Merge pull request #28 from dom-muston/main

After CRAN submission

Author: dom-muston

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.4.0
-Date: 2026-01-07 00:45:35 UTC
-SHA: 986f44179c3fb67d474c9a965f5643004c47e70c
+Version: 0.4.1
+Date: 2026-01-10 23:19:31 UTC
+SHA: ed329f5dac07bdbb36b0093216bc30c4d0a57514

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dynamicpv
 Title: Evaluates Present Values and Health Economic Models with Dynamic Pricing and Uptake
-Version: 0.4.1
+Version: 0.4.1.9000
 Authors@R: c(
     person("Dominic", "Muston", , "dominic.muston@msd.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-4876-7940")),

NEWS.md

@@ -1,3 +1,7 @@
+# dynamicpv (development version)
+
+* So far, only minor changes to the readme page
+
 # dynamicpv 0.4.1
 
 * Revised vignettes

R/dynamic.R

@@ -98,11 +98,34 @@
 dynpv <- function(
     uptakes = 1,
     payoffs,
-    horizon = length(payoffs),
+    horizon = NA,
     tzero = 0,
-    prices = rep(1, length(payoffs)+tzero),
+    prices = NA,
     discrate = 0
     ){
+  # If payoffs are discrete
+  if (class(payoffs)=="numeric") {
+    # Horizon defaults to length of payoffs
+    if (class(horizon)=="logical") {horizon <- length(payoffs)}
+    # Price index defaults to (1, ..., 1)
+    if (class(prices)=="logical") {prices <- rep(1, length(payoffs)+tzero)}
+    # Call calculation
+    dpv <- dynpv_discrete(uptakes, payoffs, horizon, tzero, prices, discrate)
+  }
+  # If payoffs are not discrete and uptake is discrete
+  if ((class(uptakes)=="numeric") & (class(payoffs)=="function")) {
+    dpv <- dynpv_semicts(uptakes, payoffs, horizon, tzero, prices, discrate)
+  }
+  # If payoffs and uptake are not discrete
+  if ((class(uptakes)=="function") & (class(payoffs)=="function")) {
+    dpv <- dynpv_fullycts(uptakes, payoffs, horizon, tzero, prices, discrate)
+  }
+  # Return
+  return(dpv)
+}
+
+# Discrete function
+dynpv_discrete <- function(uptakes, payoffs, horizon, tzero, prices, discrate){
   # Avoid no visible binding note
   j <- k <- l <- uj <- pk <- R <- v <- NULL
   # Trim
@@ -137,3 +160,42 @@ trim_vec <- function(vec){
   # Return trimmed vector
   return(vec[1:trimto])
 }
+
+# Function if payoffs, prices and discounting are functions; but uptakes is a vector
+dynpv_semicts <- function(uptakes, payoffs, horizon, tzero, prices, discrate){
+  # Avoid no visible binding note
+  j <- uj <- pRv <- pv <- NULL
+  # Trim
+  uptakes <- trim_vec(uptakes)
+  # Integrand function  
+  integrand <- function(k, j) {
+    payoffs(k) * prices(j+k+tzero) * discrate(j+k)
+  }
+  # Create a dataset for each combination of time
+  df <- expand_grid(j=1:length(uptakes)) |>
+    dplyr::mutate(
+      uj = uptakes[j],
+      pRv = stats::integrate(integrand, lower=0, upper=horizon-j, j=j)$value,
+      pv = uj * pRv
+    )
+  class(df) <- c("dynpv", class(df))
+  return(df)
+}
+
+# Function if uptakes, payoffs, prices and discounting are functions
+dynpv_fullycts <- function(uptakes, payoffs, horizon, tzero, prices, discrate){
+  # First integrand function - pRv, to be integrated between k=0 and k=T-j
+  integrand1 <- function(k, j) {
+    payoffs(k) * prices(j+k+tzero) * discrate(j+k)
+  }
+  # Second integrand function, uj I, to be integrated between j=0 and j=T
+  integrand2 <- function(j) {
+    pRv <- stats::integrate(integrand1, lower=0, upper=horizon-j, j=j)$value
+    uptakes(j) * pRv
+  }
+  # Needs to be vectorized before integrating
+  integrand2 <- Vectorize(integrand2, "j")
+  # Calculate double integral
+  df <- stats::integrate(integrand2, lower=0, upper=horizon)
+  return(df$value)
+}

README.Rmd

@@ -29,7 +29,7 @@ Through the [dynpv()](https://msdllcpapers.github.io/dynamicpv/reference/dynpv.h
 
 ## Installation
 
-The package should shortly be available on [CRAN](https://cran.r-project.org/web/packages/index.html). Installing from here is simplest, once available.
+The package is now available on [CRAN](https://cran.r-project.org/web/packages/index.html). Installing from here is simplest, as follows.
 
 ```{r inst_cran}
 #| eval: false
@@ -48,14 +48,7 @@ install.packages("devtools")
 pak::pak("MSDLLCpapers/dynamicpv")
 ```
 
-Note that the above does not install vignettes. Vignettes may be viewed on the [package website](https://msdllcpapers.github.io/dynamicpv/) or by instead running the following.
-
-```{r instal2}
-#| eval: false
-devtools::install_github("MSDLLCpapers/dynamicpv", build_vignettes=TRUE)
-```
-
-You should then load the package, alongside some other packages used here.
+Installing the development version in this way does not include vignettes. Vignettes may be viewed on the [package website](https://msdllcpapers.github.io/dynamicpv/). You can then load the package, alongside other packages you may find helpful.
 
 ```{r instal3}
 #| eval: false

README.md

@@ -36,9 +36,9 @@ cost-effectiveness model, such as one computed using the
 
 ## Installation
 
-The package should shortly be available on
+The package is now available on
 [CRAN](https://cran.r-project.org/web/packages/index.html). Installing
-from here is simplest, once available.
+from here is simplest, as follows.
 
 ``` r
 # CRAN installation - when available
@@ -56,16 +56,10 @@ install.packages("devtools")
 pak::pak("MSDLLCpapers/dynamicpv")
 ```
 
-Note that the above does not install vignettes. Vignettes may be viewed
-on the [package website](https://msdllcpapers.github.io/dynamicpv/) or
-by instead running the following.
-
-``` r
-devtools::install_github("MSDLLCpapers/dynamicpv", build_vignettes=TRUE)
-```
-
-You should then load the package, alongside some other packages used
-here.
+Installing the development version in this way does not include
+vignettes. Vignettes may be viewed on the [package
+website](https://msdllcpapers.github.io/dynamicpv/). You can then load
+the package, alongside other packages you may find helpful.
 
 ``` r
 # Load the dynamicpv package

cran-comments.md

@@ -1,3 +1,9 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Extended the description text in DESCRIPTION
+* Revised the vignettes
+
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note

tests/testthat/test-fullycts.R

@@ -0,0 +1,15 @@
+# Test new fullycts calculations
+
+# Example
+payoffs <- function(t) {100+50*t}
+prices <- function(t) {1.03 ^ (floor(t))}
+discrate <- function(t) {0.97 ^ t}
+uptakes <- function(t) {exp(-t/2)}
+
+# 1. Full function calls intermediate function ok
+test_that("Full function calls intermediate function ok", {
+    int <- dynpv_fullycts(uptakes=uptakes, payoffs=payoffs, horizon=5, tzero=0, prices=prices, discrate=discrate)
+    full <- dynpv(uptakes=uptakes, payoffs=payoffs, horizon=5, prices=prices, discrate=discrate)
+    expect_equal(int, full)
+  }
+)

tests/testthat/test-semicts.R

@@ -0,0 +1,19 @@
+# Test new semicts calculations
+
+# Example
+payoffs <- function(t) {100+50*t}
+prices <- function(t) {1.03 ^ (floor(t))}
+discrate <- function(t) {0.97 ^ t}
+
+# 1. Full function calls intermediate function ok
+test_that("Full function calls intermediate function ok", {
+    int <- dynpv_semicts(uptakes=1, payoffs=payoffs, horizon=5, tzero=0, prices=prices, discrate=discrate)
+    full <- dynpv(payoffs=payoffs, horizon=5, prices=prices, discrate=discrate)
+    expect_equal(int, full)
+  }
+)
+
+
+
+
+