remove warning and delete vignette

DESCRIPTION

@@ -53,7 +53,6 @@ Language: en-US
 LazyData: true
 Roxygen:
     list(markdown = TRUE, packages = "roxytypes")
-RoxygenNote: 7.3.3
 Config/Needs/documentation:
     roxytypes
 Remotes:
@@ -86,3 +85,4 @@ Collate:
     'sumBetaDiff.R'
     'sumTable.R'
 Config/testthat/edition: 3
+Config/roxygen2/version: 8.1.1

NAMESPACE

@@ -32,28 +32,34 @@ export(runShinyPhase1b)
 export(sumBetaDiff)
 export(sumTable)
 import(checkmate)
-importFrom(ggplot2,annotate)
-importFrom(ggplot2,geom_area)
-importFrom(ggplot2,geom_bar)
-importFrom(ggplot2,geom_line)
-importFrom(ggplot2,ggtitle)
-importFrom(ggplot2,theme_light)
-importFrom(ggplot2,xlab)
-importFrom(ggplot2,ylab)
-importFrom(graphics,abline)
-importFrom(graphics,axis)
-importFrom(graphics,hist)
-importFrom(graphics,lines)
-importFrom(graphics,plot)
-importFrom(graphics,polygon)
+importFrom(ggplot2,
+  annotate,
+  geom_area,
+  geom_bar,
+  geom_line,
+  ggtitle,
+  theme_light,
+  xlab,
+  ylab
+)
+importFrom(graphics,
+  abline,
+  axis,
+  hist,
+  lines,
+  plot,
+  polygon
+)
 importFrom(lifecycle,deprecated)
-importFrom(stats,acf)
-importFrom(stats,binom.test)
-importFrom(stats,dbeta)
-importFrom(stats,dbinom)
-importFrom(stats,integrate)
-importFrom(stats,optimize)
-importFrom(stats,pbeta)
-importFrom(stats,rbinom)
-importFrom(stats,uniroot)
+importFrom(stats,
+  acf,
+  binom.test,
+  dbeta,
+  dbinom,
+  integrate,
+  optimize,
+  pbeta,
+  rbinom,
+  uniroot
+)
 importFrom(tibble,remove_rownames)

R/dbetabinom.R

@@ -90,13 +90,6 @@ h_getBetamixPost <- function(x, n, par, weights) {
     finite = TRUE
   )
   assert_true(all(weights >= 0))
-  # Correcting weights that do not sum to 1
-  if (sum(weights) != 1) {
-    warning("Weights have been corrected. Advise to review allocated weights")
-    # We renormalize weights.
-    weights <- weights / sum(weights)
-  }
-
   # We now compute updated parameters.
   postPar <- par
   postPar[, 1] <- postPar[, 1] + x

tests/testthat/test-dbetabinom.R

@@ -257,14 +257,11 @@ test_that("h_getBetamixPost gives the correct beta-mixture parameters", {
 })
 
 test_that("h_getBetamixPost gives weight of 1 for a single beta distribution", {
-  expect_warning(
-    results <- h_getBetamixPost(
-      x = 16,
-      n = 23,
-      par = rbind(c(1, 2)),
-      weights = 0.1
-    ),
-    "Weights have been corrected"
+  results <- h_getBetamixPost(
+    x = 16,
+    n = 23,
+    par = rbind(c(1, 2)),
+    weights = 0.1
   )
   expected <- list(
     par = rbind(c(17, 9)),
@@ -285,14 +282,11 @@ test_that("h_getBetamixPost gives correct weights with 2 beta-mixture component"
 })
 
 test_that("h_getBetamixPost gives the correct weights when sum of weights is not 1 in beta-mixture", {
-  expect_warning(
-    result <- h_getBetamixPost(
-      x = 16,
-      n = 23,
-      par = rbind(c(1, 2), c(3, 4), c(10, 10)),
-      weights = c(0.6, 0.4, 0.5)
-    ),
-    "Weights have been corrected"
+  result <- h_getBetamixPost(
+    x = 16,
+    n = 23,
+    par = rbind(c(1, 2), c(3, 4), c(10, 10)),
+    weights = c(0.6, 0.4, 0.5)
   )
   expect_equal(
     result$weights,

tests/testthat/test-predprob.R

@@ -118,34 +118,6 @@ test_that("predprob gives an error when x exceeds interim n", {
   )
 })
 
-test_that("Warning length equal to length of x", {
-  captured_warnings <- capture_warnings({
-    result <- predprob(
-      x = 16,
-      n = 20,
-      Nmax = 22,
-      p = 0.6,
-      thetaT = 0.9,
-      parE = rbind(c(1, 1), c(25, 15)),
-      weights = c(3, 1)
-    )
-  })
-  expected <- data.frame(
-    counts = 0:2,
-    cumul_counts = c(20, 21, 22),
-    density = c(0.0738, 0.3651, 0.5611),
-    posterior = c(0.862329474749815, 0.928990451842824, 0.969938389163636),
-    success = c(FALSE, TRUE, TRUE)
-  )
-  expect_equal(
-    length(captured_warnings),
-    4,
-    info = "Should have generated one warning for each element in 'x' in the loop."
-  )
-  expect_equal(result$result, 0.9262315, tolerance = 1e-4)
-  expect_equal(result$table, expected, tolerance = 1e-4)
-})
-
 test_that("predprob gives an error when Nmax is less than n", {
   expect_error(
     predprob(

vignettes/introduction.Rmd

@@ -172,7 +172,7 @@ help(package = "phase1b")
 
 A list of functions will be displayed and you can learn more about each function,
 and see examples of its use, by clicking on its corresponding link.
-Note that this will easiest work in [R-Studio](https://posit.co/download/rstudio-desktop/), which
+Note that this will easiest work in [R-Studio](https://docs.posit.co/ide/user/#rstudio-ide-oss-downloads?ref=rstudio-legacy), which
 is the recommended software for editing and using R.
 
 # Methods and Models {#methods}