TY - JOUR AU - Fouillet, Anne AU - Ruello, Marc AU - Leon, Lucie AU - Sommen, Cecile AU - Marie, Laurent AU - Caserio-Schönemann, Céline AU - Pelat, Camille AU - Le Strat, Yann PY - 2017/05/02 Y2 - 2024/03/28 TI - User-friendly Rshiny web applications for supporting syndromic surveillance analysis JF - Online Journal of Public Health Informatics JA - OJPHI VL - 9 IS - 1 SE - Data sources, standards, exchange, visualization, and quality DO - 10.5210/ojphi.v9i1.7628 UR - https://ojphi.org/ojs/index.php/ojphi/article/view/7628 SP - AB - <div style="left: 89.1818px; top: 337.66px; font-size: 14.0379px; font-family: sans-serif; transform: scaleX(1.08186);" data-canvas-width="63.1985303030303">Objective</div><div style="left: 104.045px; top: 352.475px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.0058);" data-canvas-width="375.28022878787874">The presentation describes the design and the main functionalities</div><div style="left: 89.1818px; top: 368.991px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00173);" data-canvas-width="389.9062946969697">of two user-friendly applications developed using R-shiny to support</div><div style="left: 89.1818px; top: 385.506px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.976742);" data-canvas-width="389.4921772727272">the statistical analysis of morbidity and mortality data from the French</div><div style="left: 89.1818px; top: 402.021px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.0021);" data-canvas-width="233.94125000000003">syndromic surveillance system SurSaUD.</div><div style="left: 89.1818px; top: 433.448px; font-size: 14.0379px; font-family: sans-serif; transform: scaleX(1.11811);" data-canvas-width="81.88294696969696">Introduction</div><div style="left: 104.045px; top: 448.263px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.964825);" data-canvas-width="376.08881060606063">The French syndromic surveillance system SursaUD® has been</div><div style="left: 89.1818px; top: 464.779px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.04161);" data-canvas-width="390.8285833333334">set up by Santé publique France, the national public health agency</div><div style="left: 89.1818px; top: 481.294px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.99965);" data-canvas-width="389.93015909090906">(formerly French institute for public health - InVS) in 2004. In 2016,</div><div style="left: 89.1818px; top: 497.809px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.989829);" data-canvas-width="392.21973712121206">the system is based on three main data sources: the attendances</div><div style="left: 89.1818px; top: 514.324px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00835);" data-canvas-width="392.6675454545454">in about 650 emergency departments (ED), the consultations to</div><div style="left: 89.1818px; top: 530.839px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.07774);" data-canvas-width="394.9192212121212">62 emergency general practitioners’ (GPs) associations SOS</div><div style="left: 89.1818px; top: 547.354px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00401);" data-canvas-width="375.85016666666644">Médecins and the mortality data from 3,000 civil status offices [1].</div><div style="left: 104.045px; top: 563.869px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01361);" data-canvas-width="377.94040681818177">Daily, about 60,000 attendances in ED (88% of the national</div><div style="left: 89.1818px; top: 580.385px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.983162);" data-canvas-width="391.9375757575761">attendances), 8,000 visits in SOS Médecins associations (95% of</div><div style="left: 89.1818px; top: 596.9px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.02012);" data-canvas-width="390.60257348484845">the national visits) and 1,200 deaths (80% of the national mortality)</div><div style="left: 89.1818px; top: 613.415px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.02598);" data-canvas-width="390.8131416666665">are recorded all over the territory and transmitted to Santé publique</div><div style="left: 89.1818px; top: 629.93px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00216);" data-canvas-width="41.70653787878788">France.</div><div style="left: 104.045px; top: 646.445px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.03087);" data-canvas-width="375.8894727272725">About 100 syndromic groupings of interest are constructed from</div><div style="left: 89.1818px; top: 662.96px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.969479);" data-canvas-width="391.57259090909093">the reported diagnostic codes, and monitored daily or weekly, for</div><div style="left: 89.1818px; top: 679.476px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.02044);" data-canvas-width="390.74295227272734">different age groups and geographical scales, to characterize trends,</div><div style="left: 89.1818px; top: 695.991px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.990117);" data-canvas-width="389.4626977272726">detect expected or unexpected events (outbreaks) and assess potential</div><div style="left: 89.1818px; top: 712.506px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01814);" data-canvas-width="392.69702499999977">impact of both environmental and infectious events. All-causes</div><div style="left: 89.1818px; top: 729.021px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00242);" data-canvas-width="272.5734924242424">mortality is also monitored in similar objectives.</div><div style="left: 104.045px; top: 745.536px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.08991);" data-canvas-width="380.34228787878794">Two user-friendly interactive web applications have been</div><div style="left: 89.1818px; top: 762.051px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01889);" data-canvas-width="390.5730939393938">developed using the R shiny package [2] to provide a homogeneous</div><div style="left: 89.1818px; top: 778.566px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.987546);" data-canvas-width="392.0063613636363">framework for all the epidemiologists involved in the syndromic</div><div style="left: 89.1818px; top: 795.082px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00242);" data-canvas-width="284.60395454545454">surveillance at the national and the regional levels.</div><div style="left: 89.1818px; top: 826.509px; font-size: 14.0379px; font-family: sans-serif; transform: scaleX(1.07334);" data-canvas-width="57.70971969696969">Methods</div><div style="left: 104.045px; top: 841.324px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01699);" data-canvas-width="375.65784772727267">The first application, named MASS-SurSaUD, is dedicated to the</div><div style="left: 89.1818px; top: 857.839px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.981398);" data-canvas-width="389.17351742424245">analysis of the two morbidity data sources in Sursaud, along with data</div><div style="left: 89.1818px; top: 874.354px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00622);" data-canvas-width="390.1463424242425">provided by a network of Sentinel GPs [3]. Based on pre-aggregated</div><div style="left: 89.1818px; top: 890.869px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.04611);" data-canvas-width="391.03634393939325">data availaible daily at 10:30 am, R programs create daily, weekly</div><div style="left: 89.1818px; top: 907.385px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.980296);" data-canvas-width="389.4388333333332">and monthly time series of the proportion of each syndromic grouping</div><div style="left: 89.1818px; top: 923.9px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.963436);" data-canvas-width="391.46028787878805">among all visits/attendances with a valid code at the national and</div><div style="left: 89.1818px; top: 940.415px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01307);" data-canvas-width="390.3849863636363">regional levels. Twelve syndromic groupings (mainly infectious and</div><div style="left: 89.1818px; top: 956.93px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00832);" data-canvas-width="390.30216287878795">respiratory groups, like ILI, gastroenteritis, bronchiolitis, pulmonary</div><div style="left: 89.1818px; top: 973.445px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00178);" data-canvas-width="372.31262121212103">diseases) and 13 age groups have been chosen for this application.</div><div style="left: 104.045px; top: 989.96px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00803);" data-canvas-width="375.3742825757576">For ILI, 3 statistical methods (periodic regression, robust periodic</div><div style="left: 89.1818px; top: 1006.48px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.02006);" data-canvas-width="393.0465681818183">regression and Hidden Markov model) have been implemented</div><div style="left: 89.1818px; top: 1022.99px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.959873);" data-canvas-width="391.2441045454545">to identify outbreaks. The results of the 3 methods applied to the</div><div style="left: 89.1818px; top: 1039.51px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.981834);" data-canvas-width="392.160778030303">3 data sources are combined with a voting algorithm to compile</div><div style="left: 89.1818px; top: 1056.02px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.02841);" data-canvas-width="390.89877272727256">the influenza alarm level for each region each week: non-epidemic,</div><div style="left: 89.1818px; top: 1072.54px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00204);" data-canvas-width="173.88720454545458">pre/post epidemic or epidemic.</div><div style="left: 104.045px; top: 1089.05px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.08117);" data-canvas-width="380.4981083333332">The second application, named MASS-Euromomo, allows</div><div style="left: 89.1818px; top: 1105.57px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00444);" data-canvas-width="390.09019090909084">consulting results provided by the model developed by the European</div><div style="left: 89.1818px; top: 1122.08px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.999774);" data-canvas-width="392.327828787879">project EuroMomo for the common analysis of mortality in the</div><div style="left: 89.1818px; top: 1138.6px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.994956);" data-canvas-width="391.7971969696968">European countries (www.euromomo.eu). The Euromomo model,</div><div style="left: 89.1818px; top: 1155.11px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.988505);" data-canvas-width="392.0246106060605">initially developed using Stata software, has been transcripted in</div><div style="left: 89.1818px; top: 1171.63px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.0396);" data-canvas-width="390.8566590909093">R. The model has been adapted to run in France both at a national,</div><div style="left: 89.1818px; top: 1188.14px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.02394);" data-canvas-width="390.82156439393935">regional and other geographical administrative levels, and for 7 age</div><div style="left: 89.1818px; top: 1204.66px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.0021);" data-canvas-width="41.72057575757576">groups.</div><div style="left: 505.364px; top: 337.66px; font-size: 14.0379px; font-family: sans-serif; transform: scaleX(1.08498);" data-canvas-width="50.70481818181818">Results</div><div style="left: 520.227px; top: 352.475px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.977764);" data-canvas-width="376.7485909090907">The two applications, accessible on a web-portal, are similarly</div><div style="left: 505.364px; top: 368.991px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00217);" data-canvas-width="85.78547727272728">designed, with:</div><div style="left: 520.227px; top: 385.506px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.984268);" data-canvas-width="374.628871212121">- a dropdown menu and radio buttons on the left hand side to select</div><div style="left: 505.364px; top: 402.021px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.997799);" data-canvas-width="389.80662575757583">the data to display (e.g. filter by data source, age group, geographical</div><div style="left: 505.364px; top: 418.536px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00215);" data-canvas-width="268.6428863636363">levels, syndromic grouping and/or time period),</div><div style="left: 520.227px; top: 435.051px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01732);" data-canvas-width="375.6283681818182">- several tab panels allowing to consult data and statistical results</div><div style="left: 505.364px; top: 451.566px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.972133);" data-canvas-width="391.60768560606033">through tables, static and dynamic charts, statistical alarm matrix,</div><div style="left: 505.364px; top: 468.082px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.02131);" data-canvas-width="186.74590151515156">geographical maps,... (Figure 1),</div><div style="left: 520.227px; top: 484.597px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.980326);" data-canvas-width="376.9844272727272">- a “help” tab panel, including documentations and guidelines,</div><div style="left: 505.364px; top: 501.112px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00242);" data-canvas-width="118.53584848484846">links, contact details.</div><div style="left: 520.227px; top: 517.627px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00414);" data-canvas-width="375.2296924242424">The MASS-SurSaUD application has been deployed in December</div><div style="left: 505.364px; top: 534.142px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01796);" data-canvas-width="386.5189545454545">2015 and used during the 2015-2016 influenza season. MASS-</div><div style="left: 505.364px; top: 550.657px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.0154);" data-canvas-width="386.4796484848485">Euromomo application has been deployed in July 2016 for the heat-</div><div style="left: 505.364px; top: 567.172px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.995664);" data-canvas-width="389.7027454545454">wave surveillance period. Positive feedbacks from several users have</div><div style="left: 505.364px; top: 583.688px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00225);" data-canvas-width="80.29666666666665">been reported.</div><div style="left: 505.364px; top: 615.115px; font-size: 14.0379px; font-family: sans-serif; transform: scaleX(1.10288);" data-canvas-width="84.24131060606061">Conclusions</div><div style="left: 520.227px; top: 629.93px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.087);" data-canvas-width="379.9071136363636">Business Intelligence tools are generally focused on data</div><div style="left: 505.364px; top: 646.445px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.03957);" data-canvas-width="391.12197499999974">visualisation and are not generally tailored for providing advanced</div><div style="left: 505.364px; top: 662.96px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.01679);" data-canvas-width="390.48184772727274">statistical analysis. Web applications built with the R-shiny package</div><div style="left: 505.364px; top: 679.476px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.998621);" data-canvas-width="389.7617045454543">combining user-friendly visualisations and advanced statistics can be</div><div style="left: 505.364px; top: 695.991px; font-size: 14.0379px; font-family: serif; transform: scaleX(0.992396);" data-canvas-width="389.56517424242423">rapidly built to support timely epidemiological analyses and outbreak</div><div style="left: 505.364px; top: 712.506px; font-size: 14.0379px; font-family: serif; transform: scaleX(1.00284);" data-canvas-width="54.97233333333333">detection.</div><div style="left: 505.364px; top: 899.674px; font-size: 12.3864px; font-family: serif; transform: scaleX(1.05705);" data-canvas-width="289.3330681818181">Figure 1: screen-shots of a page of the two applications</div> ER -