From fe838e37d4b0c432531db29ce1b8d27ff09a5e40 Mon Sep 17 00:00:00 2001
From: Dominic Muston <dominic.muston@merck.com>
Date: Fri, 5 Jan 2024 22:13:24 -0500
Subject: [PATCH] News, and timevar not timepoint

---
 NEWS.md    |  9 ++++++---
 R/ppdpps.R | 20 ++++++++++----------
 2 files changed, 16 insertions(+), 13 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 4e72a45..c9a9f3d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,7 @@
-# psm3mkv 0.1.0
+## 5 Jan 2024 - Constraints implied by a PSM
 
-## Version 0.1
-* Initial release
+I’ve merged some experimental functions into the main branch following the version 0.1 release package. These functions provide analyses of the constraints on mortality hazards and therefore survival implied by a PSM. They are: [calc_haz_psm()], [calc_surv_psmpps()], [pickout_psmhaz()], [graph_psm_hazards()], and [graph_psm_survs()].
+
+# 1 Jan 2024 - Version 0.1
+
+This is the initial release of the package, rather belatedly. The code dates to October 2023.
diff --git a/R/ppdpps.R b/R/ppdpps.R
index edec91c..16058c7 100644
--- a/R/ppdpps.R
+++ b/R/ppdpps.R
@@ -163,9 +163,9 @@ calc_surv_psmpps <- function(totime, fromtime=0, ptdata, dpam, type="simple") {
 #' Graph is a line graphic of the hazards plotted against the time-range
 #' @importFrom rlang .data
 #' @return adj is the hazard adjusted for constraints, unadj is the unadjusted hazard
-pickout_psmhaz <- function(timepoint, endpoint, ptdata, dpam, psmtype) {
+pickout_psmhaz <- function(timevar, endpoint, ptdata, dpam, psmtype) {
   # Run calculation of all hazards
-  allhaz <- calc_haz_psm(timepoint, ptdata, dpam, psmtype)
+  allhaz <- calc_haz_psm(timevar, ptdata, dpam, psmtype)
   # Required hazard, unadjusted
   h_unadj <- dplyr::case_when(
     endpoint=="TTP" ~ allhaz$unadj$ttp,
@@ -216,14 +216,14 @@ pickout_psmhaz <- function(timepoint, endpoint, ptdata, dpam, psmtype) {
 #' #   dpam=params,
 #' #   psmtype="simple")
 #' # psmh_simple$graph
-graph_psm_hazards <- function(timerange, endpoint, ptdata, dpam, psmtype) {
+graph_psm_hazards <- function(timevar, endpoint, ptdata, dpam, psmtype) {
   # Convert endpoint to upper case text
   endpoint <- toupper(endpoint)
   # Pull out hazards to plot (inefficiently calls function twice, but is quite quick)
-  adjhaz <- timerange |> purrr::map_vec(~pickout_psmhaz(.x, endpoint, ptdata, dpam, psmtype)$adj)
-  unadjhaz <- timerange |> purrr::map_vec(~pickout_psmhaz(.x, endpoint, ptdata, dpam, psmtype)$unadj)
+  adjhaz <- timevar |> purrr::map_vec(~pickout_psmhaz(.x, endpoint, ptdata, dpam, psmtype)$adj)
+  unadjhaz <- timevar |> purrr::map_vec(~pickout_psmhaz(.x, endpoint, ptdata, dpam, psmtype)$unadj)
   # Create dataset for graphic
-  result_data <- dplyr::tibble(Time=timerange, Adjusted=adjhaz, Unadjusted=unadjhaz) |>
+  result_data <- dplyr::tibble(Time=timevar, Adjusted=adjhaz, Unadjusted=unadjhaz) |>
       tidyr::pivot_longer(cols=c(Adjusted, Unadjusted),
                       names_to="Method", values_to="Hazard")
   # Draw graphic
@@ -264,7 +264,7 @@ graph_psm_hazards <- function(timerange, endpoint, ptdata, dpam, psmtype) {
 #' # dpam=params,
 #' # psmtype="simple")
 #' # psms_simple$graph
-graph_psm_survs <- function(timerange, endpoint, ptdata, dpam, psmtype) {
+graph_psm_survs <- function(timevar, endpoint, ptdata, dpam, psmtype) {
   # Convert endpoint to upper case text
   endpoint <- toupper(endpoint)
   # Unadjusted hazard
@@ -286,13 +286,13 @@ graph_psm_survs <- function(timerange, endpoint, ptdata, dpam, psmtype) {
     if (intA$message=="OK") intA$value else NA
   }
   # Calculate cumulative hazards
-  cumH_unadj <- seq(timerange) |> purrr::map_dbl(~cumhaz_unadj(.x))
-  cumH_adj <- seq(timerange) |> purrr::map_dbl(~cumhaz_adj(.x))
+  cumH_unadj <- seq(timevar) |> purrr::map_dbl(~cumhaz_unadj(.x))
+  cumH_adj <- seq(timevar) |> purrr::map_dbl(~cumhaz_adj(.x))
   # Calculate survival values
   S_unadj <- exp(-cumH_unadj)
   S_adj <- exp(-cumH_adj)
   # Create dataset for graphic
-  result_data <- dplyr::tibble(Time=timerange, Adjusted=S_adj, Unadjusted=S_unadj) |>
+  result_data <- dplyr::tibble(Time=timevar, Adjusted=S_adj, Unadjusted=S_unadj) |>
     tidyr::pivot_longer(cols=c(Adjusted, Unadjusted),
                         names_to="Method", values_to="Survival")
   # Draw graphic