move .csl to inst, update readme with references

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")`'
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -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)
 <!-- badges: end -->
 
-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

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
+
+<div id="refs" class="references csl-bib-body hanging-indent">
+
+<div id="ref-bretz2005" class="csl-entry">
+
+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.
+<https://doi.org/10.1111/j.1541-0420.2005.00344.x>.
+
+</div>
+
+<div id="ref-pinheiro2014" class="csl-entry">
+
+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.
+<https://doi.org/10.1002/sim.6052>.
+
+</div>
+
+</div>

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}

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}

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}

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,

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}

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}