{"id":2620,"date":"2021-08-06T14:57:06","date_gmt":"2021-08-06T14:57:06","guid":{"rendered":"http:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=2620"},"modified":"2021-08-13T13:10:33","modified_gmt":"2021-08-13T13:10:33","slug":"nchhstp-2021","status":"publish","type":"page","link":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=2620","title":{"rendered":"NCHHSTP (2021)"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Overview<\/h2>\n\n\n\n<p><strong>Location:<\/strong>&nbsp;Online<br><strong>Date:<\/strong>&nbsp;August 9-13, 2021<br><strong>Instructors:<\/strong>&nbsp;John M. Drake (<a rel=\"noreferrer noopener\" href=\"mailto:jdrake@uga.edu\" target=\"_blank\">jdrake@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\">Schedule<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Day 1<\/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\/08\/Overview.html\">course overview<\/a><\/li><li><a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/IntroR.html\">Introduction to R programming<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/introduction.pdf\">R programming<\/a><\/li><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/The-art-of-modeling.html\">The art of modeling<\/a><\/li><li>Q&amp;A<\/li><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/Deterministic-models.html\">Deterministic compartmental models<\/a> (<a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/deterministic-models-solutions.pdf\">Solutions<\/a>)<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 2<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Discussion: <a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1007679\">Brett et al. 2020<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/deterministic-models.pdf\">Deterministic compartmental models<\/a><\/li><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/Stochastic-models.html\">Stochastic models<\/a><\/li><li>Q&amp;A<\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/stochastic-simulation.pdf\">Stochastic models<\/a> (<a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/demo.html\">Demo<\/a>) (<a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/stochastic-models-solutions.pdf\">Solutions<\/a>)<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 3<\/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\/Basic-reproduction-number.html\">The basic reproduction number R<sub>0<\/sub><\/a><\/li><li>Discussion: <a href=\"https:\/\/royalsocietypublishing.org\/doi\/10.1098\/rspb.2020.3074\">Drake et al. 2021<\/a><\/li><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/Estimation.html\">Estimation basics<\/a><\/li><li>Q&amp;A<\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/estimation.pdf\">Estimation basics<\/a> (<a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/estimation-solutions.pdf\">Solutions<\/a>) (<a href=\"http:\/\/least-squares-estimation-solutions\">Solutions<\/a>)<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 4<\/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\/Epidemic-interventions.html\">Interventions<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/pulsed-vaccination.pdf\">Interventions<\/a><\/li><li>Lecture: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/Uncertainty.html\">Uncertainty<\/a><\/li><li>Q&amp;A<\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/sensitivity.pdf\">Sensitivity analysis<\/a> (<a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/lhs-solutions.pdf\">Solutions<\/a>)<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Day 5<\/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\/maximum-likelihood.html\">Maximum likelihood estimation<\/a><\/li><li>Exercise: <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2021\/08\/likelihood.pdf\">Maximum likelihood estimation<\/a><\/li><li>Discussion: <a href=\"https:\/\/journals.plos.org\/plosbiology\/article?id=10.1371\/journal.pbio.1002056\">Drake et al. 2015<\/a><\/li><li>Q&amp;A and wrap-up<\/li><\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Additional resources<\/h3>\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=\"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=\"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><\/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>Overview Location:&nbsp;OnlineDate:&nbsp;August 9-13, 2021Instructors:&nbsp;John M. Drake (jdrake@uga.edu)Data for exercises: data.zip Schedule Day 1 Introductions and course overview Introduction to R programming Exercise: R programming Lecture:&#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-2620","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/2620","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=2620"}],"version-history":[{"count":27,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/2620\/revisions"}],"predecessor-version":[{"id":2696,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/2620\/revisions\/2696"}],"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=2620"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}