{"id":1929,"date":"2017-05-14T12:33:31","date_gmt":"2017-05-14T12:33:31","guid":{"rendered":"http:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=1929"},"modified":"2018-05-10T14:23:51","modified_gmt":"2018-05-10T14:23:51","slug":"ideas-scientific-programming","status":"publish","type":"page","link":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/?page_id=1929","title":{"rendered":"IDEAS: Scientific Programming (2017)"},"content":{"rendered":"<h2>Overview<\/h2>\n<p style=\"padding-left: 30px;\"><strong>Program:<\/strong>\u00a01st Annual IDEAS Workshop: Scientific Programming Module<br \/>\n<strong>Location:<\/strong> University of\u00a0Georgia<br \/>\n<strong>Date:<\/strong>\u00a0May 15-17, 2017<br \/>\n<strong>Instructors:<\/strong> John M. Drake (<a href=\"mailto:jdrake@uga.edu\" target=\"_blank\" rel=\"noopener\">jdrake@uga.edu<\/a>) &amp; Andrew Park (<a href=\"mailto:awpark@uga.edu\">awpark@uga.edu<\/a>)<br \/>\n<strong>Class objectives:<\/strong>\u00a0This module introduces the principles and practice of scientific computing with special emphasis on analysis of infectious disease data. Programming will be done in R. Students will be taught how to create reproducible research documents using R and R Markdown and to use git\/Github for collaborative and individual projects. An introduction to scientific programming will teach basic operations and classes of base R, installation and use of R packages, data import and transformation, flow control with loops, writing functions, calculating summary statistics, data visualization, and basic mapping. The module will alternate between lectures and computer labs.<br \/>\n<strong>Data for exercises:<\/strong>\u00a0<a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/cases.csv.zip\">cases.csv<\/a>,\u00a0<a href=\"https:\/\/raw.githubusercontent.com\/jdrakephd\/ideas-workshop\/master\/wnv.csv\">wnv.csv<\/a>, <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/lyme.csv.zip\">lyme.csv<\/a>, <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/pop.csv.zip\">pop.csv<\/a>, <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/climate.csv.zip\">climate.csv<\/a><\/p>\n<h2>Class topics<\/h2>\n<p style=\"padding-left: 30px;\"><strong>Data visualization:\u00a0<\/strong><a href=\"https:\/\/raw.githubusercontent.com\/jdrakephd\/ideas-workshop\/master\/visualization-presentation.html\">Presentation<\/a>, <a href=\"https:\/\/github.com\/jdrakephd\/ideas-workshop\/raw\/master\/visualization.pdf\">Handout<\/a><br \/>\n<strong>Scientific programming:\u00a0<\/strong><a href=\"https:\/\/raw.githubusercontent.com\/jdrakephd\/ideas-workshop\/master\/programming-presentation.html\">Presentation<\/a>, <a href=\"https:\/\/github.com\/jdrakephd\/ideas-workshop\/raw\/master\/programming.pdf\">Handout<\/a><br \/>\n<strong>Wrangling:<\/strong> <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/wrangling.html\">Presentation<\/a>, <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/wrangling.pdf\">Handout<\/a><br \/>\n<strong>Modeling:\u00a0<\/strong><a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/modeling.html\">Presentation<\/a>, <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/modeling.pdf\">Handout<\/a><br \/>\n<strong>Project management:\u00a0<\/strong><a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/project-management-presentation.html\">Presentation<\/a>, <a href=\"https:\/\/daphnia.ecology.uga.edu\/drakelab\/wp-content\/uploads\/2017\/05\/project-management.pdf\">Handout<\/a><\/p>\n<h2>Suggested reading<\/h2>\n<ul>\n<li><a href=\"http:\/\/r4ds.had.co.nz\/\">Wickham, H., &amp; G. Grolemund. 2017.<em>\u00a0R for Data Science<\/em>. O&#8217;Reilly<\/a>.<\/li>\n<li><a href=\"http:\/\/www.pnas.org\/content\/113\/32\/9081.abstract\">Cauchemez, S. et al. 2016. Unraveling the drivers of MERS-CoV transmission. <em>Proceedings of the National Academy of Sciences, USA<\/em> 113:9081\u20139086.<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview Program:\u00a01st Annual IDEAS Workshop: Scientific Programming Module Location: University of\u00a0Georgia Date:\u00a0May 15-17, 2017 Instructors: John M. Drake (jdrake@uga.edu) &amp; Andrew Park (awpark@uga.edu) Class objectives:\u00a0This&#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-1929","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/1929","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=1929"}],"version-history":[{"count":12,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/1929\/revisions"}],"predecessor-version":[{"id":2170,"href":"https:\/\/daphnia.ecology.uga.edu\/drakelab\/index.php?rest_route=\/wp\/v2\/pages\/1929\/revisions\/2170"}],"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=1929"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}