Merge pull request #8 from DeclareDesign/switch-to-marginaleffects

switch to marginaleffects
DeclareDesign · Dec 2, 2024 · e8eec55 · e8eec55
2 parents ae7efab + 26a8161
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.8
-Date: 2024-03-02 18:35:10 UTC
-SHA: be95cd907b6e1c1cb42c645a50a1a1bbb7a45486
+Version: 1.0.12
+Date: 2024-10-07 18:00:19 UTC
+SHA: 1802077891d79bc7df8b64a7d51448970b34ea27
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,17 +1,17 @@
 Package: rdss
 Title: Companion Datasets and Functions for Research Design in the Social Sciences
-Version: 1.0.8
+Version: 1.0.12
 Authors@R: 
     c(person("Graeme", "Blair", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9164-2102")),
              person("Alexander", "Coppock", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-5733-2386")),
              person("Macartan", "Humphreys", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0001-7029-2326")))
 Description: Helper functions to accompany the Blair, Coppock, and Humphreys (2022) "Research Design in the Social Sciences: Declaration, Diagnosis, and Redesign" <https://book.declaredesign.org>. 'rdss' includes datasets, helper functions, and plotting components to enable use and replication of the book. 
-Imports: dplyr, rlang (>= 1.0.0), generics, ggplot2, tibble, tidyr, dataverse, readr, prediction, broom, purrr, estimatr, randomizr
+Imports: dplyr, rlang (>= 1.0.0), generics, ggplot2, tibble, tidyr, dataverse, readr, marginaleffects, broom, purrr, estimatr, randomizr
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     testthat (>= 3.0.0),
     rdrobust, 

diff --git a/NAMESPACE b/NAMESPACE
@@ -53,7 +53,7 @@ importFrom(ggplot2,element_text)
 importFrom(ggplot2,margin)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
-importFrom(prediction,prediction)
+importFrom(marginaleffects,predictions)
 importFrom(purrr,as_vector)
 importFrom(purrr,map)
 importFrom(purrr,map_chr)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# rdss 1.0.12
+
+* address bugs with future package
+
+# rdss 1.0.10
+
+* Switch from prediction to marginaleffects.
+
 # rdss 1.0.8
 
 * Documentation updates for CRAN.

diff --git a/R/helpers-multilevel-regression-poststratification.R b/R/helpers-multilevel-regression-poststratification.R
@@ -13,18 +13,21 @@
 #'
 #' @export
 #'
-#' @importFrom prediction prediction
+#' @importFrom marginaleffects predictions
 #' @importFrom dplyr group_by summarize
 #' @importFrom stats weighted.mean
 #' @importFrom rlang `!!` enquo
 #'
 post_stratification_helper <- function(model_fit, data, group, weights) {
-  prediction(
+  predictions(
     model_fit,
-    data = data,
-    allow.new.levels = TRUE,
-    type = "response"
+    newdata = data,
+    type = "response",
+    re.form = NA
+    # For this model type, `marginaleffects` only takes into account the
+    # uncertainty in fixed-effect parameters. You can use the `re.form=NA`
+    # argument to acknowledge this explicitly and silence this warning.
   ) %>%
     group_by({{group}}) %>%
-    summarize(estimate = weighted.mean(fitted, !!enquo(weights)), .groups = "drop")
+    summarize(estimate = weighted.mean(estimate, !!enquo(weights)), .groups = "drop")
 }
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,6 @@
 ## Submission
 
-Submission to resolve internet connection-required example. 
+rdss 1.0.10 was archived off CRAN, principally because the `prediction` package was archived. This version switches to the `marginaleffects` package.
 
 ## Test environments
 

diff --git a/data/lapop_brazil.rda b/data/lapop_brazil.rda
diff --git a/tests/testthat/test-bayesian-regression.R b/tests/testthat/test-bayesian-regression.R
@@ -19,6 +19,6 @@ test_that("tidy_stan works", {
       inquiry = "mean_age"
     )
 
-  expect_error(simulate_design(declaration_9.3, sims = 1), NA)
+  expect_error(simulate_design(declaration_9.3, sims = 1, future.seed = FALSE), NA)
 
 })
diff --git a/tests/testthat/test-causal-forests.R b/tests/testthat/test-causal-forests.R
@@ -56,6 +56,6 @@ test_that("causal forest helpers work", {
     declare_estimator(handler = label_estimator(get_best_predictor),
                       inquiry = "best_predictor", label = "cf")
 
-  expect_error(simulate_design(declaration_19.1, sims = 1), NA)
+  expect_error(simulate_design(declaration_19.1, sims = 1, future.seed = FALSE), NA)
 
 })
diff --git a/tests/testthat/test-conjoint-experiments.R b/tests/testthat/test-conjoint-experiments.R
@@ -48,6 +48,6 @@ test_that("conjoint helpers work", {
                       respondent.id = "subject",
                       .method = amce)
 
-  expect_error(simulate_design(declaration_17.5, sims = 1), NA)
+  expect_error(simulate_design(declaration_17.5, sims = 1, future.seed = FALSE), NA)
 
 })
diff --git a/tests/testthat/test-difference-in-differences.R b/tests/testthat/test-difference-in-differences.R
@@ -51,11 +51,12 @@ test_that("lag_by_group and did_multiplegt_tidy work", {
       G = "units",
       T = "periods",
       D = "D",
+      mode = "old",
       handler = label_estimator(did_multiplegt_tidy),
       inquiry = c("ATT", "ATT_switchers"),
       label = "chaisemartin"
     )
 
-  expect_error(suppressWarnings(simulate_design(declaration_16.3, sims = 1)), NA)
+  expect_error(suppressWarnings(simulate_design(declaration_16.3, sims = 1, future.seed = FALSE)), NA)
 
 })
diff --git a/tests/testthat/test-experiments-over-networks.R b/tests/testthat/test-experiments-over-networks.R
@@ -55,6 +55,6 @@ test_that("interference helpers work", {
                       permutatation_matrix = permutatation_matrix,
                       adj_matrix = adj_matrix)
 
-  expect_error(simulate_design(declaration_18.13, sims = 1), NA)
+  expect_error(simulate_design(declaration_18.13, sims = 1, future.seed = FALSE), NA)
 
 })
diff --git a/tests/testthat/test-meta-analysis.R b/tests/testthat/test-meta-analysis.R
@@ -34,6 +34,6 @@ test_that("rma helpers work", {
 
   declaration_19.3 <- redesign(design, tau = c(0, 1))
 
-  expect_error(simulate_design(declaration_19.3, sims = 1), NA)
+  expect_error(simulate_design(declaration_19.3, sims = 1, future.seed = FALSE), NA)
 
 })
diff --git a/tests/testthat/test-multilevel-regression-poststratification.R b/tests/testthat/test-multilevel-regression-poststratification.R
@@ -49,6 +49,6 @@ test_that("post_stratification_helper works", {
     label = "Partial pooling",
     inquiry = "mean_policy_support")
 
-  expect_error(simulate_design(declaration_15.4, sims = 1), NA)
+  expect_error(simulate_design(declaration_15.4, sims = 1, future.seed = FALSE), NA)
 
 })
diff --git a/tests/testthat/test-process-tracing.R b/tests/testthat/test-process-tracing.R
@@ -29,6 +29,6 @@ test_that("process_tracing_estimator works", {
       query = "Y[X=1] - Y[X=0]",
       strategies = strategies)
 
-  expect_error(simulate_design(declaration_16.1, sims = 1), NA)
+  expect_error(simulate_design(declaration_16.1, sims = 1, future.seed = FALSE), NA)
 
 })
diff --git a/tests/testthat/test-regression-discontinuity.R b/tests/testthat/test-regression-discontinuity.R
@@ -33,6 +33,6 @@ test_that("tidy.rdrobust and rdrobust_helper work", {
       inquiry = "LATE",
       label = "optimal"
     )
-  expect_error(simulate_design(declaration_16.5, sims = 1), NA)
+  expect_error(simulate_design(declaration_16.5, sims = 1, future.seed = FALSE), NA)
 
 })