update shearer et al 2024

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diff --git a/docs/publications.html b/docs/publications.html
@@ -146,10 +146,10 @@ <h1 class="title">Publications</h1>
 <h2 class="anchored" data-anchor-id="pre-prints">Pre-prints</h2>
 <p><strong>Ryan, G.E.</strong>, Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). <a href="https://doi.org/10.32942/X2Q02W" target="_blank">The costs and benefits of publicising species discoveries</a>. <strong>EcoEvoRxiv</strong> 10.32942/X2Q02W</p>
 <p>Le, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., <strong>Ryan, G.</strong>, Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). <a href="https://doi.org/10.1101/2023.11.14.23298536" target="_blank">Cost-effective boosting allocations in the post-Omicron era of COVID-19 management</a>. <strong>medRxiv</strong> 2023.11.14.23298536.</p>
-<p>Shearer, F.M., McCaw, J.M., <strong>Ryan, G.E.</strong>, Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2023). <a href="https://doi.org/10.1101/2023.01.10.23284209" target="_blank">Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia</a>. <strong>medRxiv</strong> 2023.01.10.23284209</p>
 </section>
 <section id="peer-reviewed-articles" class="level2">
 <h2 class="anchored" data-anchor-id="peer-reviewed-articles">Peer-reviewed articles</h2>
+<p>20.&nbsp;Shearer, F.M., McCaw, J.M., <strong>Ryan, G.E.</strong>, Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). <a href="https://doi.org/10.1016/j.epidem.2024.100764" target="_blank">Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia</a>. <strong>Epidemics </strong> <em>In press</em> 10074</p>
 <p>19.&nbsp;<strong>Ryan, G.E.</strong>, Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). <a href="https://doi.org/10.1016/j.epidem.2024.100763" target="_blank">Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening</a>. <strong>Epidemics</strong> 47(2024): 100763</p>
 <p>18.&nbsp;Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., <strong>Ryan, G.</strong>, Cheng, A., McCaw, J.M. and Geard, N., (2023). <a href="https://doi.org/10.1016/j.vaccine.2023.09.025" target="_blank">Individual variation in vaccine immune response can produce bimodal distributions of protection</a>. <strong>Vaccine</strong> 41(45): 6630–6636.</p>
 <p>17.&nbsp;Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., <strong>Ryan, G.E.</strong>, Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, &amp; Shearer, F.M. (2023). <a href="https://doi.org/10.1098/rspb.2023.1437" target="_blank">COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting</a>. <strong>Proceedings of the Royal Society B</strong>, 290(2005): 20231437.</p>
@@ -200,6 +200,7 @@ <h2 class="anchored" data-anchor-id="archived-code">Archived code</h2>
 </section>
 <section id="published-pre-prints" class="level2">
 <h2 class="anchored" data-anchor-id="published-pre-prints">Published pre-prints</h2>
+<p>Shearer, F.M., McCaw, J.M., <strong>Ryan, G.E.</strong>, Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2023). <a href="https://doi.org/10.1101/2023.01.10.23284209" target="_blank">Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia</a>. <strong>medRxiv</strong> 2023.01.10.23284209 <em>Now Shearer et al.&nbsp;2024 Epidemics 47(2024): 100764</em></p>
 <p><strong>Ryan, G.E.</strong>, Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2022). <a href="https://doi.org/10.1101/2022.12.15.22282869" target="_blank">Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening</a>. <strong>medRxiv</strong> 12.15.22282869 <em>Now Ryan et al.&nbsp;2024 Epidemics 47(2024): 100763</em></p>
 <p>Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., <strong>Ryan, G.E.</strong>, Campbell, T., Miller, J.C., Yeung, M., Kabashima, G., Wood, J., Rebuli, N., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, &amp; Shearer, F.M. (2022) <a href="https://doi.org/10.1101/2022.12.04.22282996" target="_blank">COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting</a> medRxiv 2022.12.04.22282996 <em>Now Conway et al.2024 Proc. Roy. Soc. B. 290(2005): 20231437</em></p>
 <p>Golding, N., Price, D.J., <strong>Ryan, G.</strong>, McVernon, J., McCaw, J.M. and Shearer, F.M. (2021) <a href="https://doi.org/10.1101/2021.11.28.21264509" target="_blank">Estimating the transmissibility of SARS-CoV-2 during periods of high, low and zero case incidence</a> medRxiv 2021.11.28.21264509 <em>Now Golding et al.&nbsp;2023 eLife 12:e78089</em></p>

diff --git a/docs/search.json b/docs/search.json
@@ -18,14 +18,14 @@
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-    "text": "Pre-prints\nRyan, G.E., Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). The costs and benefits of publicising species discoveries. EcoEvoRxiv 10.32942/X2Q02W\nLe, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., Ryan, G., Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). Cost-effective boosting allocations in the post-Omicron era of COVID-19 management. medRxiv 2023.11.14.23298536.\nShearer, F.M., McCaw, J.M., Ryan, G.E., Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2023). Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia. medRxiv 2023.01.10.23284209"
+    "text": "Pre-prints\nRyan, G.E., Nicholson, E., Baker, C.M., and McCarthy, M. A. (2024). The costs and benefits of publicising species discoveries. EcoEvoRxiv 10.32942/X2Q02W\nLe, T.P., Conway, E., Akpan, E., Abell, I., Abraham, P., Baker, C.M., Campbell, P.T., Cromer, D., Lydeamore, M.J., McDonough, Y., Mueller, I., Ryan, G., Walker, C., Wang, Y., Carvalho, N., and McVernon, J. (2023). Cost-effective boosting allocations in the post-Omicron era of COVID-19 management. medRxiv 2023.11.14.23298536."
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-    "text": "Peer-reviewed articles\n19. Ryan, G.E., Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening. Epidemics 47(2024): 100763\n18. Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., Ryan, G., Cheng, A., McCaw, J.M. and Geard, N., (2023). Individual variation in vaccine immune response can produce bimodal distributions of protection. Vaccine 41(45): 6630–6636.\n17. Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., Ryan, G.E., Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2023). COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting. Proceedings of the Royal Society B, 290(2005): 20231437.\n16. Golding, N., Price, D.J., Ryan, G., McVernon, J., McCaw, J.M. and Shearer, F.M., (2023). A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence. eLife, 12: e78089.\n15. Borzée, A., McNeely, J., Magellan, K., Miller, J.R., Porter, L., Dutta, T., Kadinjappalli, K.P., Sharma, S., Shahabuddin, G., Aprilinayati, F., Ryan, G.E and others (2020). COVID-19 Highlights the Need for More Effective Wildlife Trade Legislation. Trends in Ecology and Evolution 35: 1052–1055 pdf\n14. Brownell RL Jr, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar L, Genov T, Hobbs R, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, Ryan GE, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, & Wang JY (2019). Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna. Endangered Species Research 40: 285–296\n13. Thomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, Ryan, GE, & Phay, S (2019). A review of electrofishing as a potential threat to freshwater cetaceans. Endangered Species Research 39: 207–220\n12. Ryan, GE, Nicholson, E, Eames, JC, Gray, TNE, Loveridge, R, Mahood, SP, Sum P, & McCarthy, MA (2019). Simultaneous‐count models to estimate abundance from counts of unmarked individuals with imperfect detection. Conservation Biology 33(3): 697–708\n11. Ryan, GE, & Baker, CM (2019). Corrigendum to “A general method for assessing the risks and benefits of secrecy in conserving ’Lazarus species” [Biol. Cons. 203, 186–187]. Biological Conservation 230: 47\n10. Loveridge, R, Ryan, GE, Sum P, Grey-Read, O, Mahood, SP, Mould, A, Harrison, S, Crouthers, R, Ko, S., Clements, T, Eames, JC, & Pruvot, M. (2018). Poisoning causing the decline in South-East Asia’s largest vulture population. Bird Conservation International 29(1): 41–54\n9. Krutzen, M, Beasley I, Ackermann, CY, Lieckfeldt, D, Ludwig, A, Ryan, GE, Bejder, L, Parra, GJ, Wolfensberger, R, & Spencer, PBS (2018). Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River. PLoS ONE 13(1): e0189200\n8. Brownell, RL, Reeves, RR, Thomas, PO, Smith, BD, & Ryan, GE (2017). Dams threaten rare Mekong dolphins. Science 355(6327): 805\n7. Mustika, PLK, Welters, R, Ryan, GE, D’Lima, C, Sorongon-Yap, P, Jutapruet S, & Peter, C (2017). A rapid assessment of wildlife tourism risk posed to cetaceans in Asia. Journal of Sustainable Tourism 25(8): 1138–115\n6. Ryan, GE, & Baker, CM (2016). A general method for assessing the risks and benefits of secrecy in conserving ‘Lazarus species’. Biological Conservation 203: 186–187. See also Corrigendum, Ryan & Baker (2019)\n5. Singh, R. Phan C, Prum S, Pin C, Ryan, G, & Wright, M (2013). The Serengeti of Asia: current status of the Eastern Plains Landscape protected area complex, Cambodia. PARKS 19(2): 23-32\n4. Ryan, GE (2012). Brahminy kites Haliastur indus fishing with Irrawaddy dolphins Orcaella brevirostris in the Mekong River. Forktail 28: 161-162\n3. Sok K, Claassen, AH, Wright, HL, & Ryan, GE (2012). Waterbird nest protection on the Mekong River: a preliminary evaluation, with notes on the recovery and release of white-shouldered ibis Pseudibis davisoni chicks. Cambodian Journal of Natural History 2012(1): 29-41\n2. McCarthy, MA, Garrard, GE, Moore, AL, Parris, KM, Regan, TJ, & Ryan, GE (2011). The SAFE index should not be used for prioritization. Frontiers in Ecology and the Environment 9(9): 486–487\n1. Ryan, GE, Dove, V, Trujillo, F, & Doherty, PF (2011). Irrawaddy dolphin demography in the Mekong River: an application of mark-resight models. Ecosphere 2(5): art58"
+    "text": "Peer-reviewed articles\n20. Shearer, F.M., McCaw, J.M., Ryan, G.E., Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2024). Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia. Epidemics  In press 10074\n19. Ryan, G.E., Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2024). Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening. Epidemics 47(2024): 100763\n18. Zachreson, C., Tobin, R., Szanyi, J., Walker, C., Cromer, D., Shearer, F.M., Conway, E., Ryan, G., Cheng, A., McCaw, J.M. and Geard, N., (2023). Individual variation in vaccine immune response can produce bimodal distributions of protection. Vaccine 41(45): 6630–6636.\n17. Conway, E., Walker, C.R., Baker, C., Lydeamore, M.J., Ryan, G.E., Campbell, T., Miller, J.C., Rebuli, N., Yeung, M., Kabashima, G., Geard, N., Wood, J., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2023). COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting. Proceedings of the Royal Society B, 290(2005): 20231437.\n16. Golding, N., Price, D.J., Ryan, G., McVernon, J., McCaw, J.M. and Shearer, F.M., (2023). A modelling approach to estimate the transmissibility of SARS-CoV-2 during periods of high, low, and zero case incidence. eLife, 12: e78089.\n15. Borzée, A., McNeely, J., Magellan, K., Miller, J.R., Porter, L., Dutta, T., Kadinjappalli, K.P., Sharma, S., Shahabuddin, G., Aprilinayati, F., Ryan, G.E and others (2020). COVID-19 Highlights the Need for More Effective Wildlife Trade Legislation. Trends in Ecology and Evolution 35: 1052–1055 pdf\n14. Brownell RL Jr, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar L, Genov T, Hobbs R, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, Ryan GE, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, & Wang JY (2019). Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna. Endangered Species Research 40: 285–296\n13. Thomas, PO, Gulland, FMD, Reeves, RR, Kreb, D, Ding, W, Smith, B, Malik, MI, Ryan, GE, & Phay, S (2019). A review of electrofishing as a potential threat to freshwater cetaceans. Endangered Species Research 39: 207–220\n12. Ryan, GE, Nicholson, E, Eames, JC, Gray, TNE, Loveridge, R, Mahood, SP, Sum P, & McCarthy, MA (2019). Simultaneous‐count models to estimate abundance from counts of unmarked individuals with imperfect detection. Conservation Biology 33(3): 697–708\n11. Ryan, GE, & Baker, CM (2019). Corrigendum to “A general method for assessing the risks and benefits of secrecy in conserving ’Lazarus species” [Biol. Cons. 203, 186–187]. Biological Conservation 230: 47\n10. Loveridge, R, Ryan, GE, Sum P, Grey-Read, O, Mahood, SP, Mould, A, Harrison, S, Crouthers, R, Ko, S., Clements, T, Eames, JC, & Pruvot, M. (2018). Poisoning causing the decline in South-East Asia’s largest vulture population. Bird Conservation International 29(1): 41–54\n9. Krutzen, M, Beasley I, Ackermann, CY, Lieckfeldt, D, Ludwig, A, Ryan, GE, Bejder, L, Parra, GJ, Wolfensberger, R, & Spencer, PBS (2018). Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River. PLoS ONE 13(1): e0189200\n8. Brownell, RL, Reeves, RR, Thomas, PO, Smith, BD, & Ryan, GE (2017). Dams threaten rare Mekong dolphins. Science 355(6327): 805\n7. Mustika, PLK, Welters, R, Ryan, GE, D’Lima, C, Sorongon-Yap, P, Jutapruet S, & Peter, C (2017). A rapid assessment of wildlife tourism risk posed to cetaceans in Asia. Journal of Sustainable Tourism 25(8): 1138–115\n6. Ryan, GE, & Baker, CM (2016). A general method for assessing the risks and benefits of secrecy in conserving ‘Lazarus species’. Biological Conservation 203: 186–187. See also Corrigendum, Ryan & Baker (2019)\n5. Singh, R. Phan C, Prum S, Pin C, Ryan, G, & Wright, M (2013). The Serengeti of Asia: current status of the Eastern Plains Landscape protected area complex, Cambodia. PARKS 19(2): 23-32\n4. Ryan, GE (2012). Brahminy kites Haliastur indus fishing with Irrawaddy dolphins Orcaella brevirostris in the Mekong River. Forktail 28: 161-162\n3. Sok K, Claassen, AH, Wright, HL, & Ryan, GE (2012). Waterbird nest protection on the Mekong River: a preliminary evaluation, with notes on the recovery and release of white-shouldered ibis Pseudibis davisoni chicks. Cambodian Journal of Natural History 2012(1): 29-41\n2. McCarthy, MA, Garrard, GE, Moore, AL, Parris, KM, Regan, TJ, & Ryan, GE (2011). The SAFE index should not be used for prioritization. Frontiers in Ecology and the Environment 9(9): 486–487\n1. Ryan, GE, Dove, V, Trujillo, F, & Doherty, PF (2011). Irrawaddy dolphin demography in the Mekong River: an application of mark-resight models. Ecosphere 2(5): art58"
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-    "text": "Published pre-prints\nRyan, G.E., Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2022). Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening. medRxiv 12.15.22282869 Now Ryan et al. 2024 Epidemics 47(2024): 100763\nConway, E., Walker, C.R., Baker, C., Lydeamore, M.J., Ryan, G.E., Campbell, T., Miller, J.C., Yeung, M., Kabashima, G., Wood, J., Rebuli, N., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2022) COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting medRxiv 2022.12.04.22282996 Now Conway et al.2024 Proc. Roy. Soc. B. 290(2005): 20231437\nGolding, N., Price, D.J., Ryan, G., McVernon, J., McCaw, J.M. and Shearer, F.M. (2021) Estimating the transmissibility of SARS-CoV-2 during periods of high, low and zero case incidence medRxiv 2021.11.28.21264509 Now Golding et al. 2023 eLife 12:e78089"
+    "text": "Published pre-prints\nShearer, F.M., McCaw, J.M., Ryan, G.E., Hao, T., Tierney, N., Lydeamore, M., Ellis, S., Ward, K., Wood, J., McVernon, J. and Golding, N., (2023). Estimating the impact of test-trace-isolate-quarantine systems on SARS-CoV-2 transmission in Australia. medRxiv 2023.01.10.23284209 Now Shearer et al. 2024 Epidemics 47(2024): 100764\nRyan, G.E., Shearer, F.M., McCaw, J.M., McVernon, J. and Golding, N., (2022). Estimating measures to reduce the transmission of SARS-CoV-2 in Australia to guide a ‘National Plan’ to reopening. medRxiv 12.15.22282869 Now Ryan et al. 2024 Epidemics 47(2024): 100763\nConway, E., Walker, C.R., Baker, C., Lydeamore, M.J., Ryan, G.E., Campbell, T., Miller, J.C., Yeung, M., Kabashima, G., Wood, J., Rebuli, N., McCaw, J.M., McVernon, J., Golding, N., Price, D.J, & Shearer, F.M. (2022) COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting medRxiv 2022.12.04.22282996 Now Conway et al.2024 Proc. Roy. Soc. B. 290(2005): 20231437\nGolding, N., Price, D.J., Ryan, G., McVernon, J., McCaw, J.M. and Shearer, F.M. (2021) Estimating the transmissibility of SARS-CoV-2 during periods of high, low and zero case incidence medRxiv 2021.11.28.21264509 Now Golding et al. 2023 eLife 12:e78089"
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