From 68abd24a706a3a047a3f6b1aad4a2feeb76f2e7b Mon Sep 17 00:00:00 2001
From: Dominic Muston <dominic.muston@merck.com>
Date: Fri, 5 Jan 2024 20:02:23 -0500
Subject: [PATCH] Starting to fix R upgrade issues

---
 NAMESPACE             | 1 +
 R/ppdpps.R            | 4 ++--
 R/probgraphs.R        | 1 +
 vignettes/example.Rmd | 2 ++
 4 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 0e0ad3d..f5e6fad 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -29,6 +29,7 @@ export(give_noparams)
 export(give_noparams_par)
 export(graph_psm_hazards)
 export(graph_psm_survs)
+export(graph_survs)
 export(prob_os_psm)
 export(prob_os_stm_cf)
 export(prob_os_stm_cr)
diff --git a/R/ppdpps.R b/R/ppdpps.R
index 70450be..b98a107 100644
--- a/R/ppdpps.R
+++ b/R/ppdpps.R
@@ -167,7 +167,7 @@ pickout_psmhaz <- function(timepoint, endpoint, ptdata, dpam, psmtype) {
   # Run calculation of all hazards
   allhaz <- calc_haz_psm(timepoint, ptdata, dpam, type)
   # Required hazard, unadjusted
-  h_unadj <- case_when(
+  h_unadj <- dplyr::case_when(
     endpoint=="TTP" ~ allhaz$unadj$ttp,
     endpoint=="PPD" ~ allhaz$unadj$ppd,
     endpoint=="PFS" ~ allhaz$unadj$pfs,
@@ -176,7 +176,7 @@ pickout_psmhaz <- function(timepoint, endpoint, ptdata, dpam, psmtype) {
     .default = NA
   )
   # Required hazard, adjusted
-  h_adj <- case_when(
+  h_adj <- dplyr::case_when(
     endpoint=="TTP" ~ allhaz$adj$ttp,
     endpoint=="PPD" ~ allhaz$adj$ppd,
     endpoint=="PFS" ~ allhaz$adj$pfs,
diff --git a/R/probgraphs.R b/R/probgraphs.R
index d1b9338..68f9bad 100644
--- a/R/probgraphs.R
+++ b/R/probgraphs.R
@@ -419,6 +419,7 @@ prob_os_stm_cf <- function(time, dpam, starting=c(1, 0, 0)) {
 #' @param cuttime is the cut-off time for a two-piece model (default 0, indicating a one-piece model)
 #' @param tpoints indicates how many timepoints should be included in the graphics (default 100)
 #' @return Four datasets and graphics as a list
+#' @export
 #' @importFrom rlang .data
 #' @examples
 #' bosonc <- create_dummydata("flexbosms")
diff --git a/vignettes/example.Rmd b/vignettes/example.Rmd
index 5c044ed..8c91df2 100644
--- a/vignettes/example.Rmd
+++ b/vignettes/example.Rmd
@@ -26,6 +26,8 @@ library(psm3mkv)
 library(dplyr) # for data wrangling
 library(boot) # for bootstrapping
 library(ggsci) # for nice graphics
+library(flexsurv) # for data to work
+library(survival) # for data to work
 ```
 
 ## Obtaining a suitable dataset