Starting to fix R upgrade issues

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)

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,

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")

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