Documentation fixes to correct notes

DESCRIPTION

@@ -10,7 +10,7 @@ Description: Fits and evaluates three-state partitioned survival analyses
     (PartSAs) and Markov models (clock forward or clock reset) to
     progression and overall survival data typically collected in oncology clinical trials. These model structures are typically considered in
     cost-effectiveness modeling in advanced/metastatic cancer indications.
-    Muston (2024). "Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit". Applied Health Economics and Health Policy. DOI 10.1007/s40258-024-00884-2 
+    Muston (2024). "Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit". Applied Health Economics and Health Policy. 
 License: GPL (>= 3)
 URL: https://merck.github.io/psm3mkv/, https://github.com/Merck/psm3mkv
 BugReports: https://github.com/Merck/psm3mkv/issues

R/likepsm.R

@@ -39,8 +39,10 @@
 #' parfits <- fit_ends_mods_par(bosonc)
 #' splfits <- fit_ends_mods_spl(bosonc)
 #' # Present comparison of likelihood calculations
+#' \donttest{
 #' compare_psm_likes(bosonc, parfits)
-#' # compare_psm_likes(bosonc, splfits)
+#' compare_psm_likes(bosonc, splfits)
+#' }
 compare_psm_likes <- function(ptdata, fitslist, cuttime=0) {
   # Determine whether fit is a spline, then call the right function
   if (fitslist$pfs[[1]]$result$dlist$name=="survspline") {
@@ -181,7 +183,7 @@ compare_psm_likes_spl <- function(ptdata, fitslist, cuttime=0) {
   if (length(fitslist)!=6) {stop("The list provided to fitslist must contain all 6 endpoints")}
   # Create local variables
   eps <- ndists <- aic_indbest <- bic_indbest <- bests <- res <- thisfit <- aic_jtbest <- bic_jtbest <- NULL
-  ll <- rank_aic <- ttp_meth <- pfs_dist <- os_dist <- rank_bic <- NULL
+  ll <- rank_aic <- ttp_meth <- ttp_knots <- pfs_scales <- pfs_knots <- os_scales <- os_knots <- rank_bic <- NULL
   # Best fits by AIC or BIC
   eps <- c(1, 3, 4)
   fits_aic <- eps |>