diff --git a/README.Rmd b/README.Rmd index 37b5391..ea257c3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,5 +1,8 @@ --- output: github_document +bibliography: '`r system.file("REFERENCES.bib", package = "DoseFinding")`' +link-citations: yes +csl: '`r system.file("american-statistical-association.csl", package = "DoseFinding")`' --- @@ -21,8 +24,7 @@ knitr::opts_chunk$set( [![R-CMD-check](https://github.com/openpharma/DoseFinding/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/openpharma/DoseFinding/actions/workflows/R-CMD-check.yaml) -The DoseFinding package provides functions for the design and analysis of dose-finding experiments (for example pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models, a combination of testing and dose-response modelling and calculating optimal designs, -both for normal and general response variable. +The DoseFinding package provides functions for the design and analysis of dose-finding experiments (for example pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models, a combination of testing and dose-response modelling and calculating optimal designs, both for normal and general response variable. In addition the package can be used to implement the MCP-Mod procedure, a combination of testing and dose-response modelling (@bretz2005, @pinheiro2014). ## Installation @@ -76,3 +78,5 @@ plot(fmodels, plotTD = TRUE, Delta = 0.2) weights <- rep(1/4, 4) optDesign(fmodels, weights, Delta=0.2, designCrit="TD") ``` + +## References diff --git a/README.md b/README.md index ced6d2a..49a34a4 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,10 @@ of dose-finding experiments (for example pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models, a combination of testing and dose-response modelling and calculating optimal designs, both for normal -and general response variable. +and general response variable. In addition the package can be used to +implement the MCP-Mod procedure, a combination of testing and +dose-response modelling (Bretz et al. ([2005](#ref-bretz2005)), Pinheiro +et al. ([2014](#ref-pinheiro2014))). ## Installation @@ -107,3 +110,27 @@ optDesign(fmodels, weights, Delta=0.2, designCrit="TD") #> 0 10 25 50 100 150 #> 0.34960 0.09252 0.00366 0.26760 0.13342 0.15319 ``` + +## References + +
+ +
+ +Bretz, F., Pinheiro, J. C., and Branson, M. (2005), “Combining multiple +comparisons and modeling techniques in dose-response studies,” +*Biometrics*, Wiley Online Library, 61, 738–748. +. + +
+ +
+ +Pinheiro, J., Bornkamp, B., Glimm, E., and Bretz, F. (2014), +“Model-based dose finding under model uncertainty using general +parametric models,” *Statistics in Medicine*, 33, 1646–1661. +. + +
+ +
diff --git a/vignettes/american-statistical-association.csl b/inst/american-statistical-association.csl similarity index 100% rename from vignettes/american-statistical-association.csl rename to inst/american-statistical-association.csl diff --git a/man/figures/README-example1-1.png b/man/figures/README-example1-1.png index 854d7c3..4d583b0 100644 Binary files a/man/figures/README-example1-1.png and b/man/figures/README-example1-1.png differ diff --git a/man/figures/README-example3-1.png b/man/figures/README-example3-1.png index 700bbee..7122eb5 100644 Binary files a/man/figures/README-example3-1.png and b/man/figures/README-example3-1.png differ diff --git a/vignettes/analysis_normal.Rmd b/vignettes/analysis_normal.Rmd index 989c563..67847de 100644 --- a/vignettes/analysis_normal.Rmd +++ b/vignettes/analysis_normal.Rmd @@ -2,7 +2,7 @@ title: "Continuous data MCP-Mod" output: rmarkdown::html_vignette bibliography: '`r system.file("REFERENCES.bib", package = "DoseFinding")`' -csl: american-statistical-association.csl +csl: '`r system.file("american-statistical-association.csl", package = "DoseFinding")`' link-citations: yes vignette: > %\VignetteIndexEntry{Analysis template MCP-Mod for continuous data} diff --git a/vignettes/binary_data.Rmd b/vignettes/binary_data.Rmd index 98a15c4..0bc73b2 100644 --- a/vignettes/binary_data.Rmd +++ b/vignettes/binary_data.Rmd @@ -3,7 +3,7 @@ title: "Binary Data MCP-Mod" output: rmarkdown::html_vignette bibliography: '`r system.file("REFERENCES.bib", package = "DoseFinding")`' link-citations: yes -csl: american-statistical-association.csl +csl: '`r system.file("american-statistical-association.csl", package = "DoseFinding")`' vignette: > %\VignetteIndexEntry{Design and analysis template MCP-Mod for binary data} %\VignetteEngine{knitr::rmarkdown} diff --git a/vignettes/faq.Rmd b/vignettes/faq.Rmd index fdca21c..53b31ba 100644 --- a/vignettes/faq.Rmd +++ b/vignettes/faq.Rmd @@ -6,7 +6,7 @@ output: toc_depth: 2 bibliography: '`r system.file("REFERENCES.bib", package = "DoseFinding")`' link-citations: yes -csl: american-statistical-association.csl +csl: '`r system.file("american-statistical-association.csl", package = "DoseFinding")`' vignette: > %\VignetteIndexEntry{Frequently Asked Questions for MCP-Mod} %\VignetteEngine{knitr::rmarkdown} diff --git a/vignettes/longitudinal_data.Rmd b/vignettes/longitudinal_data.Rmd index 2a116fd..04de7fc 100644 --- a/vignettes/longitudinal_data.Rmd +++ b/vignettes/longitudinal_data.Rmd @@ -3,7 +3,7 @@ title: "Longitudinal Data MCP-Mod" output: rmarkdown::html_vignette bibliography: '`r system.file("REFERENCES.bib", package = "DoseFinding")`' link-citations: yes -csl: american-statistical-association.csl +csl: '`r system.file("american-statistical-association.csl", package = "DoseFinding")`' vignette: > %\VignetteIndexEntry{Design and analysis template MCP-Mod for longitudinal data} %\VignetteEngine{knitr::rmarkdown} @@ -340,7 +340,7 @@ S01 <- diag(resultRepeated$sigma^2 / n_final) # Predictive power: predPower <- powMCTInterim( - contMat = contMat,, + contMat = contMat, mu_0t = resultRepeated$mu0t, S_0t = resultRepeated$S0t, S_01 = S01, diff --git a/vignettes/mult_regimen.Rmd b/vignettes/mult_regimen.Rmd index 17ef06a..a24aafd 100644 --- a/vignettes/mult_regimen.Rmd +++ b/vignettes/mult_regimen.Rmd @@ -3,7 +3,7 @@ title: "Multiple Regimen MCP-Mod" output: rmarkdown::html_vignette bibliography: '`r system.file("REFERENCES.bib", package = "DoseFinding")`' link-citations: yes -csl: american-statistical-association.csl +csl: '`r system.file("american-statistical-association.csl", package = "DoseFinding")`' vignette: > %\VignetteIndexEntry{Analysis template: MCP-Mod with multiple regimen} %\VignetteEngine{knitr::rmarkdown} diff --git a/vignettes/overview.Rmd b/vignettes/overview.Rmd index 0a8a44c..8aedc3c 100644 --- a/vignettes/overview.Rmd +++ b/vignettes/overview.Rmd @@ -4,7 +4,7 @@ output: rmarkdown::html_vignette: bibliography: '`r system.file("REFERENCES.bib", package = "DoseFinding")`' link-citations: yes -csl: american-statistical-association.csl +csl: '`r system.file("american-statistical-association.csl", package = "DoseFinding")`' vignette: > %\VignetteIndexEntry{Overview DoseFinding package} %\VignetteEngine{knitr::rmarkdown}