<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="margin: 0px; padding: 0px 0px 0.25em; border: 0px; font-stretch: inherit; line-height: inherit; vertical-align: baseline;" class=""><font color="#2c3032" face="Noto Sans, Arial, sans-serif" class=""><span style="caret-color: rgb(44, 48, 50);" class=""><a href="https://smw.ch/article/doi/smw.2020.20336" class="">https://smw.ch/article/doi/smw.2020.20336</a></span></font></div><div style="margin: 0px; padding: 0px 0px 0.25em; border: 0px; font-stretch: inherit; line-height: inherit; vertical-align: baseline;" class=""><font color="#2c3032" face="Noto Sans, Arial, sans-serif" class=""><span style="caret-color: rgb(44, 48, 50);" class=""><br class=""></span></font></div><div style="margin: 0px; padding: 0px 0px 0.25em; border: 0px; font-family: "Noto Sans", Arial, sans-serif; font-stretch: inherit; line-height: inherit; vertical-align: baseline; caret-color: rgb(44, 48, 50); color: rgb(44, 48, 50);" class=""></div><blockquote type="cite" class=""><div style="margin: 0px; padding: 0px 0px 0.25em; border: 0px; font-family: "Noto Sans", Arial, sans-serif; font-stretch: inherit; line-height: inherit; vertical-align: baseline; caret-color: rgb(44, 48, 50); color: rgb(44, 48, 50);" class="">In the fitting procedure used in the manuscript Fig1c_Rscript.R (available at <a href="https://github.com/ehylau/COVID-19" class="_3t5uN8xUmg0TOwRCOGQEcU" rel="noopener nofollow ugc" target="_blank" style="margin: 0px; padding: 0px; border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant-caps: inherit; font-stretch: inherit; line-height: inherit; vertical-align: baseline; color: rgba(255, 255, 255, 0);">https://github.com/ehylau/COVID-19</a>), the following condition is used in the return line of the likelihood function:</div><div style="margin: 0px; padding: 0.8em 0px 0.25em; border: 0px; font-family: "Noto Sans", Arial, sans-serif; font-stretch: inherit; line-height: inherit; vertical-align: baseline; caret-color: rgb(44, 48, 50); color: rgb(44, 48, 50);" class=""> return(-sum(lli[!is.infinite(lli)]))</div><div style="margin: 0px; padding: 0.8em 0px 0px; border: 0px; font-family: "Noto Sans", Arial, sans-serif; font-stretch: inherit; line-height: inherit; vertical-align: baseline; caret-color: rgb(44, 48, 50); color: rgb(44, 48, 50);" class="">This condition will erroneously drop any data-point that has a probability of zero (and hence a log-probability of −∞) under the current model parameters. As the optimisation is initiated with a shift value of 2.5 days, two data-points (54 and 68) are dropped from the beginning of the fit procedure. This then leads to an erroneous maximum likelihood infectiousness profile, which is displayed in figure 1C of the original manuscript [<a href="https://smw.ch/article/doi/smw.2020.20336#5573e39b6600496d40f493d00ec7658479a19607" class="_3t5uN8xUmg0TOwRCOGQEcU" rel="noopener nofollow ugc" target="_blank" style="margin: 0px; padding: 0px; border: 0px; font-family: inherit; font-size: inherit; font-style: inherit; font-variant-caps: inherit; font-stretch: inherit; line-height: inherit; vertical-align: baseline; color: rgba(255, 255, 255, 0);">1</a>].</div></blockquote><br class=""><div class=""><font color="#2c3032" face="Noto Sans, Arial, sans-serif" class="">paper tl;dr: infectivity date isn’t 2-3 days prior to symptom start, it’s 4-5.</font></div><div class=""><font color="#2c3032" face="Noto Sans, Arial, sans-serif" class=""><br class=""></font></div><div class=""><font color="#2c3032" face="Noto Sans, Arial, sans-serif" class="">Deirdre</font></div></body></html>