Update references to book, updates for roxygen

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: voi
 Title: Expected Value of Information 
-Version: 1.0.2
-Date: 2023-11-27
+Version: 1.0.3
+Date: 2024-02-17
 Authors@R: 
     c(person(given = "Christopher", family = "Jackson",role = c("aut", "cre"),email = "chris.jackson@mrc-bsu.cam.ac.uk"),
 	   person(given = "Anna", family = "Heath", role = c("aut"), email = "anna.heath@sickkids.ca"),
@@ -10,15 +10,15 @@ Authors@R:
 	   person(given="Kofi Placid", family="Adragni", role="ctb", comment="Author of code taken from the ldr package"),
 	   person(given="Andrew", family="Raim", role="ctb",comment="Author of code taken from the ldr package")
 	   )
-Description: Methods to calculate the expected value of information from a decision-analytic model.  This includes the expected value of perfect information (EVPI), partial perfect information (EVPPI) and sample information (EVSI), and the expected net benefit of sampling (ENBS).  A range of alternative computational methods are provided under the same user interface.  See Jackson et al. (2022) <doi:10.1146/annurev-statistics-040120-010730>.
+Description: Methods to calculate the expected value of information from a decision-analytic model.  This includes the expected value of perfect information (EVPI), partial perfect information (EVPPI) and sample information (EVSI), and the expected net benefit of sampling (ENBS).  A range of alternative computational methods are provided under the same user interface.  See Heath et al. (2024) <doi:10.1201/9781003156109>, Jackson et al. (2022) <doi:10.1146/annurev-statistics-040120-010730>.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Depends: R (>= 3.5.0)
 VignetteBuilder: knitr
 Imports: mgcv, earth, mvtnorm, progress, dbarts, posterior, ggplot2, gridExtra, Matrix
 Suggests: testthat, BCEA, INLA, splancs, sf, knitr, rmarkdown, rjags, truncnorm, scales, dplyr, heemod
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Roxygen: list(markdown = TRUE)
 URL: https://chjackson.github.io/voi/
 BugReports: https://github.com/chjackson/voi/issues

NEWS.md

@@ -1,3 +1,8 @@
+# Version 1.0.3
+
+* Citations to published book ([Heath et al](https://doi.org/10.1201/9781003156109)) added.
+
+
 # Version 1.0.2
 
 * Fix for test of reference option

R/evppi.R

@@ -92,7 +92,9 @@
 ##' a posterior standard deviation).  These represent uncertainty about the
 ##' parameters of the fitted regression model, and will naturally be lower when
 ##' more simulations from the decision model are used to fit it.  They do not
-##' represent uncertainty about the structure of the regression model,
+##' represent uncertainty about the structure of the regression model, and are
+##' also typically small in the context of uncertainties arising from
+##' converting individual-level to population VoI.
 ##'
 ##' @param B Number of parameter replicates for calculating the standard error.
 ##' Only applicable to \code{method="gam"}.  For \code{method="bart"} the
@@ -208,6 +210,8 @@
 #'   
 ##' @references
 ##'
+##' Heath, A., Kunst, N., & Jackson, C. (eds.). (2024). Value of Information for Healthcare Decision-Making. CRC Press.
+##'
 ##' Strong, M., Oakley, J. E., & Brennan, A. (2014). Estimating multiparameter
 ##' partial expected value of perfect information from a probabilistic
 ##' sensitivity analysis sample: a nonparametric regression approach. Medical
@@ -303,12 +307,14 @@ subset_outputs <- function(outputs, ...){
     UseMethod("subset_outputs", outputs)
 }
 
+##' @noRd
 subset_outputs.nb <- function(outputs, nsim, ...){
     outputs <- outputs[1:nsim,,drop=FALSE]
     class(outputs) <- c("nb", attr(outputs, "class"))
     outputs 
 }
 
+##' @noRd
 subset_outputs.cea <- function(outputs, nsim, ...){
     outputs$c <- outputs$c[1:nsim,,drop=FALSE]
     outputs$e <- outputs$e[1:nsim,,drop=FALSE]

R/evppi_mc.R

@@ -99,6 +99,7 @@ evppimc <- function(model_fn, ...){
     UseMethod("evppimc", model_fn)
 }
 
+##' @noRd
 evppimc.nb <- function(model_fn, par_fn, pars, pars_rep, nouter, ninner, nopt, mfargs, ...) {
     nb_current <- matrix(nrow=nouter, ncol=nopt)
     nb_ppi <- numeric(nouter)
@@ -121,6 +122,7 @@ evppimc.nb <- function(model_fn, par_fn, pars, pars_rep, nouter, ninner, nopt, m
     mean(nb_ppi) - max(colMeans(nb_current))
 }
 
+##' @noRd
 evppimc.cea <- function(model_fn, par_fn, pars, pars_rep, nouter, ninner, nopt, wtp, mfargs, ...) {
     nwtp <- length(wtp)
     if (nwtp < 1)

R/evppi_npreg.R

@@ -5,6 +5,7 @@ evppi_npreg <- function(outputs, ...){
     UseMethod("evppi_npreg", outputs)
 }
 
+##' @noRd
 evppi_npreg.nb <- function(outputs, inputs, pars, method, se, B, verbose, ...){
     if (verbose) message("Fitting nonparametric regression") 
     fit <- fitted_npreg(outputs, inputs=inputs, pars=pars, method=method, se=se, B=B, 
@@ -23,6 +24,7 @@ evppi_npreg.nb <- function(outputs, inputs, pars, method, se, B, verbose, ...){
     res
 }
 
+##' @noRd
 evppi_npreg.cea <- function(outputs, inputs, pars, method, se, B, verbose, ...){
     wtp <- outputs$k
     if (verbose) message("Fitting nonparametric regression for costs") 

R/evsi.R

@@ -238,6 +238,8 @@
 ##'   \code{k} identifies the willingness-to-pay.
 ##'
 ##' @references
+##' 
+##' Heath, A., Kunst, N., & Jackson, C. (eds.). (2024). Value of Information for Healthcare Decision-Making. CRC Press.
 ##'
 ##' Strong, M., Oakley, J. E., Brennan, A., & Breeze, P. (2015). Estimating the
 ##' expected value of sample information using the probabilistic sensitivity

R/model.R

@@ -49,10 +49,14 @@ check_model_fn <- function(model_fn, par_fn, mfargs=NULL, outputs=NULL, verbose=
 describe_modelfn <- function(model_fn, ...){
     UseMethod("describe_modelfn", model_fn)
 }
+
+##' @noRd
 describe_modelfn.nb <- function(model_fn, ...){
     plural <- if (attr(model_fn, "nopt") > 1) "s" else ""
     message(sprintf("model_fn returns net benefit for %s decision option%s", attr(model_fn, "nopt"), plural))
 }
+
+##' @noRd
 describe_modelfn.cea <- function(model_fn, ...){
     plural <- if (attr(model_fn, "nopt") > 1) "s" else ""
     message(sprintf("model_fn returns effects and costs for %s decision option%s", attr(model_fn, "nopt"), plural))

R/voi-package.R

@@ -16,6 +16,8 @@
 ##'
 ##' @references
 ##'
+##' Heath, A., Kunst, N., & Jackson, C. (eds.). (2024). Value of Information for Healthcare Decision-Making. CRC Press.
+##'
 ##' Heath, A., Manolopoulou, I., & Baio, G. (2017). A review of methods for analysis of the expected value of information. Medical Decision Making, 37(7), 747-758.
 ##' 
 ##' Heath, A., Kunst, N., Jackson, C., Strong, M., Alarid-Escudero, F., Goldhaber-Fiebert, J. D., Baio, G. Menzies, N.A, Jalal, H. (2020). Calculating the Expected Value of Sample Information in Practice: Considerations from 3 Case Studies. Medical Decision Making, 40(3), 314-326.
@@ -24,7 +26,6 @@
 ##'
 ##' @name voi-package
 ##' @aliases voi-package
-##' @docType package
 ##'
 ##' @importFrom grDevices dev.off
 ##' @importFrom graphics points hist par
@@ -35,4 +36,4 @@
 ##' @importFrom progress progress_bar
 ##' @importFrom Matrix nearPD
 ##' 
-NULL
+"_PACKAGE"