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udpated submission to be in format compliance.

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nickreich committed Nov 27, 2017
1 parent 3b0602e commit a1262d84b9e59b6ac6eaeeccfb83a3afa11f9cdb
@@ -17,7 +17,7 @@ output:
fig_height: 5
fig_width: 5
md_extensions: +implicit_figures+grid_tables
csl: emerging-infectious-diseases.csl
csl: nature.csl
bibliography: active-monitoring.bib
---
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@@ -1,6 +1,6 @@
---
title: "Quantifying the Risk and Cost of Active Monitoring for Infectious Diseases"
author: "Nicholas G Reich*, Justin Lessler, Jay K Varma, Neil M Vora"
author: "Nicholas G Reich$^{*,1}$, Justin Lessler$^{2}$, Jay K Varma$^{3,4}$, Neil M Vora$^{3,4}$"
date: "November 2017"
output:
pdf_document:
@@ -16,7 +16,7 @@ output:
md_extensions: +implicit_figures
reference_docx: aje-word-style.docx
header-includes: \usepackage{setspace}\doublespacing
csl: emerging-infectious-diseases.csl
csl: nature.csl
bibliography: active-monitoring.bib
---
@@ -50,11 +50,13 @@ source('../analysis-code/inc-per-mcmc.R')
\vspace{10em} -->
__Author Affiliations:__
University of Massachusetts, Amherst, Massachusetts, USA (N.G. Reich);
Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA (J. Lessler);
New York City Department of Health and Mental Hygiene, USA (J.K. Varma, N.M. Vora);
Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J.K. Varma, N.M. Vora)
#### Author Affiliations
1. University of Massachusetts, Amherst, Massachusetts, USA
2. Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
3. New York City Department of Health and Mental Hygiene, USA
4. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
*Correspondence to nick@schoolph.umass.edu
\
@@ -406,7 +408,7 @@ ggplot(costs, aes(x=dur*gamma_params['median'],
```
```{r optimized-cost-with-uncertainty, cache=FALSE}
```{r optimized-cost-with-uncertainty, cache=TRUE}
durs <- seq(.5, 5, by=.1)
phis <- c(1/1000, 1/10000)
@@ -13,7 +13,7 @@ @article{Reich:2017z
@article{Lessler:2009ub,
author = {Lessler, Justin and Reich, Nicholas G and Brookmeyer, Ron and Perl, Trish M and Nelson, Kenrad E and Cummings, Derek A T},
title = {{Incubation periods of acute respiratory viral infections: a systematic review.}},
journal = {The Lancet Infectious Diseases},
journal = {Lancet Infectious Diseases},
year = {2009},
volume = {9},
number = {5},
@@ -50,7 +50,7 @@ @webpage{CentersforDiseaseControlandPrevention:VbDBWqNH
@article{Yacisin:2015wm,
author = {Yacisin, Kari and Balter, Sharon and Fine, Annie and Weiss, Don and Ackelsberg, Joel and Prezant, David and Wilson, Ross and Starr, David and Rakeman, Jennifer and Raphael, Marisa and Quinn, Celia and Toprani, Amita and Clark, Nancy and Link, Nathan and Daskalakis, Demetre and Maybank, Aletha and Layton, Marcelle and Varma, Jay K and {Centers for Disease Control and Prevention (CDC)}},
title = {{Ebola virus disease in a humanitarian aid worker - New York City, October 2014.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2015},
volume = {64},
number = {12},
@@ -72,7 +72,7 @@ @article{Chung:2015hb
@article{Cardile:2015wa,
author = {Cardile, Anthony P and Murray, Clinton K and Littell, Christopher T and Shah, Neel J and Fandre, Matthew N and Drinkwater, Dennis C and Markelz, Brian P and Vento, Todd J},
title = {{Monitoring Exposure to Ebola and Health of U.S. Military Personnel Deployed in Support of Ebola Control Efforts - Liberia, October 25, 2014-February 27, 2015.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2015},
volume = {64},
number = {25},
@@ -83,7 +83,7 @@ @article{Cardile:2015wa
@article{StehlingAriza:2015vd,
author = {Stehling-Ariza, Tasha and Fisher, Emily and Vagi, Sara and Fechter-Leggett, Ethan and Prudent, Natasha and Dott, Mary and Daley, Randolph and Avchen, Rachel Nonkin},
title = {{Monitoring of Persons with Risk for Exposure to Ebola Virus Disease - United States, November 3, 2014-March 8, 2015.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2015},
volume = {64},
number = {25},
@@ -94,7 +94,7 @@ @article{StehlingAriza:2015vd
@article{Koonin:2015um,
author = {Koonin, Lisa M and Jamieson, Denise J and Jernigan, John A. and Van Beneden, Chris A and Kosmos, Christine and Harvey, Melissa Cole and Pietz, Harald and Bertolli, Jeanne and Perz, Joseph F and Whitney, Cynthia G and Halpin, Alison Sheehan-Laufer and Daley, W Randolph and Pesik, Nicki and Margolis, Gregg S and Tumpey, Abbigail and Tappero, Jordan and Damon, Inger and {Centers for Disease Control and Prevention (CDC)}},
title = {{Systems for rapidly detecting and treating persons with ebola virus disease--United States.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2015},
volume = {64},
number = {8},
@@ -123,7 +123,7 @@ @article{HodgeJr:2015tq
@article{Reich:2009jq,
author = {Reich, Nicholas G and Lessler, Justin and Cummings, Derek A T and Brookmeyer, Ron},
title = {{Estimating incubation period distributions with coarse data}},
journal = {Statistics in medicine},
journal = {Statistics in Medicine},
year = {2009},
volume = {28},
number = {22},
@@ -193,7 +193,7 @@ @article{Cowling:2015vb
@article{Benowitz:2014vy,
author = {Benowitz, Isaac and Ackelsberg, Joel and Balter, Sharon E and Baumgartner, Jennifer C and Dentinger, Catherine and Fine, Anne D and Harper, Scott A and Jones, Lucretia E and Laraque, Fabienne and Lee, Ellen H and Merizalde, Giselle and Yacisin, Kari A and Varma, Jay K and Layton, Marcelle C},
title = {{Surveillance and preparedness for Ebola virus disease -- New York City, 2014.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2014},
volume = {63},
number = {41},
@@ -204,7 +204,7 @@ @article{Benowitz:2014vy
@article{Parham:2015wf,
author = {Parham, Mary and Edison, Laura and Soetebier, Karl and Feldpausch, Amanda and Kunkes, Audrey and Smith, Wendy and Guffey, Taylor and Fetherolf, Romana and Sanlis, Kathryn and Gabel, Julie and Cowell, Alex and Drenzek, Cherie and {Centers for Disease Control and Prevention (CDC)}},
title = {{Ebola active monitoring system for travelers returning from West Africa---Georgia, 2014-2015.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2015},
volume = {64},
number = {13},
@@ -236,7 +236,7 @@ @incollection{Brookmeyer:2005bc
@article{Nishiura:2009dh,
author = {Nishiura, Hiroshi},
title = {{Determination of the appropriate quarantine period following smallpox exposure: an objective approach using the incubation period distribution.}},
journal = {International journal of hygiene and environmental health},
journal = {International Journal of Hygiene and Environmental Health},
year = {2009},
volume = {212},
number = {1},
@@ -247,7 +247,7 @@ @article{Nishiura:2009dh
@article{Velasquez:2015gv,
author = {Vel{\'a}squez, Gustavo E and Aibana, Omowunmi and Ling, Emilia J and Diakite, Ibrahim and Mooring, Eric Q and Murray, Megan B},
title = {{Time from Infection to Disease and Infectiousness for Ebola Virus Disease, a Systematic Review.}},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
journal = {Clinical Infectious Diseases},
year = {2015},
volume = {61},
number = {7},
@@ -292,7 +292,7 @@ @article{Nishiura:2007jh
@article{Litvinjenko:1972vp,
author = {Litvinjenko, S and Arsic, B and Borjanovic, S},
title = {{Epidemiologic Aspects of Smallpox in Yugoslavia in 1972}},
journal = {Bulletin of the World Health Organization},
journal = {Bull. World Health Organ},
year = {1972},
month = nov
}
@@ -332,7 +332,7 @@ @article{Fraser:2004ci
@article{Althaus:2014cw,
author = {Althaus, Christian L},
title = {{Estimating the Reproduction Number of Ebola Virus (EBOV) During the 2014 Outbreak in West Africa.}},
journal = {PLoS currents},
journal = {PLOS Currents},
year = {2014},
volume = {6}
}
@@ -370,7 +370,7 @@ @article{Chowell:2004gh
@article{Biddinger:2015bx,
author = {Biddinger, Paul D and Hooper, David C and Shenoy, Erica S and Bajwa, Ednan K and Robbins, Gregory K and Branda, John A},
title = {{CASE RECORDS of the MASSACHUSETTS GENERAL HOSPITAL. Case 28-2015. A 32-Year-Old Man with Fever, Headache, and Myalgias after Traveling from Liberia.}},
journal = {The New England journal of medicine},
journal = {The New England Journal of Medicine},
year = {2015},
volume = {373},
number = {11},
@@ -396,7 +396,7 @@ @article{Hladky:2014uo
@article{Cai:2006dm,
author = {Cai, Quan-Cai and Xu, Qin-Feng and Xu, Jian-Ming and Guo, Qiang and Cheng, Xiang and Zhao, Gen-Ming and Sun, Qing-Wen and Lu, Jian and Jiang, Qing-Wu},
title = {{Refined estimate of the incubation period of severe acute respiratory syndrome and related influencing factors.}},
journal = {American journal of epidemiology},
journal = {American Journal of Epidemiology},
year = {2006},
volume = {163},
number = {3},
@@ -484,7 +484,7 @@ @article{Brookmeyer:2001gx
@article{Millman:2016cz,
author = {Millman, Alexander J and Chamany, Shadi and Guthartz, Seth and Thihalolipavan, Sayone and Porter, Michael and Schroeder, Andrew and Vora, Neil M and Varma, Jay K and Starr, David and {MIA}},
title = {{Active Monitoring of Travelers Arriving from Ebola-Affected Countries - New York City, October 2014-April 2015.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2016},
volume = {65},
number = {3},
@@ -494,7 +494,7 @@ @article{Millman:2016cz
@article{Chevalier:2014uk,
author = {Chevalier, Michelle S and Chung, Wendy and Smith, Jessica and Weil, Lauren M and Hughes, Sonya M and Joyner, Sibeso N and Hall, Emily and Srinath, Divya and Ritch, Julia and Thathiah, Prea and Threadgill, Heidi and Cervantes, Diana and Lakey, David L and {Centers for Disease Control and Prevention (CDC)}},
title = {{Ebola virus disease cluster in the United States--Dallas County, Texas, 2014.}},
journal = {MMWR. Morbidity and mortality weekly report},
journal = {MMWR},
year = {2014},
volume = {63},
number = {46},
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