/likelihood.pdf\">Likelihood estimation<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 8 (March 3, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/03\/Lecture8_Uncertainty.pdf\">Uncertainty<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/03\/sensitivity.pdf\">Sensitivity analysis<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 9 (March 10, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/03\/Lecture9_ContactHeterogeneity.pdf\">Contact heterogeneities<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/07\/structured-models.pdf\">Structured models for host heterogeneities<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 10 (March 17, 2022)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2022\/03\/Forecasting.html\">Forecasting<\/a><\/li><li>Exercise: <a href=\"http:\/\/reichlab.io\/forecast-framework-demos\/\">Forecasting<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Additional resources<\/h3>\n\n\n\n<p><a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/IntroR.html\">Introduction to R programming<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/iqss.github.io\/dss-workshops\/R\/Rintro\/base-r-cheat-sheet.pdf\">Base R cheat sheet<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/www.rstudio.com\/wp-content\/uploads\/2015\/02\/rmarkdown-cheatsheet.pdf\">R-Markdown cheat sheet<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Suggested readings (case studies)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1603269\/pdf\/brmedj00115-0064.pdf\">Anonymous. 1978. Influenza in a boarding school.&nbsp;<em>British Medical Journal<\/em>&nbsp;1:587.<\/a><\/li><li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10649998\">Blower, S.M., H. B. Gershengorn, R.M. 2000. A tale of two futures: HIV and antiretroviral therapy in San Francisco.&nbsp;<em>Science<\/em>&nbsp;287:650-654.<\/a><\/li><li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16540134\">Grais, R.F., M.J. Ferrari, C. Dubray, O.N. Bjornstad, B.T. Grenfell, A. Djibo, F. Fermon, P.J. Guerin. 2006. Estimating transmission intensity for a measles epidemic in Niamey, Niger: Lessons for intervention.&nbsp;<em>Transactions of the Royal Society of Tropical Medicine and Hygiene<\/em>&nbsp;100:867-873.<\/a><\/li><li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2870608\/\">Legrand, J., R.F. Grais, P.Y. Boelle, A.J. Valleron, &amp; A. Flahault. 2007. Understanding the dynamics of Ebola epidemics.&nbsp;<em>Epidemiology &amp; Infection<\/em>&nbsp;135:610-621.<\/a><\/li><li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1755436521000669\">McCabe, R. et al. 2021. Communicating uncertainty in epidemic models. <em>Epidemics<\/em> 37:100520. <\/a><\/li><li><a href=\"http:\/\/www.sciencemag.org\/content\/326\/5953\/726\">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.&nbsp;<em>Science<\/em>&nbsp;326:726-728.<\/a><\/li><li><a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0042320\">Pitzer, V.E. et al. 2012. Direct and indirect effects of rotavirus vaccination: Comparing predictions from transmission dynamic models. <em>PLOS One <\/em>7(8): e42320.<\/a><\/li><li><a href=\"http:\/\/rspb.royalsocietypublishing.org\/content\/281\/1785\/20140268\">Read, J., Lessler, J., Riley, S., Wang, S., Tan, L.J., Kwok, K.O.,&nbsp;et al. 2014. Social mixing patterns in rural and urban areas of&nbsp;southern China.&nbsp;<em>Proceedings of the Royal Society B: Biological Sciences<\/em>&nbsp;281:20140268.<\/a><\/li><li><a href=\"http:\/\/www.sciencemag.org\/content\/330\/6006\/982.full\">Rohani, P., Zhong, X., &amp; King, A. A. 2010. Contact network structure&nbsp;explains the changing epidemiology of pertussis.&nbsp;<em>Science&nbsp;<\/em>330:982\u2013985.<\/a><\/li><li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/6600102\">Schenzle, D. 1984. An age-structured model of pre- and&nbsp;post-vaccination measles transmissiont.&nbsp;<em>IMA Journal of Mathematics&nbsp;Applied in Medicine and Biology<\/em>&nbsp;1:169\u2013191.<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Suggested readings (modeling)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/press.princeton.edu\/titles\/8459.html\">Keeling, M.J. &amp; P. Rohani. 2007.&nbsp;<em>Modeling infectious diseases in humans and animals<\/em>. Princeton University Press.<\/a><\/li><li><a href=\"http:\/\/www.anintroductiontoinfectiousdiseasemodelling.com\/\">Vynnyky, E., &amp; R. White. 2010.&nbsp;<em>An introduction to infectious disease modelling<\/em>. Oxford University Press.<\/a><\/li><li><a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S0025556405001549\">Heesterbeek, J. A. P., &amp; Roberts, M. G. 2007. The type-reproduction&nbsp;number T in models for infectious disease control.&nbsp;<em>Mathematical&nbsp;Biosciences<\/em>&nbsp;206(1):3\u201310.<\/a><\/li><li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC2871801\/\">Diekmann, O., Heesterbeek, J. A. P., &amp; Roberts, M. G. 2009. The&nbsp;construction of next-generation matrices for compartmental epidemic&nbsp;models.&nbsp;<em>Journal of the Royal Society Interface&nbsp;<\/em>7:873\u2013885.<\/a><\/li><li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC1578275\/\">Heffernan, J.M., R.J. Smith &amp; L. Wahl. 2005. Perspectives on the basic reproductive ratio. <em>Journal of the Royal Society Interface<\/em> 2:281-293.<\/a><\/li><li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0025556402001086?casa_token=w5dPAInmLJgAAAAA:PLhz3IV1evPAbjVHj25cdkBwM0soeEhl7wFd0jA3Cjo5kWoF5iAbrG2QcBV6jlTcUlYvwTl3AXEK\">van den Driessche, P. &amp; J. Watmough. 2002. Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. <em>Mathematical Biosciences<\/em> 180:29-48.<\/a><\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Suggested readings (R programming)<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.wiley.com\/en-us\/The+R+Book%2C+2nd+Edition-p-9780470973929\">Crawley, M.J. 2007.&nbsp;<em>The R book<\/em>. Wiley.<\/a><\/li><li><a href=\"https:\/\/nostarch.com\/artofr.htm\">Matloff, N. 2011.&nbsp;<em>The Art of R Programming<\/em>. No Starch Press.<\/a><\/li><li><a href=\"https:\/\/www.springer.com\/us\/book\/9780387954578\">Venables, W.N., &amp; B.D Ripley. 2002.&nbsp;<em>Modern Applied Statistics with S<\/em>. 4th edition. Springer.<\/a><\/li><li><a href=\"https:\/\/www.crcpress.com\/Introduction-to-Scientific-Programming-and-Simulation-Using-R-Second-Edition\/Jones-Maillardet-Robinson\/p\/book\/9781466569997\">Jones, O., R. Maillardet, &amp; A. Robinson. 2014.&nbsp;<em>Introduction to scientific programming and simulation with R<\/em>. Second edition. Chapman &amp; Hall.<\/a><\/li><li><a href=\"https:\/\/r4ds.had.co.nz\/\">Wickham, H. &amp; G. Grolemund. 2016. <em>R for Data Science<\/em>. O&#8217;Reilly.<\/a><\/li><\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Location:&nbsp;OnlineDate:&nbsp;January-March, 2022Instructors:&nbsp;John M. Drake (jdrake@uga.edu) &amp; Pej Rohani (rohani@uga.edu)Data for exercises: data.zip Syllabus Syllabus Project Assignment Schedule Day 1 (January 4, 2022) Introductions and course&#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-2710","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/2710","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=2710"}],"version-history":[{"count":35,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/2710\/revisions"}],"predecessor-version":[{"id":2795,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/2710\/revisions\/2795"}],"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=2710"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}