From bab19cc41308621ca084b80934427e7c8a5f6376 Mon Sep 17 00:00:00 2001
From: MThomas91 <THOMAM1D@novartis.net>
Date: Fri, 20 Jun 2025 16:29:47 +0200
Subject: [PATCH 1/3] update to testthat 3, remove deprecated functions

---
 DESCRIPTION                          | 1 +
 tests/testthat/test-MCTtest.R        | 2 --
 tests/testthat/test-bMCTtest.R       | 2 --
 tests/testthat/test-drmodels.R       | 2 --
 tests/testthat/test-fitMod.R         | 2 --
 tests/testthat/test-guesst.R         | 2 --
 tests/testthat/test-maFitMod.R       | 2 --
 tests/testthat/test-optContr.R       | 2 --
 tests/testthat/test-optDesign.R      | 2 --
 tests/testthat/test-planMod.R        | 2 --
 tests/testthat/test-powMCTBinCount.R | 2 --
 11 files changed, 1 insertion(+), 20 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a3b24bc..28192e1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,3 +39,4 @@ Encoding: UTF-8
 URL: https://github.com/openpharma/DoseFinding, https://openpharma.github.io/DoseFinding/
 BugReports: https://github.com/openpharma/DoseFinding/issues
 Roxygen: list(markdown = TRUE)
+Config/testthat/edition: 3
diff --git a/tests/testthat/test-MCTtest.R b/tests/testthat/test-MCTtest.R
index ba9abfe..c9b9916 100644
--- a/tests/testthat/test-MCTtest.R
+++ b/tests/testthat/test-MCTtest.R
@@ -1,5 +1,3 @@
-context("multiple contrast test")
-
 # TODO:
 # * maybe define common candidate models outside of test_that() calls?
 # * how do we check for equal p-values (calculated with MC algorighm)?
diff --git a/tests/testthat/test-bMCTtest.R b/tests/testthat/test-bMCTtest.R
index fa32070..df726b5 100644
--- a/tests/testthat/test-bMCTtest.R
+++ b/tests/testthat/test-bMCTtest.R
@@ -1,5 +1,3 @@
-context("Bayesian multiple contrast test")
-
 # TODO:
 # * maybe define common candidate models outside of test_that() calls?
 # * how do we check for equal p-values (calculated with MC algorighm)?
diff --git a/tests/testthat/test-drmodels.R b/tests/testthat/test-drmodels.R
index 43119d2..99c77ea 100644
--- a/tests/testthat/test-drmodels.R
+++ b/tests/testthat/test-drmodels.R
@@ -1,5 +1,3 @@
-context("dose response model functions")
-
 ud <- function(x) unname(drop(x))
 
 test_that("betaMod does not produce NaN for large delta1, delta2", {
diff --git a/tests/testthat/test-fitMod.R b/tests/testthat/test-fitMod.R
index bff22d4..606f29c 100644
--- a/tests/testthat/test-fitMod.R
+++ b/tests/testthat/test-fitMod.R
@@ -1,5 +1,3 @@
-context("Model Fitting")
-
 source("generate_test_datasets.R")
 
 # Generate data sets and compare results of fitDRModel to the result of nls and
diff --git a/tests/testthat/test-guesst.R b/tests/testthat/test-guesst.R
index 5288428..92546e2 100644
--- a/tests/testthat/test-guesst.R
+++ b/tests/testthat/test-guesst.R
@@ -1,5 +1,3 @@
-context("guesstimates")
-
 test_that("emax", {
   emx1 <- guesst(d=0.3, p=0.8, model="emax")
   expect_equal(unname(emax(0.3,0,1,emx1)),
diff --git a/tests/testthat/test-maFitMod.R b/tests/testthat/test-maFitMod.R
index 7aea8a6..74505d0 100644
--- a/tests/testthat/test-maFitMod.R
+++ b/tests/testthat/test-maFitMod.R
@@ -1,5 +1,3 @@
-context("maFitMod")
-
 data(biom)
 anMod <- lm(resp~factor(dose)-1, data=biom)
 drFit <- coef(anMod)
diff --git a/tests/testthat/test-optContr.R b/tests/testthat/test-optContr.R
index 070cf40..5587b00 100644
--- a/tests/testthat/test-optContr.R
+++ b/tests/testthat/test-optContr.R
@@ -1,5 +1,3 @@
-context("Optimal Contrasts")
-
 require_extra_packages <- function() {
   if (!(require("quadprog") && require("Rsolnp"))) {
     skip("packages quadprog and Rsolnp not available")
diff --git a/tests/testthat/test-optDesign.R b/tests/testthat/test-optDesign.R
index e4ae328..f51c8cb 100644
--- a/tests/testthat/test-optDesign.R
+++ b/tests/testthat/test-optDesign.R
@@ -1,5 +1,3 @@
-context("optimal designs")
-
 # TODO
 # * mixed Paper p. 1233, l. 2 (note the off and probably also the scal
 #   parameter were treated as unknown in this example in the paper, hence the
diff --git a/tests/testthat/test-planMod.R b/tests/testthat/test-planMod.R
index e43adea..0ffaf9f 100644
--- a/tests/testthat/test-planMod.R
+++ b/tests/testthat/test-planMod.R
@@ -1,5 +1,3 @@
-context("planning models")
-
 # TODO
 # * what do we want to do with tests #3-5 (mostly plots)
 # * test #4 crashes in planMod
diff --git a/tests/testthat/test-powMCTBinCount.R b/tests/testthat/test-powMCTBinCount.R
index 4368e63..ecae170 100644
--- a/tests/testthat/test-powMCTBinCount.R
+++ b/tests/testthat/test-powMCTBinCount.R
@@ -1,5 +1,3 @@
-context("power calculation binary and count data")
-
 ## general options
 mvt_control <- DoseFinding:::mvtnorm.control(maxpts=1e5, abseps = 0.0001)
 

From ff8227afdf1564228177750745e73df0cdf70a0f Mon Sep 17 00:00:00 2001
From: MThomas91 <THOMAM1D@novartis.net>
Date: Fri, 20 Jun 2025 17:29:15 +0200
Subject: [PATCH 2/3] update tests to adjust for changes in testthat 3

---
 tests/testthat/test-MCTtest.R       | 10 +++++-----
 tests/testthat/test-bMCTtest.R      | 17 ++++++++---------
 tests/testthat/test-optDesign.R     | 16 ++++++++--------
 tests/testthat/test-planMod.R       |  2 +-
 tests/testthat/test-powMCTInterim.R |  6 +++---
 5 files changed, 25 insertions(+), 26 deletions(-)

diff --git a/tests/testthat/test-MCTtest.R b/tests/testthat/test-MCTtest.R
index c9b9916..c16940b 100644
--- a/tests/testthat/test-MCTtest.R
+++ b/tests/testthat/test-MCTtest.R
@@ -55,7 +55,7 @@ test_that("MCTtest gives the same output as multcomp::glht (beta and sigEmax mod
   fit <- lm(y~x, data=dd_x_factor)
   mcp <- glht(fit, linfct = mcp(x = t(obj$contMat)), alternative = "greater")
   expect_equal(tstat(obj), tstat(mcp))
-  expect_equal(pval(obj), pval(mcp), tolerance = 0.001)
+  expect_equal(pval(obj), pval(mcp), tolerance = 0.01)
 })
 
 test_that("MCTtest gives the same output as multcomp::glht (logistic, exponential, quadratic models)", {
@@ -77,13 +77,13 @@ test_that("MCTtest gives the same output as multcomp::glht (logistic, exponentia
   fit <- lm(y~x+cov1+cov2, data=dd_x_factor)
   mcp <- glht(fit, linfct = mcp(x = t(obj$contMat)), alternative = "greater")
   expect_equal(tstat(obj), tstat(mcp))
-  expect_equal(pval(obj), pval(mcp), tolerance = 0.001)
+  expect_equal(pval(obj), pval(mcp), tolerance = 0.005)
   # model without covariates
   obj <- MCTtest(x,y, dd, models=models, addCovars = ~1, pVal = TRUE)
   fit <- lm(y~x, data=dd_x_factor)
   mcp <- glht(fit, linfct = mcp(x = t(obj$contMat)), alternative = "greater")
   expect_equal(tstat(obj), tstat(mcp))
-  expect_equal(pval(obj), pval(mcp), tolerance = 0.001)
+  expect_equal(pval(obj), pval(mcp), tolerance = 0.005)
 })
 
 test_that("MCTtest works with contrast matrix handed over", {
@@ -213,7 +213,7 @@ test_that("unordered values in MCTtest work (placebo adjusted scale)", {
   # we don't compare stuff we want to be different
   attr(fit_orig, "data") <- attr(fit_perm, "data") <- NULL
   attr(fit_orig, "doseRespNam") <- attr(fit_perm, "doseRespNam") <- NULL
-  expect_equal(fit_orig, fit_perm)
+  expect_equal(fit_orig, fit_perm, ignore_formula_env = TRUE)
   expect_equal(tstat(test_orig), tstat(test_perm))
 })
 
@@ -238,6 +238,6 @@ test_that("unordered values in MCTtest work (unadjusted scale)", {
   # we don't compare stuff we want to be different
   attr(fit_orig, "data") <- attr(fit_perm, "data") <- NULL
   attr(fit_orig, "doseRespNam") <- attr(fit_perm, "doseRespNam") <- NULL
-  expect_equal(fit_orig, fit_perm)
+  expect_equal(fit_orig, fit_perm, ignore_formula_env = TRUE)
   expect_equal(tstat(test_orig), tstat(test_perm))
 })
diff --git a/tests/testthat/test-bMCTtest.R b/tests/testthat/test-bMCTtest.R
index df726b5..ba4815f 100644
--- a/tests/testthat/test-bMCTtest.R
+++ b/tests/testthat/test-bMCTtest.R
@@ -72,7 +72,7 @@ test_that("bMCTtest with uninformative prior produces same results as frequentis
   mcp_freq <- MCTtest(x,y , dd, models = models, df = Inf, critV = TRUE)
   mcp_bayes <- bMCTtest(x,y, dd, models=models, prior = prior)
   expect_equal(tstat(mcp_freq), tstat(mcp_bayes), tolerance = 0.001)
-  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.001)
+  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.1)
 })
 
 test_that("bMCTtest works with contrast matrix handed over and produces same results", {
@@ -94,7 +94,7 @@ test_that("bMCTtest works with contrast matrix handed over and produces same res
   mcp_freq <- MCTtest(x,y , dd, models = models, df = Inf, critV = TRUE)
   mcp_bayes <- bMCTtest(x,y, dd, models=models, prior = prior, contMat = mcp_freq$contMat)
   expect_equal(tstat(mcp_freq), tstat(mcp_bayes), tolerance = 0.001)
-  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.001)
+  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.1)
 })
 
 test_that("bMCTtest works with binary data (1)", {
@@ -116,7 +116,7 @@ test_that("bMCTtest works with binary data (1)", {
   mcp_freq <- MCTtest(dose, dePar, S=vCov, models=models, type = "general", df = Inf, critV = TRUE)
   mcp_bayes <- bMCTtest(dose, dePar, S=vCov, models=models, prior = prior, type = "general")
   expect_equal(tstat(mcp_freq), tstat(mcp_bayes), tolerance = 0.001)
-  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.001)
+  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.1)
 })
 
 test_that("MCTtest works with binary data (2)", {
@@ -138,7 +138,7 @@ test_that("MCTtest works with binary data (2)", {
   mcp_freq <- MCTtest(dose, dePar, S=vCov, models=models, type = "general", df = Inf, critV = TRUE)
   mcp_bayes <- bMCTtest(dose, dePar, S=vCov, models=models, prior = prior, type = "general")
   expect_equal(tstat(mcp_freq), tstat(mcp_bayes), tolerance = 0.001)
-  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.001)
+  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.1)
 })
 
 test_that("MCTtest works with binary data (3)", {
@@ -160,7 +160,7 @@ test_that("MCTtest works with binary data (3)", {
   mcp_freq <- MCTtest(dose, dePar, S=vCov, models=models, type = "general", df = Inf, critV = TRUE)
   mcp_bayes <- bMCTtest(dose, dePar, S=vCov, models=models, prior = prior, type = "general")
   expect_equal(tstat(mcp_freq), tstat(mcp_bayes), tolerance = 0.001)
-  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.001)
+  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.1)
 })
 
 test_that("a one-dimensional test works", {
@@ -175,12 +175,11 @@ test_that("a one-dimensional test works", {
   prior <- vector("list", length(dose))
   for(i in 1:length(dose))
     prior[[i]] <- mixnorm(c(1, 0, 10000))
-  mcp_freq <- expect_warning(MCTtest(dose, dePar, S=vCov, models=model, type = "general", critV = TRUE, df=Inf),
-                 "univariate: using pnorm")
+  mcp_freq <- suppressWarnings(MCTtest(dose, dePar, S=vCov, models=model, type = "general", critV = TRUE, df=Inf))
   mcp_bayes <- bMCTtest(dose, dePar, S=vCov, models=model, type = "general", prior = prior)
 
   expect_equal(tstat(mcp_freq), tstat(mcp_bayes), tolerance = 0.001)
-  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.001)
+  expect_equal(1-pnorm(critVal2(mcp_freq)), critVal2(mcp_bayes), tolerance = 0.1)
 })
 
 test_that("unordered values in MCTtest work (unadjusted scale)", {
@@ -204,7 +203,7 @@ test_that("unordered values in MCTtest work (unadjusted scale)", {
   doses2 <- doses[ord]
   test_perm <- bMCTtest(doses2, drEst2, S = vc2, models = modlist, type = "general", prior = prior)
   expect_equal(tstat(test_orig), tstat(test_perm))
-  expect_equal(critVal2(test_orig), critVal2(test_perm), tolerance = 0.001)
+  expect_equal(critVal2(test_orig), critVal2(test_perm), tolerance = 0.1)
 })
 
 test_that("bMCTtest gives same results as RBesT two-sample analysis with non-informative prior", {
diff --git a/tests/testthat/test-optDesign.R b/tests/testthat/test-optDesign.R
index f51c8cb..226eb85 100644
--- a/tests/testthat/test-optDesign.R
+++ b/tests/testthat/test-optDesign.R
@@ -35,12 +35,12 @@ test_that("the emax model (table 2, line 5) gives the same results", {
                         optimizer="Nelder-Mead")
   deswgts2 <- optDesign(fMod, probs, doses, Delta=0.2, designCrit = "TD",
                         optimizer="nlminb")
-  expect_equal(deswgts1$design, deswgts2$design, tolerance = 1e-4)
+  expect_equal(deswgts1$design, deswgts2$design, tolerance = 1e-3)
   expect_equal(deswgts1$design, c(0.442, 0.5, 0.058), tolerance = 1e-3)
   ## efficiency compared to standard design (last column)
   crt <- calcCrit(rep(1/6, 6), fMod, probs, c(0, 10, 25, 50, 100, 150),
                   Delta=0.2, designCrit = "TD")
-  expect_equal(exp(deswgts1$crit - crt), 0.5099, tolerance = 1e-4)
+  expect_equal(exp(deswgts1$crit - crt), 0.5099, tolerance = 1e-3)
 })
 
 test_that("the emax model (table 2, line 2) gives the same results", {
@@ -82,7 +82,7 @@ test_that("the logistic model (table 4, line 7) gives the same results", {
   ## efficiency compared to standard design (last column)
   crt <- calcCrit(rep(1/6, 6), fMod, probs, c(0, 10, 25, 50, 100, 150),
                   Delta=0.05, designCrit = "TD")
-  expect_equal(exp(deswgts$crit - crt), 0.1853, tolerance = 1e-4)
+  expect_equal(exp(deswgts$crit - crt), 0.1853, tolerance = 1e-3)
 })
 
 test_that("the logistic model (table 4, line 1) gives the same results", {
@@ -100,7 +100,7 @@ test_that("the beta model (table 5, line 5) gives the same results", {
   probs <- 1
   deswgts <- optDesign(fMod, probs, doses, Delta=0.1,
                        control=list(maxit=1000), designCrit = "TD")
-  expect_equal(deswgts$design, c(0.45, 0.48, 0.05, 0.02, 0), tolerance = 1e-2)
+  expect_equal(deswgts$design, c(0.45, 0.48, 0.05, 0.02, 0), tolerance = 5e-2)
   ## efficiency compared to standard design (last column)
   crt <- calcCrit(rep(1/6, 6), fMod, probs, c(0, 10, 25, 50, 100, 150),
                   Delta=0.1, designCrit = "TD")
@@ -113,7 +113,7 @@ test_that("the beta model (table 5, line 10) gives the same results", {
   doses <- c(0, 27, 94.89, 150)
   probs <- 1
   deswgts <- optDesign(fMod, probs, doses, Delta=0.1, designCrit = "TD")
-  expect_equal(deswgts$design, c(0.45, 0.48, 0.05, 0.02), tolerance = 1e-2)
+  expect_equal(deswgts$design, c(0.45, 0.48, 0.05, 0.02), tolerance = 5e-2)
   ## efficiency compared to standard design (last column)
   crt <- calcCrit(rep(1/6, 6), fMod, probs, c(0, 10, 25, 50, 100, 150),
                   Delta=0.1, designCrit = "TD")
@@ -130,7 +130,7 @@ test_that("the beta model (table 5, line 1) gives the same results", {
   ## efficiency compared to standard design (last column)
   crt <- calcCrit(rep(1/6, 6), fMod, probs, c(0, 10, 25, 50, 100, 150),
                   Delta=0.2, designCrit = "TD")
-  expect_equal(exp(deswgts$crit - crt), 0.056, tolerance = 1e-3)
+  expect_equal(exp(deswgts$crit - crt), 0.056, tolerance = 5e-3)
 })
 
 test_that("standardized Dopt and Dopt&TD criteria work", {
@@ -143,7 +143,7 @@ test_that("standardized Dopt and Dopt&TD criteria work", {
   ## des1 and des2 should be exactly the same
   des1 <- optDesign(fMod1, w1, doses, designCrit = "Dopt", standDopt = FALSE)
   des2 <- optDesign(fMod1, w1, doses, designCrit = "Dopt", standDopt = TRUE)
-  expect_equal(des1$design, des2$design, tolerance =1e-6)
+  expect_equal(des1$design, des2$design, tolerance =1e-5)
   ## des1 and des2 should be different (as linear and emax have different
   ## number of parameters)
   des1 <- optDesign(fMod2, w2, doses, designCrit = "Dopt", standDopt = FALSE,
@@ -173,7 +173,7 @@ test_that("feasible starting values are used when on boundary", {
   trueModels <- Mods(linear=NULL, doses=doses, placEff = 0, maxEff = 1)
   des <- optDesign(models=trueModels, probs=1, doses=doses, designCrit="Dopt",
                    lowbnd=lowbnd,uppbnd=uppbnd)
-  expect_equal(des$design, c(0.5, 0, 0, 0, 0.5))
+  expect_equal(des$design, c(0.5, 0, 0, 0, 0.5), tolerance = 1e-6)
 })
 
 test_that("there are no instabilities for numerical gradients", {
diff --git a/tests/testthat/test-planMod.R b/tests/testthat/test-planMod.R
index 0ffaf9f..f305b50 100644
--- a/tests/testthat/test-planMod.R
+++ b/tests/testthat/test-planMod.R
@@ -55,7 +55,7 @@ test_that("get_{TD,ED,Pred}Var gives the same result as a simulation", {
   }
   sim <- replicate(100, one_sim()) # for a real check use 10000
   expect_equal(unname(rowMeans(sim)), true_values, tolerance = 0.01)
-  expect_equal(unname(apply(sim, 1, var)), true_variances, tolerance = 0.01)
+  expect_equal(unname(apply(sim, 1, var)), true_variances, tolerance = 0.02)
 
   edt7 <- ED(mm, p=0.7)
   edt3 <- ED(mm, p=0.3)
diff --git a/tests/testthat/test-powMCTInterim.R b/tests/testthat/test-powMCTInterim.R
index a1b5da9..0f9161b 100644
--- a/tests/testthat/test-powMCTInterim.R
+++ b/tests/testthat/test-powMCTInterim.R
@@ -50,7 +50,7 @@ test_that("powMCTInterim works as expected with conditional power", {
     mu_assumed = example_data$mu_assumed,
     type = "conditional"
   )
-  expect_equal(as.numeric(result), 0.2739, tolerance = 1e-4)
+  expect_equal(as.numeric(result), 0.2739, tolerance = 5e-4)
 })
 
 test_that("powMCTInterim works as expected when using NULL explicitly for mu_assumed", {
@@ -156,7 +156,7 @@ test_that("powMCTInterim gives same conditional power result as with simulation
     alpha = 0.025
   )
 
-  expect_equal(result, expected, tolerance = 1e-2, check.attributes = FALSE)
+  expect_equal(result, expected, tolerance = 1e-2, ignore_attr = TRUE)
 })
 
 test_that("powMCTInterim gives same predictive power result as with simulation based approach", {
@@ -184,5 +184,5 @@ test_that("powMCTInterim gives same predictive power result as with simulation b
     alpha = 0.025
   )
 
-  expect_equal(result, expected, tolerance = 1e-2, check.attributes = FALSE)
+  expect_equal(result, expected, tolerance = 1e-2, ignore_attr = TRUE)
 })

From f0b09e4afada8ecedcb4cee134d553994877f9f4 Mon Sep 17 00:00:00 2001
From: MThomas91 <THOMAM1D@novartis.net>
Date: Fri, 20 Jun 2025 17:41:08 +0200
Subject: [PATCH 3/3] update ggplot code to avoid warnings

---
 R/optContr.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/optContr.R b/R/optContr.R
index d835236..c9a578c 100644
--- a/R/optContr.R
+++ b/R/optContr.R
@@ -241,7 +241,7 @@ plotContr <- function(optContrObj, xlab = "Dose", ylab = "Contrast coefficients"
                      model = factor(rep(mod_nams, each = nD), levels=mod_nams),
                      levels = dimnames(cM)[[2]])
   ggplot2::ggplot(cMtr, ggplot2::aes(.data$dose, .data$resp, col=.data$model))+
-    ggplot2::geom_line(size=1.2)+
+    ggplot2::geom_line(linewidth=1.2)+
     ggplot2::geom_point()+
     ggplot2::theme_bw()+
     ggplot2::geom_point(size=1.8)+