115 add website content (#118)

Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>

DESCRIPTION

@@ -3,12 +3,13 @@ Package: phase1b
 Title: Calculations for decisions on Phase 1b clinical trials
 Version: 1.0.0
 Authors@R: c(
-    person("Daniel", "Sabanes Bove", , "daniel.sabanes_bove@roche.com", role = c("aut", "cre")),
+    person("Daniel", "Sabanes Bove", , "daniel@rconis.com", role = c("aut", "cre")),
     person("Markus", "Elze", , "markus.elze@roche.com", role = "aut"),
     person("Tony", "Pourmohamad", , "pourmoht@gene.com", role = "aut"),
     person("Jiawen", "Zhu", , "zhu.jiawen@gene.com", role = "aut"),
     person("James", "Lymp", role = "aut"),
     person("Anastasia", "Teterina", , "anastasia.teterina@roche.com", role = "aut"),
+    person("Audrey", "Yeo", , "audrey.yeo@roche.com", role = c("aut")),
     person("F. Hoffmann-La Roche Ltd", role = c("cph", "fnd"))
   )
 Description: The phase1b R package is intended to be used when conducting

R/plotBeta.R

@@ -2,19 +2,19 @@
 #'
 #' This function will plot the PDF of a beta distribution
 #'
-#' @inheritParams dbetabinom
 #' @typed alpha : number
 #'  first parameter of the Beta distribution
 #' @typed beta : number
 #'  second parameter of the Beta distribution
+#'
 #' @return A beta distribution density plot
 #'
 #' @importFrom graphics axis
 #'
 #' @example examples/plotBeta.R
 #' @export
 #' @keywords graphics
-plotBeta <- function(alpha, beta, ...) {
+plotBeta <- function(alpha, beta) {
   x_support <- seq(from = 0, to = 1, length = 1000)
   data <- data.frame(
     grid = x_support,

README.md

@@ -1,3 +1,59 @@
-# phase1b
+# `phase1b`
 
-Short description of the package
+<!-- markdownlint-disable -->
+
+<img src="man/figures/hex_logo3.png" align = "right" alt="hex logo" style="display: inline-block; width:200px; margin: 0 auto auto auto;" />
+<!-- markdownlint-enable -->
+
+The `phase1b` package implements a Bayesian approach to decision making
+in early development clinical trials. As a background, the main purpose
+of early trials is to determine whether a novel treatment demonstrates
+sufficient safety and efficacy signals to warrant further investment
+(Lee & Liu, 2008).
+
+The new R package `phase1b` is a flexible toolkit that calculates many
+properties to this end, especially in the oncology therapeutic area. The
+primary focus of this package is on binary endpoints. The benefit of a
+Bayesian approach is the possibility to account for prior data (Thall &
+Simon, 1994) in that a new drug may have shown some signals of efficacy
+owing to its proposed mode of action, or similar activity based on prior
+data. The concept of the `phase1b` package is to evaluate the posterior
+probability that the response rate with a novel drug is better than with
+the current standard of care treatment in early phase trials such as
+Phase I.
+
+The `phase1b` package provides a facility for early development study
+teams to decide on further development of a drug either through
+designing for phase 2 or 3, or expansion cohorts. The prior distribution
+can incorporate any previous data via mixtures of beta distributions.
+Furthermore, based on an assumed true response rate if the novel drug
+was administered in the wider population, the package calculates the
+frequentist probability that a current clinical trial would be stopped
+for efficacy or futility conditional on true values of the response,
+otherwise known as operating characteristics.
+
+The intended user is the early clinical trial statistician in the design
+and interim stage of their study and offers a flexible approach to
+setting priors and weighting.
+
+## Installation
+
+### Development
+
+You can install the development version of `phase1b` from
+[GitHub](https://github.com/) with:
+
+```r
+devtools::install_github("https://github.com/Genentech/phase1b/", force = TRUE)
+library(phase1b)
+```
+
+## Getting Started
+
+An introductory vignette is currently being prepared. Use the help
+function in your console to access the documentation.
+
+## Citing `phase1b`
+
+To cite `phase1b` please see
+[here](https://genentech.github.io/phase1b/main/authors.html#citation).

README.rmd

@@ -0,0 +1,36 @@
+---
+output: github_document
+---
+
+# `phase1b`
+<!-- markdownlint-disable -->
+<img src="man/figures/hex_logo3.png" align = "right" alt="hex logo" style="display: inline-block; width:200px; margin: 0 auto auto auto;" />
+<!-- markdownlint-enable -->
+
+The `phase1b` package implements a Bayesian approach to decision making in early development clinical trials.
+As a background, the main purpose of early trials is to determine whether a novel treatment demonstrates sufficient safety and efficacy signals to warrant further investment (Lee & Liu, 2008).
+
+The new R package `phase1b` is a flexible toolkit that calculates many properties to this end, especially in the oncology therapeutic area. The primary focus of this package is on binary endpoints. The benefit of a Bayesian approach is the possibility to account for prior data (Thall & Simon, 1994) in that a new drug may have shown some signals of efficacy owing to its proposed mode of action, or similar activity based on prior data. The concept of the `phase1b` package is to evaluate the posterior probability that the response rate with a novel drug is better than with the current standard of care treatment in early phase trials such as Phase I.
+
+The `phase1b` package provides a facility for early development study teams to decide on further development of a drug either through designing for phase 2 or 3, or expansion cohorts. The prior distribution can incorporate any previous data via mixtures of beta distributions. Furthermore, based on an assumed true response rate if the novel drug was administered in the wider population, the package calculates the frequentist probability that a current clinical trial would be stopped for efficacy or futility conditional on true values of the response, otherwise known as operating characteristics.
+
+The intended user is the early clinical trial statistician in the design and interim stage of their study and offers a flexible approach to setting priors and weighting.
+
+## Installation
+
+### Development
+
+You can install the development version of `phase1b` from [GitHub](https://github.com/) with:
+
+``` r
+devtools::install_github("https://github.com/Genentech/phase1b/", force = TRUE)
+library(phase1b)
+```
+
+## Getting Started
+
+An introductory vignette is currently being prepared. Use the help function in your console to access the documentation.
+
+## Citing `phase1b`
+
+To cite `phase1b` please see [here](https://genentech.github.io/phase1b/main/authors.html#citation).

inst/REFERENCES.bib

@@ -3,7 +3,7 @@ @book{held-sabanes-2015
   author={Held, Leonhard and {Saban\'es Bov\'e}, Daniel},
   publisher={Springer},
   year={2015},
-  url={http://www.springer.com/us/book/9783642378867}
+  url={https://link.springer.com/book/10.1007/978-3-642-37887-4}
 }
 
 @book{berry:2011,

inst/WORDLIST

@@ -1,3 +1,4 @@
+al
 analysed
 apriori
 bA
@@ -23,6 +24,7 @@ bI
 Binom
 binom
 Biometrics
+Biostatistics
 bL
 bLambda
 blambda
@@ -31,15 +33,16 @@ bmu
 boldsymbol
 bOmega
 bomega
-Bov<U+00E9>
 Bove
+Bové
 bPhi
 bphi
 bpi
 bPsi
 bpsi
 bR
 br
+Branson
 bS
 bs
 bsig
@@ -63,6 +66,7 @@ comparator
 conjugacy
 Cov
 cov
+CRC
 cutB
 cutW
 dec
@@ -77,6 +81,7 @@ diffience
 doi
 DoR
 dP
+Dunson
 dW
 dw
 dX
@@ -86,37 +91,48 @@ ee
 Elze
 eq
 estunated
+et
 EVAL
 ExpectedN
 ExpectedNactive
 ExpectedNcontrol
 frac
 funder
+gelman
+Gelman
 generalizable
 geq
 grayzone
 grey
+Gsponer
 hier
 Hoffmann
+http
+https
 hyoithesis
 hyperprior
 increasement
 inefficacious
 infty
 Integrand
 integrations
+isbn
 Jiawen
 kernal
+lccn
 LciU
 ldots
+Leonhard
 leq
 Liu
+ller
 Lymp
 Markus
 mathbb
 mathbf
 mathcal
 mbox
+Neuenschwander
 newcommand
 Nmax
 NmaxControl
@@ -136,6 +152,7 @@ ocPredprob
 ocPredprobDist
 ocRctPostprobDist
 ocRctPredprobDist
+onlinelibrary
 params
 parX
 parY
@@ -184,8 +201,9 @@ renewcommand
 reproducibility
 responder
 responders
-Saban<U+00E9>s
 Sabanes
+sabanes
+Sabanés
 SampleSize
 SampleSizeActive
 SampleSizeControl
@@ -195,6 +213,8 @@ simplifiedWeightedBayes
 simplifiedWeightedBayesone
 simplifiedWeightedBayestwo
 specialised
+springer
+Springer
 sumbetadiff
 summerize
 summerizes
@@ -223,10 +243,14 @@ USUBJID
 VAD
 vanillaBayes
 vanillaPP
+Vehtari
 WeightedBayes
 weightedBetaPrior
+wiley
 xL
 xS
 xU
 XYZ
+Yeo
 Zhu
+ZXL

vignettes/introduction.Rmd

@@ -10,7 +10,7 @@ author:
   - name: Jiawen Zhu
     email: zhu.jiawen@gene.com
   - name: Daniel Sabanes Bove
-    email: daniel.sabanes_bove@roche.com
+    email: daniel@rconis.com
 output:
   bookdown::html_document2:
           theme: "spacelab"
@@ -166,8 +166,7 @@ help(package = "phase1b")
 
 A list of functions will be displayed and you can learn more about each function,
 and see examples of its use, by clicking on its corresponding link.
-Note that this will easiest work in R-Studio
-((https://www.rstudio.com/products/rstudio/download/)), which
+Note that this will easiest work in [R-Studio](https://posit.co/download/rstudio-desktop/), which
 is the recommended software for editing and using R.
 
 # Methods and Models {#methods}
@@ -665,12 +664,12 @@ ex1_prior_myplot_cap <- paste(
 ```
 
 ```{r ex1_prior_plotBeta, echo=TRUE, fig.cap = ex1_prior_myplot_cap}
-plotBeta(alpha = 75, beta = 75, col = "darkgrey", ylim = c(0, 10), xlab = "PET-CR Rate", lwd = 2)
+plotBeta(alpha = 75, beta = 75)
 ```
 
 For the Novel combination, the following posterior has been updated.
 ```{r ex1_prior_plotBeta2, fig.cap = ex1_prior_myplot_cap}
-plotBeta(5.75, 4.25, col = "deepskyblue", ylim = c(0, 10), lwd = 2, xlab = "")
+plotBeta(alpha = 5.75, beta = 4.25)
 ```