Merge branch 'feature/marginal_effects' into develop

dmphillippo · Apr 30, 2024 · 7415cdf · 7415cdf
2 parents aaab952 + 4693cd8
commit 7415cdf
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -53,7 +53,7 @@ LinkingTo:
     rstan (>= 2.26.0),
     StanHeaders (>= 2.26.0)
 SystemRequirements: GNU make
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 Suggests: 
     testthat (>= 2.1.0),

diff --git a/NEWS.md b/NEWS.md
@@ -11,9 +11,12 @@ ratios.
 calculations with `predict()` or `marginal_effects()` from ML-NMR models that 
 may take longer to run. These can be controlled with the new `progress` 
 argument.
-* Deprecation: The `trt_ref` argument to `predict()` is now soft-deprecated, and
-the new argument `baseline_ref` is preferred. This makes way for the new 
-`marginal_effects()` functionality.
+* Deprecation: The `trt_ref` argument to `predict()` has been renamed to 
+`baseline_ref`; using `trt_ref` is now soft-deprecated. Renaming this argument 
+`baseline_ref` follows the naming convention for the other arguments 
+(`baseline_type`, `baseline_level`) that specify the details of a provided 
+`baseline` distribution. This also makes way for the new `marginal_effects()` 
+functionality.
 * Fix: Fallback formatting used by print methods when the crayon package is not 
 installed now works properly, rather than giving errors.
 * Fix: Small bug caused `predict()` for AgD meta-regression models with new data 

diff --git a/R/multinma-package.R b/R/multinma-package.R
@@ -46,7 +46,6 @@
 #'
 #'   \insertRef{methods_paper}{multinma}
 #'
-#' @docType package
 #' @name multinma-package
 #' @aliases multinma
 #' @useDynLib multinma, .registration = TRUE
@@ -69,7 +68,7 @@
 #' @references
 #'   \insertAllCited{}
 #'
-NULL
+"_PACKAGE"
 
 # Stop R CMD check thinking . used in pipes is an undeclared global variable
 if (getRversion() >= "2.15.1")  utils::globalVariables(c("."))

diff --git a/R/predict.R b/R/predict.R
@@ -109,7 +109,7 @@
 #'   computationally intensive, especially for survival outcomes. Currently the
 #'   default is to display progress only when running interactively and
 #'   producing predictions for a survival ML-NMR model.
-#' @param trt_ref Deprecated, use `baseline_trt` instead.
+#' @param trt_ref Deprecated, renamed to `baseline_trt`.
 #'
 #' @details
 #' # Aggregate-level predictions from IPD NMA and ML-NMR models

diff --git a/man/multinma-package.Rd b/man/multinma-package.Rd
diff --git a/man/predict.stan_nma.Rd b/man/predict.stan_nma.Rd
diff --git a/tests/testthat/test-example_diabetes.R b/tests/testthat/test-example_diabetes.R
@@ -126,7 +126,7 @@ plot(db_releff_RE, ref_line = 0)
 db_pred_FE <- predict(db_fit_FE, 
                       newdata = data.frame(time = 3),
                       baseline = distr(qnorm, mean = -4.2, sd = 1.11^-0.5), 
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response")
 db_pred_FE
 plot(db_pred_FE)
@@ -135,7 +135,7 @@ plot(db_pred_FE)
 db_pred_RE <- predict(db_fit_RE, 
                       newdata = data.frame(time = 3),
                       baseline = distr(qnorm, mean = -4.2, sd = 1.11^-0.5), 
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response")
 db_pred_RE
 plot(db_pred_RE)
@@ -302,58 +302,58 @@ db_pred_FE_multi1 <- as.data.frame(predict(db_fit_FE,
                       newdata = data.frame(time = times),
                       baseline = unname(bls), 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response"))
 
 db_pred_RE_multi1 <- as.data.frame(predict(db_fit_RE, 
                       newdata = data.frame(time = times),
                       baseline = unname(bls), 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response"))
 
 db_pred_FE_multi2 <- as.data.frame(predict(db_fit_FE, 
                       newdata = data.frame(time = times),
                       baseline = bls, 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response"))
 
 db_pred_RE_multi2 <- as.data.frame(predict(db_fit_RE, 
                       newdata = data.frame(time = times),
                       baseline = bls, 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response"))
 
 db_pred_FE_multi3 <- as.data.frame(predict(db_fit_FE, 
                       newdata = data.frame(time = rev(times)),
                       baseline = bls, 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response")) %>% 
   arrange(.study)
 
 db_pred_RE_multi3 <- as.data.frame(predict(db_fit_RE, 
                       newdata = data.frame(time = rev(times)),
                       baseline = bls, 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response")) %>% 
   arrange(.study)
 
 db_pred_FE_multi4 <- as.data.frame(predict(db_fit_FE, 
                       newdata = data.frame(time = times),
                       baseline = rev(bls), 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response"))
 
 db_pred_RE_multi4 <- as.data.frame(predict(db_fit_RE, 
                       newdata = data.frame(time = times),
                       baseline = rev(bls), 
                       study = time,
-                      trt_ref = "Diuretic",
+                      baseline_trt = "Diuretic",
                       type = "response"))
 
 test_that("Predictions for reordered newdata/baselines works", {

diff --git a/tests/testthat/test-example_parkinsons.R b/tests/testthat/test-example_parkinsons.R
@@ -145,15 +145,15 @@ plot(arm_releff_RE, ref_line = 0)
 arm_pred_FE <- predict(arm_fit_FE, 
                        baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                        type = "response",
-                       trt_ref = 1)
+                       baseline_trt = 1)
 arm_pred_FE
 plot(arm_pred_FE)
 
 ## ----arm_pred_RE, fig.height = 2------------------------------------------------------------------
 arm_pred_RE <- predict(arm_fit_RE, 
                        baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                        type = "response",
-                       trt_ref = 1)
+                       baseline_trt = 1)
 arm_pred_RE
 plot(arm_pred_RE)
 
@@ -283,15 +283,15 @@ plot(contr_releff_RE, ref_line = 0)
 contr_pred_FE <- predict(contr_fit_FE, 
                        baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                        type = "response",
-                       trt_ref = 1)
+                       baseline_trt = 1)
 contr_pred_FE
 plot(contr_pred_FE)
 
 ## ----contr_pred_RE, fig.height = 2----------------------------------------------------------------
 contr_pred_RE <- predict(contr_fit_RE, 
                        baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                        type = "response",
-                       trt_ref = 1)
+                       baseline_trt = 1)
 contr_pred_RE
 plot(contr_pred_RE)
 
@@ -444,15 +444,15 @@ plot(mix_releff_RE, ref_line = 0)
 mix_pred_FE <- predict(mix_fit_FE, 
                        baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                        type = "response",
-                       trt_ref = 1)
+                       baseline_trt = 1)
 mix_pred_FE
 plot(mix_pred_FE)
 
 ## ----mix_pred_RE, fig.height = 2------------------------------------------------------------------
 mix_pred_RE <- predict(mix_fit_RE, 
                        baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                        type = "response",
-                       trt_ref = 1)
+                       baseline_trt = 1)
 mix_pred_RE
 plot(mix_pred_RE)
 
@@ -727,7 +727,7 @@ test_that("Analysis of reordered contrast data gives same results", {
   expect_equivalent_nma_summary(predict(reorder_fit_FE, 
                                      baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                                      type = "response",
-                                     trt_ref = 1),
+                                     baseline_trt = 1),
                            contr_pred_FE,
                            tolerance = tol)
 
@@ -747,7 +747,7 @@ test_that("Analysis of reordered contrast data gives same results", {
   expect_equivalent_nma_summary(predict(reorder_fit_RE, 
                                      baseline = distr(qnorm, mean = -0.73, sd = 21^-0.5),
                                      type = "response",
-                                     trt_ref = 1),
+                                     baseline_trt = 1),
                            contr_pred_RE,
                            tolerance = tol)
 

diff --git a/tests/testthat/test-example_plaque_psoriasis.R b/tests/testthat/test-example_plaque_psoriasis.R
@@ -661,7 +661,7 @@ plot(pso_pred_FE_new, ref_line = c(0, 1))
 ##                         "Chiricozzi 2019" = distr(qbeta, 243, 330-243)),
 ##         baseline_type = "response",
 ##         baseline_level = "aggregate",
-##         trt_ref = "SEC_300"))
+##         baseline_trt = "SEC_300"))
 
 
 ## ----pso-full-pred-new, eval=!params$run_tests && params$eval_multinomial-------------------------