add hallal + lewis refs

README.Rmd

@@ -312,7 +312,7 @@ Feel free to fill an issue or contribute with your functions or workflows in a p
 
 Here are a list of publications with interesting approaches using R:
 
-- @Silveira2020 in the strategy 3 analysed the survey accounting for sampling design and test validity using parametric bootstraping.
+- @Silveira2020 and @Hallal2020 analysed a serological survey accounting for sampling design and test validity using parametric bootstraping, following @Lewis2012.
 
 - @Flor2020 implemented a lot of frequentist and bayesian methods for test with known sensitivity and specificity. Code is available [here](https://github.com/BfRstats/bayespem-validation-code).
 
@@ -351,12 +351,16 @@ Flor, Matthias, Michael Weiß, Thomas Selhorst, Christine Müller-Graf, and Matt
 
 Gelman, Andrew, and Bob Carpenter. 2020. “Bayesian Analysis of Tests with Unknown Specificity and Sensitivity.” Journal of the Royal Statistical Society: Series C (Applied Statistics), August. https://doi.org/10.1111/rssc.12435.
 
+Hallal, Pedro C, Fernando P Hartwig, Bernardo L Horta, Mariângela F Silveira, Claudio J Struchiner, Luı́s P Vidaletti, Nelson A Neumann, et al. 2020. “SARS-CoV-2 Antibody Prevalence in Brazil: Results from Two Successive Nationwide Serological Household Surveys.” The Lancet Global Health, September. https://doi.org/10.1016/s2214-109x(20)30387-9.
+
 Kritsotakis, Evangelos I. 2020. “On the Importance of Population-Based Serological Surveys of SARS-CoV-2 Without Overlooking Their Inherent Uncertainties.” Public Health in Practice 1 (November): 100013. https://doi.org/10.1016/j.puhip.2020.100013.
 
 Larremore, Daniel B., Bailey K Fosdick, Kate M Bubar, Sam Zhang, Stephen M Kissler, C. Jessica E. Metcalf, Caroline Buckee, and Yonatan Grad.2020.“Estimating SARS-CoV-2 Seroprevalence and Epidemiological Parameters with Uncertainty from Serological Surveys.” medRxiv, April. https://doi.org/10.1101/2020.04.15.20067066.
 
 Larremore, Daniel B., Bailey K. Fosdick, Sam Zhang, and Yonatan Grad.2020.“Jointly Modeling Prevalence, Sensitivity and Specificity for Optimal Sample Allocation.” bioRxiv, May. https://doi.org/10.1101/2020.05.23.112649.
 
+Lewis, Fraser I, and Paul R Torgerson. 2012. “A Tutorial in Estimating the Prevalence of Disease in Humans and Animals in the Absence of a Gold Standard Diagnostic.” Emerging Themes in Epidemiology 9 (1). https://doi.org/10.1186/1742-7622-9-9.
+
 Rogan, Walter J., and Beth Gladen. 1978. “Estimating Prevalence from the Results of A Screening Test.” American Journal of Epidemiology 107 (1): 71–76. https://doi.org/10.1093/oxfordjournals.aje.a112510.
 
 Silveira, Mariângela F., Aluı́sio J. D. Barros, Bernardo L. Horta, Lúcia C. Pellanda, Gabriel D. Victora, Odir A. Dellagostin, Claudio J. Struchiner, et al. 2020. “Population-Based Surveys of Antibodies Against SARS-CoV-2 in Southern Brazil.” Nature Medicine 26 (8): 1196–9. https://doi.org/10.1038/s41591-020-0992-3.

README.md

@@ -231,9 +231,10 @@ workflows in a pull request.
 
 Here are a list of publications with interesting approaches using R:
 
-  - Silveira et al. ([2020](#ref-Silveira2020)) in the strategy 3
-    analysed the survey accounting for sampling design and test validity
-    using parametric bootstraping.
+  - Silveira et al. ([2020](#ref-Silveira2020)) and Hallal et al.
+    ([2020](#ref-Hallal2020)) analysed a serological survey accounting
+    for sampling design and test validity using parametric bootstraping,
+    following Lewis and Torgerson ([2012](#ref-Lewis2012)).
 
   - Flor et al. ([2020](#ref-Flor2020)) implemented a lot of frequentist
     and bayesian methods for test with known sensitivity and
@@ -305,6 +306,12 @@ with Unknown Specificity and Sensitivity.” Journal of the Royal
 Statistical Society: Series C (Applied Statistics), August.
 <https://doi.org/10.1111/rssc.12435>.
 
+Hallal, Pedro C, Fernando P Hartwig, Bernardo L Horta, Mariângela F
+Silveira, Claudio J Struchiner, Luı́s P Vidaletti, Nelson A Neumann, et
+al. 2020. “SARS-CoV-2 Antibody Prevalence in Brazil: Results from Two
+Successive Nationwide Serological Household Surveys.” The Lancet Global
+Health, September. <https://doi.org/10.1016/s2214-109x(20)30387-9>.
+
 Kritsotakis, Evangelos I. 2020. “On the Importance of Population-Based
 Serological Surveys of SARS-CoV-2 Without Overlooking Their Inherent
 Uncertainties.” Public Health in Practice 1 (November): 100013.
@@ -321,6 +328,11 @@ Grad.2020.“Jointly Modeling Prevalence, Sensitivity and Specificity for
 Optimal Sample Allocation.” bioRxiv, May.
 <https://doi.org/10.1101/2020.05.23.112649>.
 
+Lewis, Fraser I, and Paul R Torgerson. 2012. “A Tutorial in Estimating
+the Prevalence of Disease in Humans and Animals in the Absence of a Gold
+Standard Diagnostic.” Emerging Themes in Epidemiology 9 (1).
+<https://doi.org/10.1186/1742-7622-9-9>.
+
 Rogan, Walter J., and Beth Gladen. 1978. “Estimating Prevalence from the
 Results of A Screening Test.” American Journal of Epidemiology 107 (1):
 71–76. <https://doi.org/10.1093/oxfordjournals.aje.a112510>.
@@ -373,6 +385,16 @@ Statistical Society: Series C (Applied Statistics)*, August.
 
 </div>
 
+<div id="ref-Hallal2020">
+
+Hallal, Pedro C, Fernando P Hartwig, Bernardo L Horta, Mariângela F
+Silveira, Claudio J Struchiner, Luı́s P Vidaletti, Nelson A Neumann, et
+al. 2020. “SARS-CoV-2 Antibody Prevalence in Brazil: Results from Two
+Successive Nationwide Serological Household Surveys.” *The Lancet Global
+Health*, September. <https://doi.org/10.1016/s2214-109x(20)30387-9>.
+
+</div>
+
 <div id="ref-Kritsotakis2020">
 
 Kritsotakis, Evangelos I. 2020. “On the Importance of Population-Based
@@ -401,6 +423,15 @@ Optimal Sample Allocation.” *bioRxiv*, May.
 
 </div>
 
+<div id="ref-Lewis2012">
+
+Lewis, Fraser I, and Paul R Torgerson. 2012. “A Tutorial in Estimating
+the Prevalence of Disease in Humans and Animals in the Absence of a Gold
+Standard Diagnostic.” *Emerging Themes in Epidemiology* 9 (1).
+<https://doi.org/10.1186/1742-7622-9-9>.
+
+</div>
+
 <div id="ref-ROGAN1978">
 
 Rogan, Walter J., and Beth Gladen. 1978. “Estimating Prevalence from the

references.bib

@@ -119,3 +119,27 @@ @article{Gelman2020
   title = {Bayesian analysis of tests with unknown specificity and sensitivity},
   journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)}
 }
+
+@article{Lewis2012,
+  doi = {10.1186/1742-7622-9-9},
+  url = {https://doi.org/10.1186/1742-7622-9-9},
+  year = {2012},
+  month = dec,
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {9},
+  number = {1},
+  author = {Fraser I Lewis and Paul R Torgerson},
+  title = {A tutorial in estimating the prevalence of disease in humans and animals in the absence of a gold standard diagnostic},
+  journal = {Emerging Themes in Epidemiology}
+}
+
+@article{Hallal2020,
+  doi = {10.1016/s2214-109x(20)30387-9},
+  url = {https://doi.org/10.1016/s2214-109x(20)30387-9},
+  year = {2020},
+  month = sep,
+  publisher = {Elsevier {BV}},
+  author = {Pedro C Hallal and Fernando P Hartwig and Bernardo L Horta and Mari{\^{a}}ngela F Silveira and Claudio J Struchiner and Lu{\'{\i}}s P Vidaletti and Nelson A Neumann and Lucia C Pellanda and Odir A Dellagostin and Marcelo N Burattini and Gabriel D Victora and Ana M B Menezes and Fernando C Barros and Alu{\'{\i}}sio J D Barros and Cesar G Victora},
+  title = {{SARS}-{CoV}-2 antibody prevalence in Brazil: results from two successive nationwide serological household surveys},
+  journal = {The Lancet Global Health}
+}