diff --git a/README.Rmd b/README.Rmd index 2995362..9fc82b0 100644 --- a/README.Rmd +++ b/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. diff --git a/README.md b/README.md index 1cc44e0..dbaa6ac 100644 --- a/README.md +++ b/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. . +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. . + 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. . +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). +. + Rogan, Walter J., and Beth Gladen. 1978. “Estimating Prevalence from the Results of A Screening Test.” American Journal of Epidemiology 107 (1): 71–76. . @@ -373,6 +385,16 @@ Statistical Society: Series C (Applied Statistics)*, August. +
+ +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. . + +
+
Kritsotakis, Evangelos I. 2020. “On the Importance of Population-Based @@ -401,6 +423,15 @@ Optimal Sample Allocation.” *bioRxiv*, May.
+
+ +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). +. + +
+
Rogan, Walter J., and Beth Gladen. 1978. “Estimating Prevalence from the diff --git a/docs/articles/howto-reprex.html b/docs/articles/howto-reprex.html index 6074f99..1a45b0c 100644 --- a/docs/articles/howto-reprex.html +++ b/docs/articles/howto-reprex.html @@ -455,7 +455,7 @@

} toc() -#> 367.84 sec elapsed +#> 241 sec elapsed outcome_01_adj <- out %>% mutate(rowname=as.numeric(rowname)) %>% @@ -530,35 +530,35 @@

E outcome_one positive -75.9% (65.3 - 84.6) -78.9% ( 67.5 - 87) -83.157% (65.90 - 95.5) +75.9 (65.3 - 84.6) +78.9 ( 67.5 - 87) +83.140 (65.87 - 95.5) covariate_01 H outcome_one positive -25.0% ( 8.7 - 49.1) -14.8% ( 3.8 - 44) -0.421% ( 0.28 - 29.9) +25.0 ( 8.7 - 49.1) +14.8 ( 3.8 - 44) +0.423 ( 0.27 - 29.8) covariate_01 M outcome_one positive -65.2% (42.7 - 83.6) -44.8% ( 16.0 - 78) -31.544% ( 0.40 - 81.1) +65.2 (42.7 - 83.6) +44.8 ( 16.0 - 78) +31.450 ( 0.41 - 81.1) covariate_01 E outcome_two positive -6.0% ( 2.0 - 13.5) -18.2% ( 5.0 - 49) +6.0 ( 2.0 - 13.5) +18.2 ( 5.0 - 49) NA @@ -566,8 +566,8 @@

H outcome_two positive -5.0% ( 0.1 - 24.9) -7.7% ( 0.9 - 44) +5.0 ( 0.1 - 24.9) +7.7 ( 0.9 - 44) NA @@ -575,17 +575,17 @@

Yes outcome_one positive -93.3% (85.9 - 97.5) -96.7% ( 88.2 - 99) -99.900% (97.02 - 100.0) +93.3 (85.9 - 97.5) +96.7 ( 88.2 - 99) +99.903 (97.00 - 100.0) covariate_02 No outcome_two positive -8.1% ( 1.7 - 21.9) -21.8% ( 6.7 - 52) +8.1 ( 1.7 - 21.9) +21.8 ( 6.7 - 52) NA @@ -593,8 +593,8 @@

Yes outcome_two positive -3.4% ( 0.7 - 9.5) -9.1% ( 2.1 - 32) +3.4 ( 0.7 - 9.5) +9.1 ( 2.1 - 32) NA @@ -602,8 +602,8 @@

positive covariate_02 Yes -100.0% (95.7 - 100.0) -100.0% (100.0 - 100) +100.0 (95.7 - 100.0) +100.0 (100.0 - 100) NA @@ -611,8 +611,8 @@

positive covariate_02 No -50.0% (11.8 - 88.2) -54.9% ( 29.4 - 78) +50.0 (11.8 - 88.2) +54.9 ( 29.4 - 78) NA @@ -620,8 +620,8 @@

positive covariate_02 Yes -50.0% (11.8 - 88.2) -45.1% ( 21.9 - 71) +50.0 (11.8 - 88.2) +45.1 ( 21.9 - 71) NA diff --git a/docs/index.html b/docs/index.html index 41d2ea8..8c14605 100644 --- a/docs/index.html +++ b/docs/index.html @@ -259,7 +259,7 @@

Feel free to fill an issue or contribute with your functions or workflows in a pull request.

Here are a list of publications with interesting approaches using R:

    -

  • Silveira et al. (2020) in the strategy 3 analysed the survey accounting for sampling design and test validity using parametric bootstraping.

    • +

  • Silveira et al. (2020) and Hallal et al. (2020) analysed a serological survey accounting for sampling design and test validity using parametric bootstraping, following Lewis and Torgerson (2012).

  • Flor et al. (2020) implemented a lot of frequentist and bayesian methods for test with known sensitivity and specificity. Code is available here.

  • Gelman and Carpenter (2020) also applied Bayesian inference with hierarchical regression and post-stratification to account for test uncertainty with unknown specificity and sensitivity. Here a case-study.

@@ -304,9 +304,11 @@

Diggle, Peter J. 2011. “Estimating Prevalence Using an Imperfect Test.” Epidemiology Research International 2011: 1–5. https://doi.org/10.1155/2011/608719.

Flor, Matthias, Michael Weiß, Thomas Selhorst, Christine Müller-Graf, and Matthias Greiner. 2020. “Comparison of Bayesian and Frequentist Methods for Prevalence Estimation Under Misclassification.” BMC Public Health 20 (1). https://doi.org/10.1186/s12889-020-09177-4.

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.

Takahashi, Saki, Bryan Greenhouse, and Isabel Rodríguez-Barraquer. 2020. “Are SARS-CoV-2 seroprevalence estimates biased?” The Journal of Infectious Diseases, August. https://doi.org/10.1093/infdis/jiaa523.

@@ -352,6 +354,17 @@

+
+ +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. . + + +
+
Kritsotakis, Evangelos I. 2020. “On the Importance of Population-Based @@ -383,6 +396,16 @@

+
+ +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). +. + + +
+
Rogan, Walter J., and Beth Gladen. 1978. “Estimating Prevalence from the diff --git a/docs/reference/figures/README-unnamed-chunk-10-1.png b/docs/reference/figures/README-unnamed-chunk-10-1.png index 39dfc0d..74beebb 100644 Binary files a/docs/reference/figures/README-unnamed-chunk-10-1.png and b/docs/reference/figures/README-unnamed-chunk-10-1.png differ diff --git a/docs/reference/figures/README-unnamed-chunk-14-1.png b/docs/reference/figures/README-unnamed-chunk-14-1.png index 1541450..4e63f6c 100644 Binary files a/docs/reference/figures/README-unnamed-chunk-14-1.png and b/docs/reference/figures/README-unnamed-chunk-14-1.png differ diff --git a/docs/reference/unite_dotwhiskers.html b/docs/reference/unite_dotwhiskers.html index 7c4edb6..7c8649c 100644 --- a/docs/reference/unite_dotwhiskers.html +++ b/docs/reference/unite_dotwhiskers.html @@ -122,7 +122,8 @@

Miscellaneous function

unite_dotwhiskers(data, variable_dot, variable_low, variable_upp,
-  digits_dot = 3, digits_low = 2, digits_upp = 3)
+  digits_dot = 3, digits_low = 2, digits_upp = 3,
+  decimal_to_percent = TRUE)
 
 serosvy_extract_posterior(data, variable)
@@ -157,6 +158,10 @@

Arg digits_upp

digits of upper interval to round

+ + decimal_to_percent +

logical to multiply values by 100. TRUE by default.

+ variable

variable to extract from posterior distributions

diff --git a/man/figures/README-unnamed-chunk-10-1.png b/man/figures/README-unnamed-chunk-10-1.png index 39dfc0d..74beebb 100644 Binary files a/man/figures/README-unnamed-chunk-10-1.png and b/man/figures/README-unnamed-chunk-10-1.png differ diff --git a/man/figures/README-unnamed-chunk-14-1.png b/man/figures/README-unnamed-chunk-14-1.png index 1541450..4e63f6c 100644 Binary files a/man/figures/README-unnamed-chunk-14-1.png and b/man/figures/README-unnamed-chunk-14-1.png differ diff --git a/references.bib b/references.bib index 31de3ce..93d24f3 100644 --- a/references.bib +++ b/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} +}