Additional check() fixes

R/datasets.R

@@ -82,5 +82,5 @@ create_dummydata_flexbosms <- function() {
         ) |>
         dplyr::select(id, pfs.durn, pfs.flag,
                       os.durn, os.flag, ttp.durn, ttp.flag) |>
-        dplyr::rename(ptid = .data$id)
+        dplyr::rename(ptid = "id")
 }

R/ppdpps.R

@@ -32,7 +32,7 @@
 #' @examples
 #' bosonc <- create_dummydata("flexbosms")
 #' fits <- fit_ends_mods_spl(bosonc)
-#' Pick out best distribution according to min AIC
+#' # Pick out best distribution according to min AIC
 #' params <- list(
 #'   ppd = find_bestfit_spl(fits$ppd, "aic")$fit,
 #'   ttp = find_bestfit_spl(fits$ttp, "aic")$fit,
@@ -44,6 +44,13 @@
 #' calc_haz_psm(0:10, ptdata=bosonc, dpam=params, type="simple")
 #' calc_haz_psm(0:10, ptdata=bosonc, dpam=params, type="complex")
 calc_haz_psm <- function(timevar, ptdata, dpam, type) {
+  # Declare local variables
+  pfs.ts <- pfs.type <- pfs.spec <- NULL
+  os.ts <- os.type <- os.spec <- NULL
+  ttp.ts <- ttp.type <- ttp.spec <- NULL
+  ne_pfs <- ne_ttp <- progfrac <- NULL
+  http <- hpf <- hos <- sos <- spf <- NULL
+  hppd_simple <- hppd_complex <- hppd <- hpps <- hdiff <- NULL
   # PFS
   pfs.ts <- convert_fit2spec(dpam$pfs)
   pfs.type <- pfs.ts$type
@@ -104,6 +111,8 @@ calc_haz_psm <- function(timevar, ptdata, dpam, type) {
 #'     dpam=params,
 #'     type="simple")
 calc_surv_psmpps <- function(totime, fromtime=0, ptdata, dpam, type="simple") {
+  # Declare local variables
+  cumH <- NULL
   # Hazard function
   hazfn <- function(x) {
     calc_haz_psm(timevar=x, ptdata=ptdata, dpam=dpam, type=type)$post

R/resmeans.R

@@ -453,16 +453,16 @@ calc_allrmds <- function(simdat,
     pfdat <- tidyr::as_tibble(cbind(time=pf_km$time, surv=pf_km$surv)) |>
       dplyr::mutate(
         row = dplyr::row_number(),
-        itime = if_else(.data$row==1, .data$time, time-lag(.data$time)),
-        incl = if_else(.data$time<cuttime, 1, 0),
+        itime = dplyr::if_else(.data$row==1, .data$time, .data$time-dplyr::lag(.data$time)),
+        incl = dplyr::if_else(.data$time<cuttime, 1, 0),
         area = .data$incl*.data$surv*.data$itime
       )
     pfarea <- sum(pfdat$area)
     pfsurv <- min(pfdat[pfdat$incl==1,]$surv)
     # OS calculations
     osdat <- tidyr::as_tibble(cbind(time=os_km$time, surv=os_km$surv)) |>
-      mutate(
-        row = row_number(),
+      dplyr::mutate(
+        row = dplyr::row_number(),
         itime = if_else(.data$row==1, .data$time, .data$time-lag(.data$time)),
         incl = if_else(.data$time<cuttime, 1, 0),
         area = .data$incl*.data$surv*.data$itime

tests/testthat/test-resmeans.R

@@ -57,9 +57,9 @@ rmd_all <- calc_allrmds(bosonc,
 Ty <- 10
 Tw <- Ty * weeks_in_year
 # params$pfs$dlist$name is "exp"
-exp_psm_pf <- rmst_exp(Tw, rate=params$pfs$res[1])
+exp_psm_pf <- flexsurv::rmst_exp(Tw, rate=params$pfs$res[1])
 # params$os$dlist$name is "weibullPH"
-exp_psm_os <- rmst_weibullPH(Tw, shape=params$os$res[1,1], scale=params$os$res[2,1])
+exp_psm_os <- flexsurv::rmst_weibullPH(Tw, shape=params$os$res[1,1], scale=params$os$res[2,1])
 exp_psm_pd <- exp_psm_os - exp_psm_pf
 
 test_that("PSM results match expected durations", {
@@ -167,8 +167,8 @@ exp_stmcf_pf2 <- stats::integrate(int1, 0, 10*weeks_in_year)$value
 S <- cbind(c(0,0),c(0, Tw),c(Tw, Tw))
 exp_stmcr_pd2 <- SimplicialCubature::adaptIntegrateSimplex(int3, S)$integral
 exp_stmcf_pd2 <- SimplicialCubature::adaptIntegrateSimplex(int2, S)$integral
-exp_psm_pf2 <- rmst_exp(Tw, rate=params$pfs$res[1]) # Exp
-exp_psm_os2 <- rmst_weibullPH(Tw,
+exp_psm_pf2 <- flexsurv::rmst_exp(Tw, rate=params$pfs$res[1]) # Exp
+exp_psm_os2 <- flexsurv::rmst_weibullPH(Tw,
                              shape=params$os$res[1,1],
                              scale=params$os$res[2,1]) # WeibullPH