From d32122086bdd516fa2d2857817123e35c2d9a035 Mon Sep 17 00:00:00 2001
From: Quentin Marcou <18257721+qmarcou@users.noreply.github.com>
Date: Thu, 30 May 2024 12:34:21 +0200
Subject: [PATCH] fix missing namespace

---
 R/renewnetTPreg.R    | 10 +++----
 R/survexp_wrappers.R | 69 +-------------------------------------------
 2 files changed, 6 insertions(+), 73 deletions(-)

diff --git a/R/renewnetTPreg.R b/R/renewnetTPreg.R
index 19b5d51..76ec9b8 100644
--- a/R/renewnetTPreg.R
+++ b/R/renewnetTPreg.R
@@ -28,7 +28,7 @@ mod.glm.fit.errorwrapper <-
            response,
            family,
            weights,
-           maxit = glm.control()$maxit,
+           maxit = stats::glm.control()$maxit,
            maxmaxit = 1000,
            warning_str = "",
            ...) {
@@ -41,7 +41,7 @@ mod.glm.fit.errorwrapper <-
           family = family,
           weights = weights,
           start = rep.int(0, times = ncol(X)),
-          control = glm.control(maxit = maxit)
+          control = stats::glm.control(maxit = maxit)
         )
       },
       warning = function(warn) {
@@ -138,7 +138,7 @@ mod.glm.fit.callingwrapper <-
            response,
            family,
            weights,
-           maxit = glm.control()$maxit,
+           maxit = stats::glm.control()$maxit,
            maxmaxit = 1000,
            warning_str = "",
            ...) {
@@ -591,8 +591,8 @@ estimate_censoring_dist <-
 get_survival_at <- function(t, survfit_data, safe = TRUE) {
   # Return the `surv` value for the row with greatest time lower than t using a
   # step function
-  if (is(survfit_data, "survfit")) survfit_data <- summary(survfit_data)
-  if (is(survfit_data, "summary.survfit")) {
+  if (isa(survfit_data, "survfit")) survfit_data <- summary(survfit_data)
+  if (isa(survfit_data, "summary.survfit")) {
     survfit_data <- tibble::tibble(
       time = survfit_data$time,
       surv = survfit_data$surv
diff --git a/R/survexp_wrappers.R b/R/survexp_wrappers.R
index 839693a..e079e24 100644
--- a/R/survexp_wrappers.R
+++ b/R/survexp_wrappers.R
@@ -236,7 +236,7 @@ dftoRatetable <- function(
       list(relsurv::transrate(
         lifetable[
           sexe == "M" & dept == dep,
-          .(agerev, annee, yearsurv = 1 - mua)
+          list(agerev, annee, yearsurv = 1 - mua)
         ] %>%
           tidyr::pivot_wider(
             id_cols = agerev,
@@ -350,70 +350,3 @@ dftoRatetable <- function(
   }
 }
 
-
-
-# nessie function from the relsurv package, under GNU GPL
-nessie <- function (formula = formula(data), data = parent.frame(), ratetable = relsurv::slopop,
-          times, rmap)
-{
-  call <- match.call()
-  if (!missing(rmap)) {
-    rmap <- substitute(rmap)
-  }
-  na.action <- NA
-  rform <- rformulate(formula, data, ratetable, na.action,
-                      rmap)
-  templab <- attr(rform$Terms, "term.labels")
-  if (!is.null(attr(rform$Terms, "specials")$ratetable))
-    templab <- templab[-length(templab)]
-  nameslist <- vector("list", length(templab))
-  for (it in 1:length(nameslist)) {
-    valuetab <- table(data[, match(templab[it], names(data))])
-    nameslist[[it]] <- paste(templab[it], names(valuetab),
-                             sep = "")
-  }
-  names(nameslist) <- templab
-  data <- rform$data
-  p <- rform$m
-  if (p > 0) {
-    data$Xs <- my.strata(rform$X[, , drop = F], nameslist = nameslist)
-  }
-  else data$Xs <- rep(1, nrow(data))
-  if (!missing(times))
-    tis <- times
-  else tis <- unique(sort(floor(rform$Y/365.241)))
-  tis <- unique(c(0, tis))
-  tisd <- tis * 365.241
-  out <- NULL
-  out$n <- table(data$Xs)
-  out$sp <- out$strata <- NULL
-  for (kt in order(names(table(data$Xs)))) {
-    inx <- which(data$Xs == names(out$n)[kt])
-    temp <- exp.prep(rform$R[inx, , drop = FALSE], rform$Y[inx],
-                     rform$ratetable, rform$status[inx], times = tisd,
-                     fast = FALSE)
-    out$time <- c(out$time, tisd)
-    out$sp <- c(out$sp, temp$sis)
-    out$strata <- c(out$strata, length(tis))
-    temp <- exp.prep(rform$R[inx, , drop = FALSE], rform$Y[inx],
-                     rform$ratetable, rform$status[inx], times = (seq(0,
-                                                                      100, by = 0.5) * 365.241)[-1], fast = FALSE)
-    out$povp <- c(out$povp, mean(temp$sit/365.241))
-  }
-  names(out$strata) <- names(out$n)[order(names(table(data$Xs)))]
-  if (p == 0)
-    out$strata <- NULL
-  mata <- matrix(out$sp, ncol = length(tis), byrow = TRUE)
-  mata <- data.frame(mata)
-  mata <- cbind(mata, out$povp)
-  row.names(mata) <- names(out$n)[order(names(table(data$Xs)))]
-  names(mata) <- c(tis, "c.exp.surv")
-  cat("\n")
-  print(round(mata, 1))
-  cat("\n")
-  out$mata <- mata
-  out$n <- as.vector(out$n)
-  class(out) <- "nessie"
-  invisible(out)
-}
-