From 57f3515a4f4a784cee52b2815d3715e70b8e7afd Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Mon, 2 Feb 2026 17:43:38 +0100 Subject: [PATCH] move .csl to inst, update readme with references --- README.Rmd | 8 +++-- README.md | 29 +++++++++++++++++- .../american-statistical-association.csl | 0 man/figures/README-example1-1.png | Bin 7520 -> 7523 bytes man/figures/README-example3-1.png | Bin 7865 -> 7866 bytes vignettes/analysis_normal.Rmd | 2 +- vignettes/binary_data.Rmd | 2 +- vignettes/faq.Rmd | 2 +- vignettes/longitudinal_data.Rmd | 4 +-- vignettes/mult_regimen.Rmd | 2 +- vignettes/overview.Rmd | 2 +- 11 files changed, 41 insertions(+), 10 deletions(-) rename {vignettes => inst}/american-statistical-association.csl (100%) 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. +. + +
+ +
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