From 646c30b65bfcd7109759c4e6904529157543231a Mon Sep 17 00:00:00 2001 From: MoserGitHub <33371420+MoserGitHub@users.noreply.github.com> Date: Mon, 24 Jun 2024 15:14:22 +0200 Subject: [PATCH] Update Sylvain --- 01-SampleSize.qmd | 2 +- ...pleSize_Bayesian_power_basics_examples.qmd | 75 ++ _quarto.yml | 1 + docs/01-SampleSize.html | 8 +- ...leSize_Bayesian_power_basics_examples.html | 656 ++++++++++++++++++ docs/search.json | 57 +- 6 files changed, 796 insertions(+), 3 deletions(-) create mode 100755 01-SampleSize_Bayesian_power_basics_examples.qmd create mode 100644 docs/01-SampleSize_Bayesian_power_basics_examples.html diff --git a/01-SampleSize.qmd b/01-SampleSize.qmd index d16981f..00488e4 100644 --- a/01-SampleSize.qmd +++ b/01-SampleSize.qmd @@ -1,3 +1,3 @@ # Sample size -This section covers examples related to the topic of sample size. \ No newline at end of file +This section covers specific the examples related to the topic of 'sample size'. \ No newline at end of file diff --git a/01-SampleSize_Bayesian_power_basics_examples.qmd b/01-SampleSize_Bayesian_power_basics_examples.qmd new file mode 100755 index 0000000..31e22e6 --- /dev/null +++ b/01-SampleSize_Bayesian_power_basics_examples.qmd @@ -0,0 +1,75 @@ +# External resources and references + +## Peer-reviewed articles + + +- A Review of Bayesian Perspectives on Sample Size Derivation for Confirmatory Trials (2021). \ + + +- Bayesian sample size determination for diagnostic accuracy studies (2022). \ + + +- Bayesian estimation supersedes the t test (2013). \ + + +- The Bayesian New Statistics: Hypothesis testing, estimation, meta-analysis, and power analysis from a Bayesian perspective (2017) + + +- Bayesian and mixed bayesian/likelihood criteria for sample size determination + + + + +## Blog posts + +- Introduction to bayesian clinical trial designs (detailed - including R code examples)\ + + + +- Introduction to bayesian sample size calculation (including R code example) + + + +- Introduction to bayesian "power" and comparison with frequentist approaches (including R code example):\ + + + +- Brief introduction to bayesian power - including comparison with frequentist terms:\ + + +- Stopping rules using bayesian analyses + + + + +## R packages and online tools + +- **Package ‘SampleSizeProportions’ (2023)** \ +Calculating Sample Size Requirements when Estimating the Difference Between Two Binomial Proportions + + +- **Package ‘BayesPPD’ (2021)** \ +Bayesian sample size determination using the power and normalized power prior for generalized linear models + + +- **Package ‘BayesPPDSurv’ (2024)** \ +Bayesian power/type I error calculation and model fitting using the power prior and the normalized power prior for proportional hazards models with piecewise constant hazard. + +- **Package ‘BayesCTDesign’ (2021)** \ +Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data + + +- **Package ‘BayesFactor’ (2024)** \ +A suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression. + + +- **trialdesign.org** \ +An online resource platform for several phase-I and phase-II designs. + + +## Author {-} + +Sylvain Losdat, PhD\ +Department of Clinical Research\ +University of Bern\ +3012 Bern, Switzerland \ No newline at end of file diff --git a/_quarto.yml b/_quarto.yml index cd3664c..d074840 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -15,6 +15,7 @@ book: chapters: - 01-SampleSize-BinaryOutcome.qmd - 01-SampleSize-ContinuousOutcome.qmd + - 01-SampleSize_Bayesian_power_basics_examples.qmd - references.qmd format: diff --git a/docs/01-SampleSize.html b/docs/01-SampleSize.html index e3f8a04..8fd9256 100644 --- a/docs/01-SampleSize.html +++ b/docs/01-SampleSize.html @@ -123,6 +123,12 @@

Sample size

2  Two-arm study with a continuous primary outcome + +
  • +
    + + 3  External resources and references +
    • @@ -147,7 +153,7 @@

    Sample size

    -

    This section covers examples related to the topic of sample size.

    +

    This section covers specific the examples of the topic of ‘sample size’.

    diff --git a/docs/01-SampleSize_Bayesian_power_basics_examples.html b/docs/01-SampleSize_Bayesian_power_basics_examples.html new file mode 100644 index 0000000..623f901 --- /dev/null +++ b/docs/01-SampleSize_Bayesian_power_basics_examples.html @@ -0,0 +1,656 @@ + + + + + + + + + +Bayesian Toolbox – 3  External resources and references + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + +
    + +
    +
    +
    +

    3  External resources and references

    +
    +
    + + +
    + + + + +
    + + +
    + + +
    + + + +
    + + + + + +
    +

    3.1 Peer-reviewed articles

    + +
    +
    +

    3.2 Blog posts

    + +
    +
    +

    3.3 R packages and online tools

    + +
    +
    +

    Author

    +

    Sylvain Losdat, PhD
    +Department of Clinical Research
    +University of Bern
    +3012 Bern, Switzerland

    + + +
    + +
    + + +
    + + + + + \ No newline at end of file diff --git a/docs/search.json b/docs/search.json index c6cecef..3e90a2c 100644 --- a/docs/search.json +++ b/docs/search.json @@ -293,9 +293,64 @@ "href": "01-SampleSize.html", "title": "Sample size", "section": "", - "text": "This section covers examples related to the topic of sample size.", + "text": "This section covers specific the examples of the topic of ‘sample size’.", "crumbs": [ "Sample size" ] + }, + { + "objectID": "01-SampleSize_Bayesian_power_basics_examples.html", + "href": "01-SampleSize_Bayesian_power_basics_examples.html", + "title": "3  External resources and references", + "section": "", + "text": "3.1 Peer-reviewed articles", + "crumbs": [ + "Sample size", + "3  External resources and references" + ] + }, + { + "objectID": "01-SampleSize_Bayesian_power_basics_examples.html#peer-reviewed-articles", + "href": "01-SampleSize_Bayesian_power_basics_examples.html#peer-reviewed-articles", + "title": "3  External resources and references", + "section": "", + "text": "A Review of Bayesian Perspectives on Sample Size Derivation for Confirmatory Trials (2021).\nhttps://pubmed.ncbi.nlm.nih.gov/34992303/\nBayesian sample size determination for diagnostic accuracy studies (2022).\nhttps://onlinelibrary.wiley.com/doi/10.1002/sim.9393\nBayesian estimation supersedes the t test (2013).\nhttps://psycnet.apa.org/doiLanding?doi=10.1037%2Fa0029146\nThe Bayesian New Statistics: Hypothesis testing, estimation, meta-analysis, and power analysis from a Bayesian perspective (2017) https://link.springer.com/article/10.3758/s13423-016-1221-4\nBayesian and mixed bayesian/likelihood criteria for sample size determination https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0258(19970415)16:7%3C769::AID-SIM495%3E3.0.CO;2-V", + "crumbs": [ + "Sample size", + "3  External resources and references" + ] + }, + { + "objectID": "01-SampleSize_Bayesian_power_basics_examples.html#blog-posts", + "href": "01-SampleSize_Bayesian_power_basics_examples.html#blog-posts", + "title": "3  External resources and references", + "section": "3.2 Blog posts", + "text": "3.2 Blog posts\n\nIntroduction to bayesian clinical trial designs (detailed - including R code examples)\nhttps://hbiostat.org/bayes/bet/design\nIntroduction to bayesian sample size calculation (including R code example) https://www.rdatagen.net/post/2021-06-01-bayesian-power-analysis/\nIntroduction to bayesian “power” and comparison with frequentist approaches (including R code example):\nhttps://solomonkurz.netlify.app/blog/bayesian-power-analysis-part-i/ https://solomonkurz.netlify.app/blog/bayesian-power-analysis-part-ii/\nBrief introduction to bayesian power - including comparison with frequentist terms:\nhttps://anatomisebiostats.com/biostatistics-blog/bayesian-sample-size-estimation-in-clinical-study-design-rtcs/\nStopping rules using bayesian analyses https://statmodeling.stat.columbia.edu/2014/02/13/stopping-rules-bayesian-analysis/ http://varianceexplained.org/r/bayesian-ab-testing/", + "crumbs": [ + "Sample size", + "3  External resources and references" + ] + }, + { + "objectID": "01-SampleSize_Bayesian_power_basics_examples.html#r-packages-and-online-tools", + "href": "01-SampleSize_Bayesian_power_basics_examples.html#r-packages-and-online-tools", + "title": "3  External resources and references", + "section": "3.3 R packages and online tools", + "text": "3.3 R packages and online tools\n\nPackage ‘SampleSizeProportions’ (2023)\nCalculating Sample Size Requirements when Estimating the Difference Between Two Binomial Proportions https://cran.rstudio.com/web/packages/SampleSizeProportions/index.html\nPackage ‘BayesPPD’ (2021)\nBayesian sample size determination using the power and normalized power prior for generalized linear models https://rdrr.io/cran/BayesPPD/man/BayesPPD-package.html\nPackage ‘BayesPPDSurv’ (2024)\nBayesian power/type I error calculation and model fitting using the power prior and the normalized power prior for proportional hazards models with piecewise constant hazard. https://cran.r-project.org/web/packages/BayesPPDSurv/index.html\nPackage ‘BayesCTDesign’ (2021)\nTwo Arm Bayesian Clinical Trial Design with and Without Historical Control Data https://cran.r-project.org/web/packages/BayesCTDesign/index.html\nPackage ‘BayesFactor’ (2024)\nA suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression. https://cran.r-project.org/web/packages/BayesFactor/index.html\ntrialdesign.org\nAn online resource platform for several phase-I and phase-II designs. https://www.trialdesign.org", + "crumbs": [ + "Sample size", + "3  External resources and references" + ] + }, + { + "objectID": "01-SampleSize_Bayesian_power_basics_examples.html#author", + "href": "01-SampleSize_Bayesian_power_basics_examples.html#author", + "title": "3  External resources and references", + "section": "Author", + "text": "Author\nSylvain Losdat, PhD\nDepartment of Clinical Research\nUniversity of Bern\n3012 Bern, Switzerland", + "crumbs": [ + "Sample size", + "3  External resources and references" + ] } ] \ No newline at end of file