Merge branch 'main' into 137_hardcoded_params

Author: audreyyeoCH

R/betadiff.R

@@ -19,7 +19,7 @@
 #' @typed eps : number
 #'  lowest floating point number as lower bound of integration
 #' @typed rel.tol : number
-#'  used in [stats::integrate()]
+#'  used in `[stats::integrate()]`
 #' @return The density values
 #'
 #' @note `X` and `Y` can be either Control or Treatment and `Z = X-Y`, subject to assumptions.

R/plotBeta.R

@@ -81,12 +81,12 @@ plotBetaDiff <- function(
   diff <- seq(from = -1, to = 1, length = 1000)
   data <- data.frame(
     grid = diff,
-    density = dbetadiff(z = diff, parY = parY, parX = parX)
+    density = phase1b::dbetadiff(z = diff, parY = parY, parX = parX)
   )
   data$stop <- ifelse(diff > -1 & diff < stop_cut, TRUE, FALSE)
   data$go <- ifelse(diff > go_cut & diff < 1, TRUE, FALSE)
 
-  temp <- sumBetaDiff(
+  temp <- phase1b::sumBetaDiff(
     parX = parX,
     parY = parY,
     go_cut = go_cut, # in response rate
@@ -102,7 +102,7 @@ plotBetaDiff <- function(
     stop_label
   )
 
-  pbetadiff_plot <- if (shade) {
+   pbetadiff_plot <- if (shade) {
     ggplot2::ggplot(
       data = data,
       mapping = ggplot2::aes(x = grid, y = density)

man/dbetadiff.Rd

@@ -328,11 +328,11 @@ test_that("plotOc gives expected results for `ocPostprob` and `ocPredprob`", {
     all_looks = res5$Looks,
     wiggle_status = res5$params$wiggle
   )
-  vdiffr::expect_doppelganger(
+  vdiffr::expect_doppelganger( ##
     title = "plot of simulation result for single arm posterior probability",
     fig = result1
   )
-  vdiffr::expect_doppelganger(
+  vdiffr::expect_doppelganger( ##
     title = "plot of simulation result for single arm posterior predictive probability",
     fig = result2
   )